N,N-bis(2-mercaptoethyl)methylamine: a new coligand for Tc-99m labeling of hydrazinonicotinamide peptides - Banerjee, S. R.; Maresca, K. P.; Stephenson, K. A.; Valliant, J. F.; Babich, J. W.; Graham, W. A.; Barzana, M.; Dong, Q.; Fischman, A. J.; Zubieta, J. (Bioconjugate Chem., 2005)
Hydrazinonicotinamide (HYNIC) forms stable coordination complexes with Tc-99m when reacted with Tc(V)oxo species such as Tc-mannitol or other Tc-polyhydric complexes. However, radio-HPLC of [Tc-For-MLFK-HYNIC] labeled via Tc-polyhydric ligands demonstrated multiple radiochemical species each with unique biodistribution patterns. This is likely due to the fact that Tc can bind to the hydrazino moiety, as well as polyhydric ligands, in a variety of coordination geometries. Tridentate ligands, such as bis(mercaptoethyl)methylamine (NS2), may constrain the possible coordination geometries and improve overall stability. To investigate this, we synthesized NS2, converted the [Tc-mannitol-For-MLFK-HYNIC] to the corresponding NS2-containing complex [Tc-NS2-For-MLFK-HYNIC], and compared its infection imaging and biodistribution properties with [Tc-mannitol-For-MLFK-HYNIC]. Conversion to the NS2 complex was confirmed by HPLC which showed a single unique hydrophobic species with retention time greater than the [Tc-mannitol-For-MLFK-HYNIC] complex. Imaging experiments with both preparations were performed in rabbits with E. coli infections in the left thigh. Tissue radioactivity measurements demonstrated that compared to Tc-mannitol-peptide, accumulation of Tc-NS2-peptide was lower in blood, heart, and normal muscle and higher in spleen, infected muscle, and pus (p < 0.01). These results indicate that the Tc-NS2-peptide complex is chemically more homogeneous and exhibits improved infection localization and biodistribution properties. In an effort to model the interactions of the metal-HYNIC core with NS2 and related ligand types, the reactions of [ReCl3(NNC5H4NH)(NHNC5H4N)] and [99TcCl3(NNC5H4NH)(NHNC5H4N)], effective structural analogues for the [M(NNC5H4NH(x))2] core, with NS2, C5H3N-2,6-(CH2SH)2, O(CH2CH2SH)2, and S(CH2CH2SH)2 were investigated and the compounds [M[CH3N(CH2CH2S)2](NNC5H4N)(NHNC5H4N] (M = 99Tc (5a), Re (5b)), [Re[C5H3N-2,6-(CH2S)2](NNC5H4N)(NHNC5H4N)].CH2Cl2.0.5MeOH (7), [Re[SCH2CH2)2O] (NNC5H4N)(NHNC5H4N)] (8), and [Re[(SCH2CH2)2S](NNC5H4NH)(NHNC5H4N)]Cl (9) were isolated. Similarly, the reaction of [ReCl3(NNC5H4NH)(NHNC5H4N)] with the bidentate ligands pyridine-2-methanethiol and 3-(trimethlysilyl)pyridine-2-thiol led to the isolation of [ReCl(C5H4N-2-CH2S) (NNC5H4N)(NHNC5H4N)] (10) and [Re(2-SC5H3N-3-SiMe3)2 (NNC5H4N)(NHNC5H4N)] (11), respectively, while reaction with N-methylimidazole-2-thiol yielded the binuclear complex [Re(OH)Cl(SC3H2N2CH3)2(NNC5H4N)2 (NHNC5H4N)2] (12). The analogous metal-(HYNIC-OH) precursor, [ReCl3[NNC5H3NH(CO2R)] [NHNC5H3N(CO2R)]] (R = H, 13a; R = CH3, 13b) has been prepared and coupled to lysine to provide [RCl3[NNC5H3NH(CONHCH2CH2CH2CH2CH(NH2)CO2H)] [NHNC5H3NH(CONHCH2CH2CH2CH2CH(NH2)CO2H)]].2HCl (14.2HCl), while the reaction of the methyl ester 13b with 2-mercaptopyridine yields [Re(2-SC5H4N)2[NNC5H3N(CO2Me)][NHNC5H3N(CO2Me)]] (15). While the chemical studies confirm the robustness of the M-HYNIC core (M = Tc, Re) and its persistence in ligand substitution reactions at adjacent coordination sites of the metal, the isolation of oligomeric structures and the insolubility of the peptide conjugates of 13, 14, and 15 underscore the difficulty of characterizing these materials on the macroscopic scale, an observation relevant to the persistent concerns with reagent purity and identity on the tracer level.
1043-1802 (Print) 1043-1802 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA. number: 4 accession-num: 16029030
Keywords: Animals; Models, Molecular; Molecular Structure; Chromatography, High Pressure Liquid; Crystallography, X-Ray; Magnetic Resonance Spectroscopy; Ligands; Spectrophotometry, Infrared; Hydrazines/*chemistry/pharmacokinetics; Male; Mercaptoethylamines/*chemistry; Niacinamide/*analogs & derivatives/chemistry/pharmacokinetics; Organotechnetium Compounds/*chemistry/pharmacokinetics; Peptides/*chemistry/pharmacokinetics; Rabbits; Tissue Distribution

Backbone amide linker strategies for the solid-phase synthesis of C-terminal modified peptides - Alsina, J.; Kates, S. A.; Barany, G.; Albericio, F. (Methods Mol. Biol., 2005)
This chapter describes backbone amide linker (BAL) strategies for the Nalpha-Fmoc solid-phase synthesis of C-terminal modified peptides. Most solid-phase protocols for the assembly of such peptides have limited generality, because they rely on the Calpha-carboxyl for attachment to the solid support. In the BAL approach, the growing peptide chain is anchored through a backbone nitrogen, thus allowing significant flexibility for chemical modification of the C-termini. In effect, any peptide containing C-terminal variations can be prepared in overall good purity and yield, with minimal side reactions, by using one or more of three variations (original and two modifications) of the BAL strategy.
Alsina, Jordi Kates, Steven A Barany, George Albericio, Fernando Clifton, N.J. Methods Mol Biol. 2005;298:195-208.
The following values have no corresponding Zotero field: auth-address: Eli Lily and Company, Indianapolis, IN, USA. edition: 2005/07/27 accession-num: 16044548
Keywords: Acylation; Peptides/*chemical synthesis/*chemistry; Amides/chemistry; Resins, Synthetic; Molecular Biology/*methods

Total chemical synthesis of N-myristoylated HIV-1 matrix protein p17: structural and mechanistic implications of p17 myristoylation - Wu, Z.; Alexandratos, J.; Ericksen, B.; Lubkowski, J.; Gallo, R. C.; Lu, W. (Proc. Natl. Acad. Sci. U. S. A., 2004)
The HIV-1 matrix protein p17, excised proteolytically from the N terminus of the Gag polyprotein, forms a protective shell attached to the inner surface of the plasma membrane of the virus. During the late stages of the HIV-1 replication cycle, the N-terminally myristoylated p17 domain targets the Gag polyprotein to the host-cell membrane for particle assembly. In the early stages of HIV-1 replication, however, some p17 molecules dissociate from the viral membrane to direct the preintegration complex to the host-cell nucleus. These two opposing targeting functions of p17 require that the protein be capable of reversible membrane interaction. It is postulated that a significant structural change in p17 triggered by proteolytic cleavage of the Gag polyprotein sequesters the N-terminal myristoyl group, resulting in a weaker membrane binding by the matrix protein than the Gag precursor. To test this "myristoyl switch" hypothesis, we obtained highly purified synthetic HIV-1 p17 of 131 amino acid residues and its N-myristoylated form in large quantity. Both forms of p17 were characterized by circular dichroism spectroscopy, protein chemical denaturation, and analytical centrifugal sedimentation. Our results indicate that although N-myristoylation causes no spectroscopically discernible conformational change in p17, it stabilizes the protein by 1 kcal/mol and promotes protein trimerization in solution. These findings support the premise that the myristoyl switch in p17 is triggered not by a structural change associated with proteolysis, but rather by the destabilization of oligomeric structures of membrane-bound p17 in the absence of downstream Gag subdomains.
R21 AI056264/AI/NIAID NIH HHS/United States R21 AI058939/AI/NIAID NIH HHS/United States AI056264/AI/NIAID NIH HHS/United States AI058939/AI/NIAID NIH HHS/United States Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Institute of Human Virology, University of Maryland Biotechnology Institute, and School of Medicine, University of Maryland, 725 West Lombard Street, Baltimore, MD 21201, USA. alt-title: Proceedings of the National Academy of Sciences of the United States of America number: 32 accession-num: 15280532
Keywords: Protein Conformation; Protein Binding; Dimerization; Protein Denaturation; Cell Membrane/metabolism; gag Gene Products, Human Immunodeficiency Virus; Gene Products, gag/*chemical synthesis/chemistry/metabolism; HIV Antigens/chemistry/metabolism; Myristates/*chemical synthesis; Spectrum Analysis; Viral Proteins/*chemical synthesis/chemistry/metabolism

Backbone thioester exchange: A new approach to evaluating higher order structural stability in polypeptides - Woll, Matthew G.; Gellman, Samuel H. (J. Am. Chem. Soc., 2004)
An amide bond has been replaced by a thioester in bovine pancreatic polypeptide (bPP) to allow rapid and reversible (dynamic) exchange of the α-helical segment with other thiols in solution. We have begun to study the higher order structural stability of bPP by measuring the equilibrium constant of the “backbone thioester exchange” (BTE) reaction. The extent to which the equilibrium (KBTE) favors one set of peptides over the other, which can be easily measured, can be directly correlated to the energy gained from favorable noncovalent interactions that occur between peptide segments on either side of the thioester bond (Kfold).
The following values have no corresponding Zotero field: number: 36 publisher: American Chemical Society

Toward fully synthetic glycoproteins by ultimately convergent routes: a solution to a long-standing problem - Warren, J. D.; Miller, J. S.; Keding, S. J.; Danishefsky, S. J. (J. Am. Chem. Soc., 2004)
A method is disclosed for the convergent synthesis of multiply glycosylated peptides. The approach centers on a convergent technique for generating masked, complex glycopeptide-containing C-terminal acyl donors. Activation of the latent donor in situ and use directly in segment coupling with a second peptide bearing a complex carbohydrate produces a completely unprotected, bifunctional glycopeptide. The system demonstrates a minimum level of hydrolysis and epimerization at the C-terminal amino acid residue of the acyl donor during fully convergent segment coupling and is therefore a powerful tool for the synthesis of glycoproteins.
0002-7863 (Print) 0002-7863 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10021, USA. number: 21 accession-num: 15161285
Keywords: Amino Acid Sequence; Models, Molecular; Protein Conformation; Molecular Sequence Data; Acylation; Erythropoietin/chemistry; Carbohydrate Sequence; Polysaccharides/chemistry; Carbohydrate Conformation; Glycoproteins/*chemical synthesis

Direct detection of homocysteine - Wang, W.; Escobedo, J. O.; Lawrence, C. M.; Strongin, R. M. (J. Am. Chem. Soc., 2004)
Homocysteine (Hcy) is a biomarker for significant disorders including Alzheimer's and cardiovascular disease. The monitoring of Hcy levels in plasma is of current concern. We describe highly selective colorimetric methods for the direct detection of Hcy. Inexpensive, commercially available materials are employed. The results show potential application for the detection of Hcy in human blood plasma.
R01 EB002044/EB/NIBIB NIH HHS/United States R01 EB002044/EB/NIBIB NIH HHS/United States R15 EB016870/EB/NIBIB NIH HHS/United States Journal Article Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA. alt-title: Journal of the American Chemical Society number: 11 accession-num: 15025448
Keywords: Humans; Hydrogen-Ion Concentration; Spectrophotometry, Ultraviolet/methods; Colorimetry/*methods; Homocysteine/*blood; Paraquat/chemistry

On-resin native chemical ligation for cyclic peptide synthesis - Tulla-Puche, J.; Barany, G. (J. Org. Chem., 2004)
A novel cysteine derivative, N(alpha)-trityl-S-(9H-xanthen-9-yl)-l-cysteine [Trt-Cys(Xan)-OH] has been introduced for peptide synthesis, specifically for application to a new strategy for the preparation of cyclic peptides. The following steps were carried out to synthesize the cyclic model peptide cyclo(Cys-Thr-Abu-Gly-Gly-Ala-Arg-Pro-Asp-Phe): (i). side-chain anchoring of Fmoc-Asp-OAl via its free beta-carboxyl as a p-alkoxybenzyl ester to a solid support; (ii). stepwise chain elongation of the peptide by standard Fmoc/tBu solid-phase chemistry; (iii). removal of the N-terminal Fmoc group; (iv). coupling of Trt-Cys(Xan)-OH; (v). selective Pd(0)-promoted cleavage of the C-terminal allyl ester; (vi). coupling of the C-terminal residue, i.e., H-Phe-SBzl, preactivated as a thioester; (vii). selective removal of the N(alpha)-Trt and S-Xan protecting groups under very mild acid conditions; (viii). on-resin cyclization by native chemical ligation in an aqueous milieu; and (ix). final acidolytic cleavage of the cyclic peptide from the resin. The strategy was evaluated for three supports: poly[N,N-dimethacrylamide-co-poly(ethylene glycol)] (PEGA), cross-linked ethoxylate acrylate resin (CLEAR), and poly(ethylene glycol)-polystyrene (PEG-PS) graft resin supports. For PEGA and CLEAR, the desired cyclic product was obtained in 76-86% overall yield with initial purities of approximately 70%, whereas for PEG-PS (which does not swell nearly as well in water), results were inferior. Solid-phase native chemical ligation/cyclization methodology appears to have advantages of convenience and specificity, which make it promising for further generalization.
0022-3263 (Print) 0022-3263 (Linking) Journal Article Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, University of Minnesota, 207 Pleasant Street S E, Minneapolis, Minnesota 55455, USA. number: 12 accession-num: 15176835
Keywords: Cyclization; Peptides, Cyclic/*chemical synthesis/chemistry; Cysteine/chemistry/metabolism

Direct determination of thiol pKa by isothermal titration microcalorimetry - Tajc, Stephen G.; Tolbert, Blanton S.; Basavappa, Ravi; Miller, Benjamin L. (J. Am. Chem. Soc., 2004)
doi: 10.1021/ja047929u 0002-7863 doi: 10.1021/ja047929u
The following values have no corresponding Zotero field: number: 34 publisher: American Chemical Society

Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor - Stamos, J.; Lazarus, R. A.; Yao, X.; Kirchhofer, D.; Wiesmann, C. (EMBO J., 2004)
The Met tyrosine kinase receptor and its ligand, hepatocyte growth factor (HGF), play important roles in normal development and in tumor growth and metastasis. HGF-dependent signaling requires proteolysis from an inactive single-chain precursor into an active alpha/beta-heterodimer. We show that the serine protease-like HGF beta-chain alone binds Met, and report its crystal structure in complex with the Sema and PSI domain of the Met receptor. The Met Sema domain folds into a seven-bladed beta-propeller, where the bottom face of blades 2 and 3 binds to the HGF beta-chain 'active site region'. Mutation of HGF residues in the area that constitutes the active site region in related serine proteases significantly impairs HGF beta binding to Met. Key binding loops in this interface undergo conformational rearrangements upon maturation and explain the necessity of proteolytic cleavage for proper HGF signaling. A crystallographic dimer interface between two HGF beta-chains brings two HGF beta:Met complexes together, suggesting a possible mechanism of Met receptor dimerization and activation by HGF.
0261-4189 (Print) 0261-4189 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Protein Engineering, Genentech Inc., South San Francisco, CA 94080, USA. number: 12 accession-num: 15167892
Keywords: Amino Acid Sequence; Models, Molecular; Sequence Homology, Amino Acid; Protein Binding; Molecular Sequence Data; Base Sequence; Crystallography, X-Ray; Surface Plasmon Resonance; Hepatocyte Growth Factor/*chemistry/metabolism; DNA Primers

Novel and efficient synthesis of difficult sequence-containing peptides through O-N intramolecular acyl migration reaction of O-acyl isopeptides - Sohma, Youhei; Sasaki, Masato; Hayashi, Yoshio; Kimura, Tooru; Kiso, Yoshiaki (Chem. Commun., 2004)
A novel and efficient method for the synthesis of difficult sequence-containing peptides has been developed based on the synthesis of O-acyl isopeptides followed by an O-N intramolecular acyl migration reaction, resulting in a remarkable improvement of the yields.
1359-7345 10.1039/B312129A
The following values have no corresponding Zotero field: number: 1 publisher: The Royal Society of Chemistry

Ninhydrin as a reversible protecting group of amino-terminal cysteine - Pool, C. T.; Boyd, J. G.; Tam, J. P. (J. Pept. Res., 2004)
The proximity of the alpha-amine and beta-thiol of alpha-amino terminal-cysteine (NT-Cys) residues in peptides imparts unique chemical properties that have been exploited for inter- and intra-molecular ligation of unprotected peptides obtained through both synthetic and biological means. A reversible protecting group orthogonal to other protection strategies and reversible under mild conditions would be useful in simplifying the synthesis, cleavage, purification and handling of such NT-Cys peptides. It could also be useful for the sequential ligation of peptides. To this end, we explored tri-one chemistry and found that ninhydrin (indane-1,2,3 trione) reacted readily with cysteine or an NT-Cys-containing peptide on- or off-resin at pH 2-5 to form Ninhydrin-protected Cys (Nin-Cys) as a thiazolidine (Thz). The Thz ring, protecting both the amino and thiol groups in Nin-Cys, completely avoids the formylation and Thz side reactions found during hydrofluoric acid (HF) cleavage when N-pi-benzyloxymethyl histidine groups are present. Nin-Cys is stable during coupling reactions and various cleavage conditions with trifluoroacetic acid or HF, but is deprotected under thiolytic or reducing conditions. These properties enable a facile one-step deprotection and end-to-end-cyclization reaction of Nin-Cys peptides containing C-terminal thioesters.
Journal Article Denmark official journal of the American Peptide Society
The following values have no corresponding Zotero field: auth-address: Department of Microbiology/Immunology, Vanderbilt University, Nashville, TN, USA. number: 3 accession-num: 15049834
Keywords: Molecular Structure; Cysteine/*chemistry; Peptides, Cyclic/*chemical synthesis/chemistry; Ninhydrin/*chemistry

Conformational analysis and derivation of molecular mechanics parameters for esters and thioesters - Nagy, Peter I.; Tejada, Frederick R.; Sarver, Jeffrey G.; Messer, William S. (J. Phys. Chem. A, 2004)
doi: 10.1021/jp0490251 1089-5639 doi: 10.1021/jp0490251
The following values have no corresponding Zotero field: number: 46 publisher: American Chemical Society

Modular assembly of glycoproteins: towards the synthesis of GlyCAM-1 by using expressed protein ligation - Macmillan, D.; Bertozzi, C. R. (Angew. Chem. Int. Ed., 2004)
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Germany
The following values have no corresponding Zotero field: auth-address: School of Chemistry, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh, EH9 3JJ GB. derek.macmillan@ed.ac.uk alt-title: Angewandte Chemie (International ed number: 11 accession-num: 15368405
Keywords: Amino Acid Sequence; Molecular Sequence Data; Glycosylation; Ligands; Glycopeptides/chemical synthesis/chemistry; Glycoproteins/*chemical synthesis/*chemistry; Mucins/*chemical synthesis/*chemistry; Protein Structure, Tertiary/physiology

Catalytic self-screening of cholinesterase substrates from a dynamic combinatorial thioester library - Larsson, R.; Pei, Z.; Ramstrom, O. (Angew. Chem. Int. Ed., 2004)
Larsson, Rikard Pei, Zhichao Ramstrom, Olof Germany International ed. in English Angew Chem Int Ed Engl. 2004 Jul 12;43(28):3716-8.
The following values have no corresponding Zotero field: auth-address: Royal Institute of Technology, Department of Chemistry, Teknikringen 36, 10044 Stockholm, Sweden. number: 28 edition: 2004/07/13 accession-num: 15248281
Keywords: Catalysis; Hydrolysis; Sulfhydryl Compounds/*chemistry; Esters/*chemistry; Proteomics; *Combinatorial Chemistry Techniques; Cholinesterases/chemistry/*metabolism

Synthesis of 3-acyl-1-alkyl-2-alkylseleno-1-cyclobutene using alkyneselenolate - Koketsu, Mamoru; Mizutani, Kayo; Ogawa, Tomoko; Takahashi, Ayako; Ishihara, Hideharu (J. Org. Chem., 2004)
The following values have no corresponding Zotero field: number: 25 publisher: American Chemical Society

Total chemical synthesis of large CCK isoforms using a thioester segment condensation approach - Kitagawa, Kouki; Adachi, Hiroshi; Sekigawa, Yumi; Yagami, Takeshi; Futaki, Shiroh; Gu, Yuan Jun; Inoue, Kazutomo (Tetrahedron, 2004)
The following values have no corresponding Zotero field: number: 4
Keywords: Peptide thioester; 2-Chlorotrityl chloride resin; Cholecystokinin (CCK); Fmoc-based SPPS; Silver-ion mediated thioester segment condensation; Sulfated peptide

A new convenient preparation of thiol esters utilizing N-acylbenzotriazoles - Katritzky, Alan R.; Shestopalov, Aleksandr A.; Suzuki, Kazuyuki (Synthesis, 2004)
The following values have no corresponding Zotero field: number: 11 edition: 01.07.2004 section: 1806
Keywords: #nosource

Structural characterization of recombinant soluble rat neuroligin 1: mapping of secondary structure and glycosylation by mass spectrometry - Hoffman, R. C.; Jennings, L. L.; Tsigelny, I.; Comoletti, D.; Flynn, R. E.; Sudhof, T. C.; Taylor, P. (Biochemistry, 2004)
Neuroligins (NLs) are a family of transmembrane proteins that function in synapse formation and/or remodeling by interacting with beta-neurexins (beta-NXs) to form heterophilic cell adhesions. The large N-terminal extracellular domain of NLs, required for beta-NX interactions, has sequence homology to the alpha/beta hydrolase fold superfamily of proteins. By peptide mapping and mass spectrometric analysis of a soluble recombinant form of NL1, several structural features of the extracellular domain have been established. Of the nine cysteine residues in NL1, eight are shown to form intramolecular disulfide bonds. Disulfide pairings of Cys 117 to Cys 153 and Cys 342 to Cys 353 are consistent with disulfide linkages that are conserved among the family of alpha/beta hydrolase proteins. The disulfide bond between Cys 172 and Cys 181 occurs within a region of the protein encoded by an alternatively spliced exon. The disulfide pairing of Cys 512 and Cys 546 in NL1 yields a structural motif unique to the NLs, since these residues are highly conserved. The potential N-glycosylation sequons in NL1 at Asn 109, Asn 303, Asn 343, and Asn 547 are shown occupied by carbohydrate. An additional consensus sequence for N-glycosylation at Asn 662 is likely occupied. Analysis of N-linked oligosaccharide content by mass matching paradigms reveals significant microheterogeneous populations of complex glycosyl moieties. In addition, O-linked glycosylation is observed in the predicted stalk region of NL1, prior to the transmembrane spanning domain. From predictions based on sequence homology of NL1 to acetylcholinesterase and the molecular features of NL1 established from mass spectrometric analysis, a novel topology model for NL three-dimensional structure has been constructed.
0006-2960 (Print) 0006-2960 (Linking) Journal Article Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Pharmacology and Howard Hughes Medical Institute Mass Spectrometry Facility, University of California, San Diego, La Jolla 92093, USA. number: 6 accession-num: 14769026
Keywords: Amino Acid Sequence; Animals; Molecular Sequence Data; Chromatography, High Pressure Liquid; Mass Spectrometry; Glycosylation; Membrane Proteins/*chemistry/metabolism; Protein Structure, Secondary; Disulfides/chemistry; Peptide Fragments/chemistry; Rats; *Peptide Mapping/methods; Asparagine/chemistry; Cell Adhesion Molecules, Neuronal/chemistry; Extracellular Space/chemistry; Mucins/chemistry; Nerve Tissue Proteins/*chemistry/metabolism; Oligosaccharides/chemistry; Recombinant Proteins/*chemistry; Solubility; Trypsin/chemistry

Copper(I)-Catalyzed Synthesis of Azoles. DFT Study Predicts Unprecedented Reactivity and Intermediates - Himo, Fahmi; Lovell, Timothy; Hilgraf, Robert; Rostovtsev, Vsevolod V.; Noodleman, Louis; Sharpless, K. Barry; Fokin, Valery V. (J. Am. Chem. Soc., 2013)
doi: 10.1021/ja0471525
The following values have no corresponding Zotero field: number: 1 publisher: American Chemical Society

Direct production of proteins with N-terminal cysteine for site-specific conjugation - Gentle, I. E.; De Souza, D. P.; Baca, M. (Bioconjugate Chem., 2004)
Proteins with N-terminal cysteine can undergo native chemical ligation and are useful for site-specific N-terminal labeling or protein semisynthesis. Recombinant production of these has usually been by site-specific cleavage of a precursor fusion protein at an internal cysteine residue. Here we describe a simpler route to producing these proteins. Overexpression in E. coli of several proteins containing cysteine as the second amino acid residue yielded products in which the initiating methionine residue had been completely cleaved by endogenous methionine aminopeptidase. While secondary modification of the terminal cysteine was a complicating factor, conditions were identified to eliminate or minimize this problem. Recombinant proteins produced in this way were suitable for site-specific modification of the amino terminus via native chemical ligation technology, as demonstrated by conjugation of a thioester-containing derivative of fluorescein to one such protein. The ability to directly produce proteins with N-terminal cysteine should simplify the application of native chemical ligation technology to recombinant proteins and make the technique more amenable to researchers with limited expertise in protein chemistry.
1043-1802 (Print) 1043-1802 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia. number: 3 accession-num: 15149194
Keywords: Structure-Activity Relationship; Ligands; Cysteine/chemical synthesis/*chemistry; Fluorescein; Proteins/*chemical synthesis/isolation & purification

Synthesis of a thioester linker precursor for a general preparation of peptide C-terminal thioacids - Gaertner, Hubert; Villain, Matteo; Botti, Paolo; Canne, Lynne (Tetrahedron Lett., 2004)
The following values have no corresponding Zotero field: number: 10
Keywords: C-terminal modified peptides; Thioacids; Thioesters

Synthesis of glyoxylyl peptides using a phosphine labile-diaminoacetic acid derivative - Far, Samia; Melnyk, Oleg (Tetrahedron Lett., 2004)
We describe in this letter the preparation of a novel protected α,α′-diaminoacetic acid derivative that acts as a masked glyoxylic acid equivalent. The reagent could easily be introduced on a peptide chain using standard Fmoc/tert-butyl solid-phase methods and resisted to the TFA treatment allowing the deprotection and cleavage of the peptide. Unmasking of the glyoxylyl group was performed in solution in the presence of a phosphine.
0040-4039
The following values have no corresponding Zotero field: number: 38
Keywords: Peptide; Î±-Oxo aldehyde; Phosphine

Gas electron diffraction analysis on S-methyl thioacetate, CH3C(O)SCH3 - Della Védova, Carlos O.; Romano, Rosana M.; Oberhammer, Heinz (J. Org. Chem., 2004)
doi: 10.1021/jo0493828 0022-3263 doi: 10.1021/jo0493828
The following values have no corresponding Zotero field: number: 16 publisher: American Chemical Society

New water-soluble phosphines as reductants of peptide and protein disulfide bonds: reactivity and membrane permeability - Cline, D. J.; Redding, S. E.; Brohawn, S. G.; Psathas, J. N.; Schneider, J. P.; Thorpe, C. (Biochem., 2004)
Tris(2-carboxyethyl)phosphine (TCEP) is a widely used substitute for dithiothreitol (DTT) in the reduction of disulfide bonds in biochemical systems. Although TCEP has been recently shown to be a substrate of the flavin-dependent sulfhydryl oxidases, there is little quantitative information concerning the rate by which TCEP reduces other peptidic disulfide bonds. In this study, mono-, di-, and trimethyl ester analogues of TCEP were synthesized to evaluate the role of carboxylate anions in the reduction mechanism, and to expand the range of phosphine reductants. The effectiveness of all four phosphines relative to DTT has been determined using model disulfides, including a fluorescent disulfide-containing peptide (H(3)N(+)-VTWCGACKM-NH(2)), and with protein disulfide bonds in thioredoxin and sulfhydryl oxidase. Mono-, di-, and trimethyl esters exhibit phosphorus pK values of 6.8, 5.8, and 4.7, respectively, extending their reactivity with the model peptide to correspondingly lower pH values relative to that of TCEP (pK = 7.6). At pH 5.0, the order of reactivity is as follows: trimethyl- > dimethyl- > monomethyl- > TCEP >> DTT; tmTCEP is 35-fold more reactive than TCEP, and DTT is essentially unreactive. Esterification also increases lipophilicity, allowing tmTCEP to penetrate phospholipid bilayers rapidly (>30-fold faster than DTT), whereas the parent TCEP is impermeant. Although more reactive than DTT toward small-molecule disulfides at pH 7.5, all phosphines are markedly less reactive toward protein disulfides at this pH. Molecular modeling suggests that the nucleophilic phosphorus of TCEP is more sterically crowded than the thiolate of DTT, contributing to the lower reactivity of the phosphine with protein disulfides. In sum, these data suggest that there is considerable scope for the synthesis of phosphine analogues tailored for specific applications in biological systems.
Cline, Daniel J Redding, Sarah E Brohawn, Stephen G Psathas, James N Schneider, Joel P Thorpe, Colin 1-T32-GM08550/GM/NIGMS NIH HHS/ GM26643/GM/NIGMS NIH HHS/ Biochemistry. 2004 Dec 7;43(48):15195-203.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA. alt-title: Biochemistry number: 48 edition: 2004/12/01 accession-num: 15568811 work-type: Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
Keywords: Models, Molecular; Hydrogen-Ion Concentration; Proteins/*chemistry/metabolism; Esters; Lipid Bilayers/*chemistry/metabolism; Esterification; Solubility; *Water; Disulfides/*chemistry/metabolism; Dithiothreitol/chemistry; Escherichia coli/chemistry/metabolism; Oligopeptides/*chemistry/metabolism; Permeability; Phosphines/chemical synthesis/*chemistry; Reducing Agents/*chemistry; Thioredoxins/chemistry/metabolism

Biomimetic monoacylation of diols in water. Lanthanide-promoted reactions of methyl benzoyl phosphate - Cameron, Lisa L.; Wang, Sheila C.; Kluger, Ronald (J. Am. Chem. Soc., 2004)
doi: 10.1021/ja049538l 0002-7863 doi: 10.1021/ja049538l
The following values have no corresponding Zotero field: number: 34 publisher: American Chemical Society

Fmoc-based synthesis of peptide α-thioesters using an aryl hydrazine support - Camarero, Julio A.; Hackel, Benjamin J.; de Yoreo, James J.; Mitchell, Alexander R. (J. Org. Chem., 2004)
C-Terminal peptide thioesters are key intermediates in the synthesis/semisynthesis of proteins and of cyclic peptides by native chemical ligation. They are prepared by solid-phase peptide synthesis (SPPS) or biosynthetically by protein splicing techniques. Until recently, the chemical synthesis of C-terminal α-thioester peptides by SPPS was largely restricted to the use of Boc/Benzyl chemistry due to the poor stability of the thioester bond to the basic conditions required for the deprotection of the Nα-Fmoc group. In the present work, we describe a new method for the SPPS of C-terminal thioesters using Fmoc/t-Bu chemistry. This method is based on the use of an aryl hydrazine linker, which is totally stable to conditions required for Fmoc-SPPS. When the peptide synthesis has been completed, activation of the linker is achieved by mild oxidation. This step converts the acyl hydrazine group into a highly reactive acyl diazene intermediate which reacts with an α-amino acid alkyl thioester (H-AA-SR) to yield the corresponding peptide α-thioester in good yield. This method has been successfully used to prepare a variety of peptide thioesters, cyclic peptides, and a fully functional Src homology 3 (SH3) protein domain.
The following values have no corresponding Zotero field: number: 12 publisher: American Chemical Society

Native chemical ligation through in situ O to S acyl shift - Botti, P.; Villain, M.; Manganiello, S.; Gaertner, H. (Org. Lett., 2004)
Keywords: #nosource

A one-pot total synthesis of crambin - Bang, D.; Kent, S. B. H. (Angew. Chem. Int. Ed., 2004)
1433-7851 (Print) 1433-7851 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S.
The following values have no corresponding Zotero field: auth-address: Institute for Biophysical Dynamics, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. number: 19 accession-num: 15127445
Keywords: Amino Acid Sequence; Models, Molecular; Protein Conformation; Cysteine/chemistry; Molecular Sequence Data; Chromatography, High Pressure Liquid; Peptides/chemical synthesis/chemistry; Protein Folding; Gas Chromatography-Mass Spectrometry; Crystallography, X-Ray; Nuclear Magnetic Resonance, Biomolecular; Plant Proteins/*chemical synthesis/chemistry; Thiazoles/chemistry; Thiazolidines

Total chemical synthesis of crambin - Bang, D.; Chopra, N.; Kent, S. B. H. (J. Am. Chem. Soc., 2004)
Crambin is a small (46 amino acids) protein isolated from the seeds of the plant Crambe abyssinica. Crambin has been extensively used as a model protein for the development of advanced crystallography and NMR techniques and for computational folding studies. We set out to establish synthetic access to crambin. Initially, we synthesized the 46 amino acid polypeptide by native chemical ligation of two distinct sets of peptide segments (15 + 31 and 31 + 15 residues). The synthetic polypeptide chain folded in good yield to give native crambin containing three disulfide bonds. The chemically synthesized crambin was characterized by LC-MS and by 2D-NMR. However, the 31-residue peptide segments were difficult to purify, and this caused an overall low yield for the synthesis. To overcome this problem, we synthesized crambin by the native chemical ligation of three segments (15 + 16 + 15 residues). Total synthesis using the ligation of three segments gave more than a 10-fold increase in yield and a protein product of exceptionally high purity. This work demonstrates the efficacy of chemical protein synthesis by the native chemical ligation of three segments and establishes efficient synthetic access to the important model protein crambin for experimental studies of protein folding and stability.
0002-7863 (Print) 0002-7863 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S.
The following values have no corresponding Zotero field: auth-address: Institute for Biophysical Dynamics, and Department of Chemistry, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA. number: 5 accession-num: 14759195
Keywords: Amino Acid Sequence; Models, Molecular; Molecular Sequence Data; Mass Spectrometry; Nuclear Magnetic Resonance, Biomolecular; Protein Isoforms; Plant Proteins/*chemical synthesis/chemistry; Crambe Plant/chemistry

Explanation of the anomalous complexation of silver(I) with ammonia in terms of the poor affinity of the ion for water - Antolovich, Michael; Lindoy, Leonard F.; Reimers, Jeffrey R. (J. Chem. Phys. A, 2004)
The following values have no corresponding Zotero field: number: 40 publisher: American Chemical Society

A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems - Agard, Nicholas J.; Prescher, Jennifer A.; Bertozzi, Carolyn R. (J. Am. Chem. Soc., 2013)
doi: 10.1021/ja044996f
The following values have no corresponding Zotero field: number: 46 publisher: American Chemical Society

Cell-permeable small molecule probes for site-specific labeling of proteins - Yeo, D. S.; Srinivasan, R.; Uttamchandani, M.; Chen, G. Y.; Zhu, Q.; Yao, S. Q. (Chem. Commun., 2003)
We have successfully synthesized a number of small molecule probes designed for site-specific labeling of N-terminal cysteine-containing proteins expressed in live cells. Their utility for site-specific, covalent modifications of proteins was successfully demonstrated with purified proteins in vitro, and with live bacterial cells in vivo.
The following values have no corresponding Zotero field: auth-address: Department of Biological Sciences, National University of Singapore, 3 Science Drive 3, Singapore 117543, Republic of Singapore. number: 23 edition: 2003/12/19 accession-num: 14680216 work-type: Research Support, Non-U.S. Gov't
Yeo, Dawn S Y Srinivasan, Rajavel Uttamchandani, Mahesh Chen, Grace Y J Zhu, Qing Yao, Shao Q England Cambridge, England Chem Commun (Camb). 2003 Dec 7;(23):2870-1.
Keywords: Cysteine/chemistry; Molecular Structure; Gene Expression Regulation; Fluorescent Dyes/chemistry; *Cell Membrane Permeability; Escherichia coli/chemistry; Molecular Probes/chemical synthesis/*chemistry; Proteins/*chemistry/*metabolism

Peptide αthioester formation using standard Fmoc-chemistry - von Eggelkraut-Gottanka, Regula; Klose, Annerose; Beck-Sickinger, Annette G.; Beyermann, Michael (Tetrahedron Lett., 2003)
The following values have no corresponding Zotero field: number: 17

Native chemical ligation with aspartic and glutamic acids as C-terminal residues: Scope and limitations - Villain, Matteo; Gaertner, Hubert; Botti, Paolo (Eur. J. Org. Chem., 2003)
1099-0690
The following values have no corresponding Zotero field: number: 17 publisher: WILEY-VCH Verlag
Keywords: Native chemical ligation; Peptides; Isomerization; Protecting groups

Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions - Scheibner, K. A.; Zhang, Z.; Cole, P. A. (Anal. Biochem., 2003)
Determination of protein oligomerization state can be technically challenging. We have combined the methods of expressed protein ligation (EPL) and fluorescence resonance energy transfer (FRET) for the analysis of protein homo-oligomerization states. We have attached fluorescein (donor) and rhodamine (acceptor) chromophores via dipeptide linkages to the C-termini of three recombinant proteins and examined the potential for FRET between mixtures of these semisynthetic proteins. The known protein dimer (glutathione S-transferase) showed evidence of FRET and the known protein monomer (SH2 domain phosphatase-1) did not display FRET. Using this method, the previously uncharacterized circadian rhythm enzyme, serotonin N-acetyltransferase, displayed significant FRET, indicating its likely propensity for dimerization or more complex oligomerization. These results establish the potential of the union of EPL and FRET in the analysis of protein-protein interactions and provide insight into the unusual enzymatic behavior of a key circadian rhythm enzyme.
Scheibner, Kara A Zhang, Zhongsen Cole, Philip A Anal Biochem. 2003 Jun 15;317(2):226-32.
The following values have no corresponding Zotero field: auth-address: Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Rm. 316, Hunterian Bldg., Baltimore, MD 21205, USA. alt-title: Analytical biochemistry number: 2 edition: 2003/05/22 accession-num: 12758261 work-type: Comparative Study Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
Keywords: Amino Acid Sequence; Protein Binding; Molecular Sequence Data; Rhodamines/chemistry; Spectrometry, Fluorescence; Gene Expression; Arylamine N-Acetyltransferase/chemistry/genetics/metabolism; Escherichia coli/genetics; Fluorescein/chemistry; Fluorescence Resonance Energy Transfer/*methods; Glutathione Transferase/chemistry/genetics/metabolism; Intracellular Signaling Peptides and Proteins; Protein Phosphatase 1; Protein Tyrosine Phosphatase, Non-Receptor Type 11; Protein Tyrosine Phosphatases/chemistry/genetics/metabolism; Recombinant Fusion Proteins/chemistry/genetics/*metabolism; SH2 Domain-Containing Protein Tyrosine Phosphatases

A novel small molecule met inhibitor induces apoptosis in cells transformed by the oncogenic TPR-MET tyrosine kinase - Sattler, M.; Pride, Y. B.; Ma, P.; Gramlich, J. L.; Chu, S. C.; Quinnan, L. A.; Shirazian, S.; Liang, C.; Podar, K.; Christensen, J. G.; Salgia, R. (Cancer Res., 2003)
The Met receptor tyrosine kinase has been shown to be overexpressed or mutated in a variety of solid tumors and has, therefore, been identified as a good candidate for molecularly targeted therapy. Activation of the Met tyrosine kinase by the TPR gene was originally described in vitro through carcinogen-induced rearrangement. The TPR-MET fusion protein contains constitutively elevated Met tyrosine kinase activity and constitutes an ideal model to study the transforming activity of the Met kinase. We found, when introduced into an interleukin 3-dependent cell line, TPR-MET induces factor independence and constitutive tyrosine phosphorylation of several cellular proteins. One major tyrosine phosphorylated protein was identified as the TPR-MET oncoprotein itself. Inhibition of the Met kinase activity by the novel small molecule drug SU11274 [(3Z)-N-(3-chlorophenyl)-3-([3,5-dimethyl-4-[(4-methylpiperazin-1-yl)carbo nyl]-1H-pyrrol-2-yl]methylene)-N-methyl-2-oxo-2,3-dihydro-1H-indole-5-sulf onamide] led to time- and dose-dependent reduced cell growth. The inhibitor did not affect other tyrosine kinase oncoproteins, including BCR-ABL, TEL-JAK2, TEL-PDGFbetaR, or TEL-ABL. The Met inhibitor induced G(1) cell cycle arrest and apoptosis with increased Annexin V staining and caspase 3 activity. The autophosphorylation of the Met kinase was reduced on sites that have been shown previously to be important for activation of pathways involved in cell growth and survival, especially the phosphatidylinositol-3'-kinase and the Ras pathway. In particular, we found that the inhibitor blocked phosphorylation of AKT, GSK-3beta, and the pro-apoptotic transcription factor FKHR. The characterization of SU11274 as an effective inhibitor of Met tyrosine kinase activity illustrates the potential of targeting for Met therapeutic use in cancers associated with activated forms of this kinase.
0008-5472 (Print) 0008-5472 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. number: 17 accession-num: 14500382
Keywords: Animals; Mice; Apoptosis/*drug effects; B-Lymphocytes/cytology/drug effects/enzymology; Cell Cycle/drug effects; Cell Division/drug effects/physiology; Cell Transformation, Neoplastic/drug effects/metabolism; Indoles/*pharmacology; Phosphorylation/drug effects; Piperazines/*pharmacology; Proto-Oncogene Proteins c-met/*antagonists & inhibitors/physiology; Sulfonamides/*pharmacology; Tyrosine/metabolism

Synthesis of methionine containing peptides related to native chemical ligation - Pachamuthu, Kandasamy; Schmidt, Richard R. (Synlett, 2003)
The following values have no corresponding Zotero field: number: 5
Keywords: #nosource

Protein assembly by orthogonal chemical ligation methods - Nilsson, B. L.; Hondal, R. J.; Soellner, M. B.; Raines, R. T. (J. Am. Chem. Soc., 2003)
Chemical synthesis harbors the potential to provide ready access to natural proteins as well as to create nonnatural ones. The Staudinger ligation of a peptide containing a C-terminal phosphinothioester with a peptide containing an N-terminal azide gives an amide with no residual atoms. This method for amide bond formation is orthogonal and complementary to other ligation methods. Herein, we describe the first use of the Staudinger ligation to couple peptides on a solid support. The fragment thus produced is used to assemble functional ribonuclease A via native chemical ligation. The synthesis of a protein by this route expands the versatility of chemical approaches to protein production.
0002-7863 (Print) 0002-7863 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA. number: 18 accession-num: 12720426
Keywords: Protein Conformation; Kinetics; Amino Acids/chemistry; Nuclear Magnetic Resonance, Biomolecular; Peptide Fragments/*chemical synthesis; Ribonuclease, Pancreatic/*chemical synthesis/chemistry/metabolism

Coordination properties of tris(2-carboxyethyl)phosphine, a newly Introduced thiol reductant, and its oxide - Krezel, Artur; Latajka, RafaÅ‚; Bujacz, Grzegorz D.; Bal, Wojciech (Inorg. Chem., 2014)
doi: 10.1021/ic025969y
The following values have no corresponding Zotero field: number: 6 publisher: American Chemical Society

Design and chemical synthesis of a homogeneous polymer-modified erythropoiesis protein - Kochendoerfer, G. G.; Chen, S. Y.; Mao, F.; Cressman, S.; Traviglia, S.; Shao, H.; Hunter, C. L.; Low, D. W.; Cagle, E. N.; Carnevali, M.; Gueriguian, V.; Keogh, P. J.; et al. (Science, 2003)
We report the design and total chemical synthesis of "synthetic erythropoiesis protein" (SEP), a 51-kilodalton protein-polymer construct consisting of a 166-amino-acid polypeptide chain and two covalently attached, branched, and monodisperse polymer moieties that are negatively charged. The ability to control the chemistry allowed us to synthesize a macromolecule of precisely defined covalent structure. SEP was homogeneous as shown by high-resolution analytical techniques, with a mass of 50,825 +/-10 daltons by electrospray mass spectrometry, and with a pI of 5.0. In cell and animal assays for erythropoiesis, SEP displayed potent biological activity and had significantly prolonged duration of action in vivo. These chemical methods are a powerful tool in the rational design of protein constructs with potential therapeutic applications.
1095-9203 (Electronic) 0036-8075 (Linking) Journal Article
The following values have no corresponding Zotero field: auth-address: Gryphon Therapeutics, 250 East Grand Avenue, Suite 90, South San Francisco, CA 94080, USA. Gkochendoerfer@gryphonRX.com number: 5608 accession-num: 12574628
Keywords: Amino Acid Sequence; Animals; Humans; Cell Line; Molecular Structure; Molecular Sequence Data; Circular Dichroism; Protein Folding; Mice; Spectrometry, Mass, Electrospray Ionization; Rats; Drug Stability; *Drug Design; *Erythropoiesis; *Polymers/*chemical synthesis/*chemistry/pharmacokinetics/pharmacology; Electrophoresis, Polyacrylamide Gel; Erythropoietin/chemistry/pharmacology; Hematocrit; Isoelectric Point; Molecular Weight; Proteins/*chemical synthesis/*chemistry/pharmacokinetics/pharmacology; Receptors, Erythropoietin/drug effects/metabolism; Recombinant Proteins

Chemoselective peptide bond formation using formyl-substituted nitrophenylthio ester - Ishiwata, Akihiro; Ichiyanagi, Tsuyoshi; Takatani, Maki; Ito, Yukishige (Tetrahedron Lett., 2003)
0040-4039
The following values have no corresponding Zotero field: number: 15

Effect of copper salts on peptide bond formation using peptide thioesters - Ingenito, Raffaele; Wenschuh, Holger (Org. Lett., 2003)
In the present paper, systematic studies revealed that Cu(I) salts in general and Cu(II) salts under certain circumstances promote effective reaction between peptide thiol esters and the N-terminal amino function of a second peptide segment to give the native amide bond for both solution- and solid-phase syntheses. Chiral integrity was retained. Reaction conditions were optimized and applied to the synthesis of a small protein, the identity of which was confirmed by NMR analysis.
The following values have no corresponding Zotero field: number: 24 publisher: American Chemical Society

Computational study of the aminolysis of esters. The reaction of methylformate with ammonia - Ilieva, Sonia; Galabov, Boris; Musaev, Djamaladdin G.; Morokuma, Keiji; Schaefer, Henry F. (J. Org. Chem., 2003)
doi: 10.1021/jo0263723 0022-3263 doi: 10.1021/jo0263723
The following values have no corresponding Zotero field: number: 4 publisher: American Chemical Society

An electronic effect on protein structure - Hinderaker, M. P.; Raines, R. T. (Protein Sci., 2003)
The well-known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N-formyl group (H(i-1)-C'(i-1)=O(i-1)), in which H(i-1) presents less steric hindrance than does O(i-1), likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n --> pi* interaction between the oxygen of the peptide bond (O(i-1)), and the subsequent carbonyl carbon in the polypeptide chain (C'(i)) also contributes to this preference. The O(i-1) and C'(i) distance and O(i-1).C'(i)=O(i) angle are especially favorable for such an n --> pi* interaction in a polyproline II helix. We propose that this electronic effect provides substantial stabilization to this and other elements of protein structure.
S10 RR013790/RR/NCRR NIH HHS/United States S10 RR13790/RR/NCRR NIH HHS/United States AR447276/AR/NIAMS NIH HHS/United States S10 RR04981/RR/NCRR NIH HHS/United States GM08506/GM/NIGMS NIH HHS/United States S10 RR04981-01/RR/NCRR NIH HHS/United States Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. United States a publication of the Protein Society
The following values have no corresponding Zotero field: auth-address: Department of Chemistry and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA. number: 6 accession-num: 12761389
Keywords: Protein Conformation; Stereoisomerism; Solvents/chemistry; Esters/chemistry; Molecular Structure; Proteins/*chemistry; *Electrons; Peptides/chemistry; Magnetic Resonance Spectroscopy/methods; Amides/chemical synthesis; Proline/chemistry

Aromatic thiol pKa effects on the folding rate of a disulfide containing protein - Gough, J. D.; Gargano, J. M.; Donofrio, A. E.; Lees, W. J. (Biochemistry, 2003)
The production of proteins via recombinant DNA technology often requires the in vitro folding of inclusion bodies, which are protein aggregates. To create a more efficient redox buffer for the in vitro folding of disulfide containing proteins, aromatic thiols were investigated for their ability to increase the folding rate of scrambled RNase A. Scrambled RNase A is fully oxidized RNase A with a relatively random distribution of disulfide bonds. The importance of the thiol pK(a) value was investigated by the analysis of five para-substituted aromatic thiols with pK(a) values ranging from 5.2 to 6.6. Folding was measured at pH 6.0 where the pK(a) value of the thiols would be higher, lower, or equal to the solution pH. Thus, relative concentrations of thiol and thiolate would vary across the series. At pH 6.0, the aromatic thiols increased the folding rate of RNase A by a factor of 10-23 over that observed for glutathione, the standard additive. Under optimal conditions, the apparent rate constant increased as the thiol pK(a) value decreased. Optimal conditions occurred when the concentration of protonated thiol in solution was approximately 2 mM, although the total thiol concentration varied considerably. The importance of the concentration of protonated thiol in solution can be understood based on equilibrium effects. Kinetic studies suggest that the redox buffer participates as the nucleophile and/or the center thiol in the key rate determining thiol disulfide interchange reactions that occur during protein folding. Aromatic thiols proved to be kinetically faster and more versatile than classical aliphatic thiol redox buffers.
Journal Article Research Support, U.S. Gov't, Non-P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA. alt-title: Biochemistry number: 40 accession-num: 14529290
Keywords: Hydrogen-Ion Concentration; *Protein Folding; Sulfhydryl Compounds/*chemistry; Oxidation-Reduction; Time Factors; Disulfides/*chemistry; Models, Chemical; Buffers; Glutathione Disulfide/chemistry; Glutathione/chemistry; Ribonuclease, Pancreatic/*chemistry

Diketopiperazines in peptide and combinatorial chemistry - Fischer, P. M. (J. Pept. Sci., 2003)
Diketopiperazines (DKPs), the smallest cyclic peptides, represent an important class of biologically active natural products and their research has been fundamental to many aspects of peptide chemistry. The advent of combinatorial chemistry has revived interest in DKPs for two reasons: firstly, they are simple heterocyclic scaffolds in which diversity can be introduced and stereochemically controlled at up to four positions; secondly, they can be prepared from readily available alpha-amino acids using very robust chemistry. Here synthetic methods, conformation, as well as applications of DKPs are summarized and discussed critically.
Fischer, Peter M Review England Journal of peptide science : an official publication of the European Peptide Society J Pept Sci. 2003 Jan;9(1):9-35.
The following values have no corresponding Zotero field: auth-address: Cyclacel Limited, Dundee, Scotland, UK. pfischer@cyclacel.com number: 1 edition: 2003/02/18 accession-num: 12587880
Keywords: Amino Acids/chemistry; Peptides/chemical synthesis/*chemistry; *Combinatorial Chemistry Techniques; Diketopiperazines; Piperazines/chemical synthesis/*chemistry

tris(2-Carboxyethyl)phosphine (TCEP) for the reduction of sulfoxides, sulfonylchlorides, N-oxides, and azides - Faucher, Anne-Marie; Grand-Maître, Chantal (Synth. Commun., 2003)
doi: 10.1081/SCC-120024730 0039-7911 doi: 10.1081/SCC-120024730
The following values have no corresponding Zotero field: number: 20 publisher: Taylor & Francis

Large-scale manufacture of peptide therapeutics by chemical synthesis - Bray, B. L. (Nat. Rev. Drug Discov., 2003)
The large-scale commercial production of a 36-amino-acid peptide by chemical synthesis has been demonstrated in the development of enfuvirtide (T-20 or Fuzeon), a first-in-class membrane fusion inhibitor for the treatment of HIV. The rationale behind route selection and the scale-up of the process used to manufacture enfuvirtide are discussed.
Bray, Brian L England Nat Rev Drug Discov. 2003 Jul;2(7):587-93. doi: 10.1038/nrd1133.
The following values have no corresponding Zotero field: auth-address: Trimeris, Inc., 3518 West Gate Drive, Durham, Noth Carolina NC27707, USA. bbray@trimeris.com alt-title: Nature reviews. Drug discovery number: 7 edition: 2003/06/20 accession-num: 12815383 work-type: Review
Keywords: Peptide Fragments/*chemical synthesis; Anti-HIV Agents/*chemical synthesis; HIV Envelope Protein gp41

Fmoc solid-phase synthesis of peptide thioesters by masking as trithioortho esters - Brask, J.; Albericio, F.; Jensen, K. J. (Org. Lett., 2003)
[reaction: see text] Total chemical synthesis of proteins by chemoselective ligation relies on C-terminal peptide thioesters as building blocks. Their preparation by standard Fmoc solid-phase peptide synthesis is made difficult by the lability of thioesters to aminolysis by the secondary amines used for removal of the Fmoc group. Here we present a novel backbone amide linker (BAL) strategy for their synthesis in which the thioester functionality is masked as a trithioortho ester throughout the synthesis.
1523-7060 (Print) 1523-7052 (Linking) Journal Article
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, Royal Veterinary and Agricultural University, DK-1871 Frederiksberg, Denmark. number: 16 accession-num: 12889916

Met, metastasis, motility and more - Birchmeier, C.; Birchmeier, W.; Gherardi, E.; Vande Woude, G. F. (Nat. Rev. Mol. Cell Biol., 2003)
1471-0072 (Print) 1471-0072 (Linking) Journal Article Review
The following values have no corresponding Zotero field: auth-address: Department of Neuroscience, Max-Delbruck-Center for Molecular Medicine, Robert-Rossle-Strasse 10, 13122 Berlin, Germany. number: 12 accession-num: 14685170
Keywords: Animals; Models, Molecular; Cell Line; Binding Sites; Morphogenesis; Signal Transduction/*physiology; Proto-Oncogene Proteins c-met/chemistry/genetics/*metabolism; Intracellular Signaling Peptides and Proteins; Protein Tyrosine Phosphatase, Non-Receptor Type 11; *Cell Movement; *Neoplasm Metastasis; Cell Size; Hepatocyte Growth Factor/chemistry/genetics/*metabolism; Neoplasms/genetics/metabolism/*pathology; Phosphoproteins/metabolism; Protein Tyrosine Phosphatases/metabolism

Total chemical synthesis of a functional interacting protein pair: the protooncogene H-Ras and the Ras-binding domain of its effector c-Raf1 - Becker, C. F.; Hunter, C. L.; Seidel, R.; Kent, S. B. H.; Goody, R. S.; Engelhard, M. (Proc. Natl. Acad. Sci. U. S. A., 2003)
Generation of biological function by chemical methods is potentially of great importance for the understanding and targeting of physiological processes. Chemical synthesis of proteins offers the ability to alter the properties of target protein molecules in a tailor-made fashion. In the present work it is demonstrated that this methodology can be expanded to the elucidation of protein-protein interactions as exemplified by the complete chemical synthesis of the protooncogene product H-Ras as well as of the Ras-binding domain (RBD) of its effector c-Raf1. The 166-aa polypeptide chain of H-Ras was synthesized by native chemical ligation of three unprotected peptide segments. Similarly, the 81-aa RBD was prepared by ligation of two peptide segments. Both RBD and Ras displayed functional and spectroscopic properties indistinguishable from their recombinant forms as judged by CD spectroscopy and from transient kinetic measurements of the Ras-RBD interaction as well as from nucleotide replacement reactions in Ras. An unnatural amino acid bearing a nitrobenzofurazan side chain was introduced into position 91 of the RBD, providing unique fluorescence properties. The association transient of nitrobenzofurazan labeled with Ras.guanosine 5'-beta,gamma-imidotriphosphate showed a slow phase that had not been detected in earlier work by using other signals.
0027-8424 (Print) 0027-8424 (Linking) Journal Article
The following values have no corresponding Zotero field: auth-address: Max-Planck-Institut fur Molekulare Physiologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany. number: 9 accession-num: 12704243
Keywords: Kinetics; Chromatography, High Pressure Liquid; Protein Folding; Protein Structure, Secondary; Proto-Oncogene Proteins c-raf/chemistry/*metabolism; Proto-Oncogene Proteins p21(ras)/chemistry/*metabolism

Oxidation of thiol compounds by molecular oxygen in aqueous solutions - Bagiyan, G. A.; Koroleva, I. K.; Soroka, N. V.; Ufimtsev, A. V. (Russ. Chem. Bull., 2003)
Side self-oxidation of thiols was studied. It was found that these reactions in neutral and alkaline solutions are induced by impurities of variable-valence metals. The ability of transition metals to catalyze oxidation of thiols changes in the order Cu > Mn > Fe > Ni â‰« Co. The plot of the self-oxidation rate vs. pH passes through a maximum whose position on the pH scale depends on both the nature of metal and the structure of the thiol oxidized. For thiols having different structures, the kinetic orders in reactions catalyzed by copper ions differently vary with pH, which is apparently associated with the formation of complexes possessing different catalytic activity.
The following values have no corresponding Zotero field: number: 5 label: Bagiyan2003 work-type: journal article

Protein prosthesis: a nonnatural residue accelerates folding and increases stability - Arnold, U.; Hinderaker, M. P.; Koditz, J.; Golbik, R.; Ulbrich-Hofmann, R.; Raines, R. T. (J. Am. Chem. Soc., 2003)
Nonnatural residues can endow proteins with desirable properties. Here, replacing a proline residue that has a cis peptide bond in native ribonuclease A with 5,5-dimethyl-l-proline is shown to accelerate protein folding by 6-fold and enhance conformational stability by DeltaTm = 2.8 +/- 0.3 degrees C while having no effect on enzymatic activity. The rational use of this and other prosthetic segments could enable chemotherapeutic proteins to survive longer in vivo or retain activity after oral administration.
GM 08506/GM/NIGMS NIH HHS/United States GM 44783/GM/NIGMS NIH HHS/United States Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Biochemistry/Biotechnology, Martin-Luther University, 06099 Halle, Germany. alt-title: Journal of the American Chemical Society number: 25 accession-num: 12812474
Keywords: Kinetics; *Protein Folding; Thermodynamics; Ribonuclease, Pancreatic/*chemistry; Proline/*analogs & derivatives/*chemistry

Rapid induction of cell death by selenium-compromised thioredoxin reductase 1 but not by the fully active enzyme containing selenocysteine - Anestal, K.; Arner, E. S. (J. Biol. Chem., 2003)
Mammalian thioredoxin reductases are selenoproteins. For native catalytic activity, these enzymes utilize a C-terminal -Gly-Cys-Sec-Gly-COOH sequence (where Sec is selenocysteine) forming a redox active selenenylsulfide/selenolthiol motif. A range of cellular systems depend upon or are regulated by thioredoxin reductase and its major protein substrate thioredoxin, including apoptosis signal-regulating kinase 1, peroxiredoxins, methionine sulfoxide reductase, and several transcription factors. Cytosolic thioredoxin reductase 1 (TrxR1) is moreover inhibited by various electrophilic anticancer compounds. TrxR1 is hence generally considered to promote cell viability. However, several recent studies have suggested that TrxR1 may promote apoptosis, and the enzyme was identified as GRIM-12 (gene associated with retinoid interferon-induced mortality 12). Transient transfection with GRIM-12/TrxR1 was also shown to directly induce cell death. To further analyze such effects, we have here employed lipid-mediated delivery of recombinant TrxR1 preparations into human A549 cells, thereby bypassing selenoprotein translation to facilitate assessment of the protein-related effects on cell viability. We found that selenium-deficient TrxR1, having a two-amino acid-truncated C-terminal -Gly-Cys-COOH motif, rapidly induced cell death (38 +/- 29% apoptotic cells after 4 h; p < 0.005 compared with controls). Cell death induction was also promoted by selenium-compromised TrxR1 derivatized with either cis-diamminedichloroplatinum (II) (cisplatin) or dinitrophenyl moieties but not by the structurally related non-selenoprotein glutathione reductase. In contrast, TrxR1 with intact selenocysteine could not promote cell death. The direct cellular effects of selenium-compromised forms of TrxR1 may be important for the pathophysiology of selenium deficiency as well as for the efficacy of antiproliferative drugs targeting the selenocysteine moiety of this enzyme.
Journal Article Research Support, Non-U.S. Gov't United States
The following values have no corresponding Zotero field: auth-address: Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden. alt-title: The Journal of biological chemistry number: 18 accession-num: 12574159
Keywords: Humans; Cell Survival; Apoptosis; Cisplatin/pharmacology; NADPH Oxidase/metabolism; Selenium/*physiology; Selenocysteine/*physiology; Thioredoxin Reductase 1; Thioredoxin-Disulfide Reductase/*physiology; Tumor Cells, Cultured

Granulysin crystal structure and a structure-derived lytic mechanism - Anderson, D. H.; Sawaya, M. R.; Cascio, D.; Ernst, W.; Modlin, R.; Krensky, A.; Eisenberg, D. (J. Mol. Biol., 2003)
Our crystal structure of granulysin suggests a mechanism for lysis of bacterial membranes by granulysin, a 74-residue basic protein from human cytolytic T lymphocyte and natural killer cells. We determined the initial crystal structure of selenomethionyl granulysin by MAD phasing at 2A resolution. We present the structure model refined using native diffraction data to 0.96A resolution. The five-helical bundle of granulysin resembles other "saposin folds" (such as NK-lysin). Positive charges distribute in a ring around the granulysin molecule, and one face has net positive charge. Sulfate ions bind near the segment of the molecule identified as most membrane-lytic and of highest hydrophobic moment. The ion locations may indicate granulysin's orientation of initial approach towards the membrane. The crystal packing reveals one way to pack a sheet of granulysin molecules at the cell surface for a concerted lysis effort. The energy of binding granulysin charges to the bacterial membrane could drive the subsequent lytic processes. The loosely packed core facilitates a hinge or scissors motion towards exposure of hydrophobic surface that we propose tunnels the granulysin into the fracturing target membrane.
AI07118/AI/NIAID NIH HHS/United States AI43348/AI/NIAID NIH HHS/United States AR40312/AR/NIAMS NIH HHS/United States Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. England
The following values have no corresponding Zotero field: auth-address: Howard Hughes Medical Institute, 5-748 MacDonald, Box 951662, Los Angeles, CA 90095-1662, USA. dha@mbi.ucla.edu alt-title: Journal of molecular biology number: 2 accession-num: 12488100
Keywords: Humans; Models, Molecular; Solvents/chemistry; Protein Binding; Hydrogen Bonding; Protein Folding; Crystallography, X-Ray; *Protein Structure, Tertiary; Binding Sites; Antigens, Differentiation, T-Lymphocyte/*chemistry; Anti-Infective Agents/*chemistry; Killer Cells, Natural/metabolism; Sulfates/chemistry; T-Lymphocytes, Cytotoxic/metabolism

Synthesis and application of an auxiliary group for chemical ligation at the X-gly site - Vizzavona, Jean; Dick, Fritz; Vorherr, Thomas (Bioorg. Med. Chem. Lett., 2002)
The following values have no corresponding Zotero field: number: 15

Semisynthesis and folding of the potassium channel KcsA - Valiyaveetil, Francis I.; MacKinnon, Roderick; Muir, Tom W. (J. Am. Chem. Soc., 2002)
doi: 10.1021/ja0266722 0002-7863 doi: 10.1021/ja0266722
The following values have no corresponding Zotero field: number: 31 publisher: American Chemical Society

Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides - Tornoe, Christian W.; Christensen, Caspar; Meldal, Morten (J. Org. Chem., 2013)
doi: 10.1021/jo011148j
The following values have no corresponding Zotero field: number: 9 publisher: American Chemical Society

Staudinger ligation of alpha-azido acids retains stereochemistry - Soellner, M. B.; Nilsson, B. L.; Raines, R. T. (J. Org. Chem., 2002)
The Staudinger ligation of peptides with a C-terminal phosphinothioester and N-terminal azide is an emerging method in protein chemistry. Here, the first Staudinger ligations of nonglycyl azides are reported and shown to proceed both in nearly quantitative yield and with no detectable effect on the stereochemistry at the alpha-carbon of the azide. These results demonstrate further the potential of the Staudinger ligation as a general method for the total synthesis of proteins from peptide fragments.
0022-3263 (Print) 0022-3263 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. number: 14 accession-num: 12098322
Keywords: Stereoisomerism; Molecular Structure; Catalysis; Chromatography, High Pressure Liquid; Proteins/*chemistry; Amino Acids/*chemistry; Azides/*chemistry; Peptide Fragments/chemistry; Chemistry, Organic/methods

Peptide-small molecule hybrids via orthogonal deprotection-chemoselective conjugation to cysteine-anchored scaffolds. A model study - Smith, Amos B.; Savinov, Sergey N.; Manjappara, Uma V.; Chaiken, Irwin M. (Org. Lett., 2002)
doi: 10.1021/ol026736d 1523-7060 doi: 10.1021/ol026736d
The following values have no corresponding Zotero field: number: 23 publisher: American Chemical Society

Dynamic covalent chemistry - Rowan, S. J.; Cantrill, S. J.; Cousins, G. R.; Sanders, J. K.; Stoddart, J. F. (Angew. Chem. Int. Ed., 2002)
Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.
Rowan, Stuart J Cantrill, Stuart J Cousins, Graham R L Sanders, Jeremy K M Stoddart, J Fraser Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Review Germany Angewandte Chemie (International ed. in English) Angew Chem Int Ed Engl. 2002 Mar 15;41(6):898-952.
The following values have no corresponding Zotero field: auth-address: Department of Macromolecular Science, Case Western Reserve University, Cleveland, OH, USA. sjr4@po.cwru.edu number: 6 edition: 2002/12/20 accession-num: 12491278
Keywords: Kinetics; Thermodynamics; Combinatorial Chemistry Techniques; Macromolecular Substances; Organic Chemicals/*chemical synthesis

A stepwise Huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes - Rostovtsev, Vsevolod V.; Green, Luke G.; Fokin, Valery V.; Sharpless, K. Barry (Angew. Chem. Int. Ed., 2002)
The following values have no corresponding Zotero field: number: 14 publisher: WILEY-VCH Verlag GmbH
Keywords: azides; copper; cycloaddition; homogeneous catalysis; nitrogen heterocycles

Drug discovery by dynamic combinatorial libraries - Ramstrom, O.; Lehn, J. M. (Nat. Rev. Drug Discov., 2002)
Dynamic combinatorial chemistry is a recently introduced supramolecular approach that uses self-assembly processes to generate libraries of chemical compounds. In contrast to the stepwise methodology of classical combinatorial techniques, dynamic combinatorial chemistry allows for the generation of libraries based on the continuous interconversion between the library constituents. Spontaneous assembly of the building blocks through reversible chemical reactions virtually encompasses all possible combinations, and allows the establishment of adaptive processes owing to the dynamic interchange of the library constituents. Addition of the target ligand or receptor creates a driving force that favours the formation of the best-binding constituent--a self-screening process that is capable, in principle, of accelerating the identification of lead compounds for drug discovery.
Ramstrom, Olof Lehn, Jean-Marie Review England Nature reviews. Drug discovery Nat Rev Drug Discov. 2002 Jan;1(1):26-36.
The following values have no corresponding Zotero field: auth-address: Laboratoire de Chimie Supramoleculaire, ISIS-Universite Louis Pasteur, 4 rue Blaise Pascal, F-67000, Strasbourg, France. number: 1 edition: 2002/07/18 accession-num: 12119606
Keywords: Molecular Conformation; *Combinatorial Chemistry Techniques; *Drug Design

Selenocysteine-mediated backbone cyclization of unprotected peptides followed by alkylation, oxidative elimination or reduction of the selenol - Quaderer, R.; Hilvert, D. (Chem. Commun., 2002)
An unprotected 16 residue peptide containing a C-terminal thioester and an N-terminal selenocysteine residue efficiently cyclizes in the presence of thiophenol; subsequent reduction, elimination or alkylation of the selenol yields modified cyclic peptides with alanine, dehydroalanine or a non-natural amino acid at the site of ligation.
1359-7345 (Print) 1359-7345 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Laboratory of Organic Chemistry, Swiss Federal Institute of Technology, ETH-Honggerberg, CH-8093 Zurich, Switzerland. number: 22 accession-num: 12510266
Keywords: Amino Acid Sequence; Peptides/*chemistry; Molecular Sequence Data; Oxidation-Reduction; Selenocysteine/*chemistry; Selenium Compounds/*chemistry; Cyclization; Alkylation

Extending synthetic access to proteins with a removable acyl transfer auxiliary - Offer, J.; Boddy, C. N.; Dawson, P. E. (J. Am. Chem. Soc., 2002)
A chemo- and regioselective auxiliary-mediated peptide ligation has been developed that is effective under nonidealized conditions for the synthesis of proteins. This general amide bond ligation utilizes a removable auxiliary that is analogous to the role of cysteine in native chemical ligation, combining chemoselective thioester exchange with efficient regioselective intramolecular acyl transfer. Acid lability and improved ligation efficiency were introduced into the 2-mercaptobenzyl auxiliary by increasing the electron density of the aromatic ring. The 62 amino acid SH3 domain from alpha-spectrin was synthesized using the auxiliary-mediated ligation at a Lys-Gly sequence. The auxiliary was removed with TFA and scavengers from the ligated product. This methodology enables unprotected peptides to be coupled at noncysteine ligation sites expanding the scope of protein synthesis and semisynthesis.
GM59380/GM/NIGMS NIH HHS/United States MH62261/MH/NIMH NIH HHS/United States Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Cell Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. alt-title: Journal of the American Chemical Society number: 17 accession-num: 11971712
Keywords: Amino Acid Sequence; Cysteine/chemistry; Molecular Sequence Data; Proteins/*chemical synthesis; Chromatography, High Pressure Liquid; Peptides/chemistry; src Homology Domains

Designing heterodimeric two-stranded alpha-helical coiled-coils. Effects of hydrophobicity and alpha-helical propensity on protein folding, stability, and specificity - Litowski, J. R.; Hodges, R. S. (J. Biol. Chem., 2002)
The E/K coil, a heterodimeric coiled-coil, has been designed as a universal peptide capture and delivery system for use in applications such as biosensors and as an expression and affinity purification tag. In this design, heterodimer formation is specified through the placement of charged residues at the e and g positions of the heptad repeat such that the E coil contains all glutamic acid residues at these positions, and the K coil contains all lysine residues at these positions. The affinity and stability of the E/K coil have been modified to allow a greater range of conditions for association and dissociation. Increasing the hydrophobicity of the coiled-coil core, by substituting isoleucine for valine, gave increases in stability of 2.81 and 3.73 kcal/mol (0.47 kcal/mol/substitution). Increasing the alpha-helical propensity of residues outside the core, by substituting alanine for serine, yielded increases in stability of 2.68 and 3.28 kcal/mol (0.41 and 0.45 kcal/mol/substitution). These sequence changes yielded a series of heterodimeric coiled-coils whose stabilities varied from 6.8 to 11.2 kcal/mol, greatly expanding their scope for use in protein engineering and biomedical applications.
Litowski, Jennifer R Hodges, Robert S J Biol Chem. 2002 Oct 4;277(40):37272-9. Epub 2002 Jul 22.
The following values have no corresponding Zotero field: auth-address: Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7 Canada. alt-title: The Journal of biological chemistry number: 40 edition: 2002/07/26 accession-num: 12138097 work-type: Research Support, Non-U.S. Gov't
Keywords: Amino Acid Sequence; Models, Molecular; Molecular Sequence Data; Chromatography, High Pressure Liquid; Peptides/chemical synthesis/*chemistry; Circular Dichroism; Protein Folding; Dimerization; *Protein Structure, Secondary; Indicators and Reagents; Drug Stability; Helix-Turn-Helix Motifs

Activation of acyl phosphate monoesters by lanthanide ions: Enhanced reactivity of benzoyl methyl phosphate - Kluger, Ronald; Cameron, Lisa L. (J. Am. Chem. Soc., 2002)
doi: 10.1021/ja016600v 0002-7863 doi: 10.1021/ja016600v
The following values have no corresponding Zotero field: number: 13 publisher: American Chemical Society

Preparation of phosphopeptide thioesters by Fmoc- and Fmoc(2-F)-solid phase synthesis - Hasegawa, K.; Sha, Y. L.; Bang, J. K.; Kawakami, T.; Akaji, K.; Aimoto, S. (Lett. Pept. Sci., 2002)
Keywords: #nosource

Folding disulfide-containing proteins faster with an aromatic thiol - Gough, J. D.; Williams, R. H.; Donofrio, A. E.; Lees, W. J. (J. Am. Chem. Soc., 2002)
The traditional method for in vitro folding of disulfide-containing proteins is slow and involves a redox buffer of glutathione and glutathione disulfide. To increase the folding rate and to gain insight into the folding process, we replaced glutathione, an aliphatic thiol, with a commercially available aromatic thiol, 4-mercaptobenzeneacetate (1). Aromatic thiol 1 was selected due to its enhanced nucleophilicity and its enhanced leaving-group ability relative to glutathione at pH 7.7. To demonstrate the advantages of 1, the folding of reduced and scrambled RNase A at pH 7.0 and 7.7 in the presence of 1 and glutathione was investigated. For each set of folding conditions, the optimum concentration of each thiol was initially determined and then the folding rates in the presence of each thiol were measured concurrently. In all cases examined, the folding rate enhancement with the aromatic thiol was 5- 6-fold. Furthermore, under similar conditions folding rates were almost identical with either reduced or scrambled RNase A. In addition the 5-6-fold folding rate enhancement varied only slightly with pH, 7.0 vs 7.7.
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA. alt-title: Journal of the American Chemical Society number: 15 accession-num: 11942825
Keywords: Kinetics; Hydrogen-Ion Concentration; Oxidation-Reduction; Sulfhydryl Compounds/*chemistry/metabolism; Protein Folding; Glutathione Disulfide/*chemistry/metabolism; Glutathione/*chemistry/metabolism; Phenylacetates/*chemistry/metabolism; Ribonuclease, Pancreatic/*chemistry/metabolism

Kinetics and mechanism of phosphate-catalyzed hydrolysis of benzoate esters: comparison with nucleophilic catalysis by imidazole and o-iodosobenzoate - El Seoud, Omar A.; Ruasse, Marie-Francoise; Rodrigues, Wagner A. (J. Chem. Soc., Perkin Trans. 2, 2002)
Phosphate-catalyzed hydrolysis of 2,4-dinitrophenyl 4-X-benzoate, and 3- or 4-Y-phenyl 3,5-dinitrobenzoates, where X and Y are substituents, has been studied spectrophotometrically. The following conclusions are based on catalytic rate constants, solvent kinetic isotope effect, detection of a mixed anhydride by FTIR, and application of the Hammett equation: (i) the catalytically active species is HPO42-, (ii) the mechanism of catalysis is nucleophilic, the reaction proceeds via the irreversible formation of acyl phosphate, (iii) the formation of a tetrahedral species by attack of the HPO42- on the ester CO group is rate limiting. Comparison of these results with our previous data on hydrolysis of benzoate esters with imidazole, or o-iodosobenzoate anion showed that: (i) the catalytic efficiency observed, o-iodosobenzoate > imidazole > phosphate, is due to a combination of steric and solvation effects, and the enhancement of the nucleophilicity of the former catalyst by the [small alpha]-effect, (ii) the nonlinear Bronsted-type plot between log (catalytic constant) and pKa of the leaving 4-Y-phenol indicates that the rate-limiting step for o-iodosobenzoate changes as a function of changing Y, (iii) the reaction rate-limiting steps are different for the above-mentioned nucleophiles.
1472-779X 10.1039/B202728N
The following values have no corresponding Zotero field: number: 6 publisher: The Royal Society of Chemistry

Hepatocyte growth factor/scatter factor binds to small heparin-derived oligosaccharides and stimulates the proliferation of human HaCaT keratinocytes - Delehedde, M.; Lyon, M.; Vidyasagar, R.; McDonnell, T. J.; Fernig, D. G. (J. Biol. Chem., 2002)
Hepatocyte growth factor/scatter factor (HGF/SF) acts via a dual receptor system consisting of the MET tyrosine kinase receptor and heparan sulfate or dermatan sulfate proteoglycans. In optical biosensor binding assays, competition by oligosaccharides for binding of HGF/SF to immobilized heparin showed that disaccharides failed to compete, whereas tetrasaccharides inhibited HGF/SF binding (IC(50) 8 microg/ml). The inhibitory potency of the oligosaccharides increased as their length increased by successive disaccharide units, to reach a maximum (IC(50) 1 microg/ml) at degree of polymerization (dp) 10. In binding assays, HGF/SF was found to bind directly to oligosaccharides as small as dp 4, and the binding parameters were similar for oligosaccharides of dp 4-14 (k(a) 2.2-45.3 x 10(6) m(-1) s(-1), k(d) 0.033-0.039 s(-1), and K(d) 9-16 nm). In human keratinocytes, HGF/SF stimulated DNA synthesis, and this was dependent on a sustained phosphorylation of p42/44(MAPK). In chlorate-treated and hence sulfated glycosaminoglycan-deficient HaCaT cells, the stimulation of DNA synthesis by HGF/SF was almost abolished. Heparin-derived oligosaccharides from dp 2 to dp 24 were added together with HGF/SF to chlorate-treated cells to determine the minimum size of oligosaccharides able to restore HGF/SF activity. At restricted concentrations of oligosaccharides (4 ng/ml), HGF/SF required decasaccharides, whereas at higher concentrations (100 ng/ml) even tetrasaccharides were able to partly restore DNA synthesis. The results suggest that HGF/SF binds to a tetrasaccharide and that although this is sufficient to enable the stimulation of DNA synthesis, longer oligosaccharides are more efficient, perhaps by virtue of their ability to bind more easily other molecules.
0021-9258 (Print) 0021-9258 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: School of Biological Sciences, Life Science Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom. number: 14 accession-num: 11799124
Keywords: Humans; Kinetics; Dose-Response Relationship, Drug; Protein Binding; Phosphorylation; Time Factors; Protein Structure, Tertiary; Biotinylation; Dimerization; Oligosaccharides/*chemistry; Binding, Competitive; Biosensing Techniques; Cell Division; Chlorates/pharmacology; DNA/biosynthesis; Glycosaminoglycans/chemistry; Heparin/*metabolism; Hepatocyte Growth Factor/*chemistry/*metabolism; Inhibitory Concentration 50; Keratinocytes/*metabolism; Mitogen-Activated Protein Kinase 1/metabolism; Mitogen-Activated Protein Kinase 3; Mitogen-Activated Protein Kinases/metabolism

An improved deblocking agent for direct Fmoc solid-phase synthesis of peptide thioesters - Bu, Xianzhang; Xie, Guiyang; Law, Chi Wang; Guo, Zhihong (Tetrahedron Lett., 2002)
To synthesize peptide thioesters directly on a solid support for use as substrate analogues for thioesterases in non-ribosomal peptide synthases, we modified a reagent compatible with Fmoc solid-phase peptide synthesis that efficiently removes the protecting group while keeping the thioester intact. The deprotecting reagent, consisting of DBU and HOBt, was successfully used to prepare a decapeptide in high yield.
The following values have no corresponding Zotero field: number: 13

In vitro quantification of hydrolysis-induced racemization of amino acid enantiomers in environmental samples using deuterium labeling and electron-impact ionization mass spectrometry - Amelung, W.; Brodowski, S. (Anal. Chem., 2002)
D-amino acids indicate aging, bacterial origin, and pathogenic properties of peptides in the environment, but the reliable assessment of D-enantiomers must account for a yet unknown formation during hydrolyses. Here, we introduce a method for the in vitro determination of the hydrolysis-induced racemization (HIR) of amino acids in environmental samples. It involves hydrolyses with hydro- and deuteriochloric acid (6 M, 12 h, 105 degrees C), desalting, and selective detection of chiral mass fragments of amino acid-N-pentafluoropropionyl derivatives. D-Amino acids formed in 2HCl incorporated deuterium into their C(alpha) position. This resulted in a relative signal loss of the nondeuterated fragment compared with the 1HCl hydrolysate. Mathematically evaluating the relative target signal intensities of both hydrolysates allowed the quantification of the proportion of D-amino acids formed during sample processing. Side-chain incorporations of deuterium were no limitations for this method as they could be estimated from that of the respective L-enantiomers. In soil and litter samples, between 0 (D-glutamic acid) and 85% (D-alloisoleucine) of the detected D-amino acids were formed upon hydrolysis (standard error, 5-11%). For a given amino acid, the HIR varied by a factor of 2-10 between samples, thereby confirming that HIR must be individually assessed for samples from different environments.
0003-2700 (Print) 0003-2700 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Institute of Soil Science and Soil Geography, University of Bayreuth, Germany. wulf.amelung@tu-berlin.de number: 13 accession-num: 12141688
Keywords: Stereoisomerism; Hydrolysis; Gas Chromatography-Mass Spectrometry; Isotope Labeling; Amino Acids/*analysis; Deuterium; Environmental Pollution/*analysis; Soil Pollutants/*analysis

Tris(2-carboxyethyl)phosphine hydrochloride - Yost, Julianne M.; Knight, John D.; Coltart, Don M. (e-EROS, 2001)
Keywords: #nosource

Understanding the relative acyl-transfer reactivity of oxoesters and thioesters: Computational analysis of transition state delocalization effects - Yang, Wei; Drueckhammer, Dale G. (J. Am. Chem. Soc., 2001)
doi: 10.1021/ja010726a 0002-7863 doi: 10.1021/ja010726a
The following values have no corresponding Zotero field: number: 44 publisher: American Chemical Society

Synthesis of peptides and proteins without cysteine residues by native chemical ligation combined with desulfurization - Yan, L. Z.; Dawson, P. E. (J. Am. Chem. Soc., 2001)
The highly chemoselective reaction between unprotected peptides bearing an N-terminal Cys residue and a C-terminal thioester enables the total and semi-synthesis of complex polypeptides. Here we extend the utility of this native chemical ligation approach to non-cysteine containing peptides. Since alanine is a common amino acid in proteins, ligation at this residue would be of great utility. To achieve this goal, a specific alanine residue in the parent protein is replaced with cysteine to facilitate synthesis by native chemical ligation. Following ligation, selective desulfurization of the resulting unprotected polypeptide product with H(2)/metal reagents converts the cysteine residue to alanine. This approach, which provides a general method to prepare alanyl proteins from their cysteinyl forms, can be used to chemically synthesize a variety of polypeptides, as demonstrated by the total chemical syntheses of the cyclic antibiotic microcin J25, the 56-amino acid streptococcal protein G B1 domain, and a variant of the 110-amino acid ribonuclease, barnase.
0002-7863 (Print) 0002-7863 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Departments of Cell Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, CVN-6, La Jolla, California 92037, USA. number: 4 accession-num: 11456564
Keywords: Cysteine/*chemistry; Proteins/*chemical synthesis; Methods; Peptides/*chemical synthesis; Aminobutyric Acids/chemistry; Bacterial Proteins/chemical synthesis; Bacteriocins/chemical synthesis; Ribonucleases/chemical synthesis

Covalent capture: a new tool for the purification of synthetic and recombinant polypeptides - Villain, M.; Vizzavona, J.; Rose, K. (Chem. Biol., 2001)
BACKGROUND: Purification of polypeptides and proteins derived from recombinant DNA techniques and of long synthetic polypeptides often represents a challenge. Affinity methods exist, but generally require addition of a large recognition unit to the target protein and use of expensive purification media. Use of large units is dictated by the characteristics of non-covalent complexes, where the energy necessary to form the complex derives from the sum of multiple weak energy interactions. Covalent interactions in contrast are of high energy, even when only a few bonds are formed. We decided to explore the use of the reversible covalent bond formed between N-terminal cysteine and threonine residues with an aldehyde as a method of protein purification. RESULTS: A series of test peptides with N-terminal cysteine and threonine were captured by a polyethyleneglycol-polyacrylamide resin to which an aldehyde function had been grafted. Peptides with other amino acids at the N-terminus did not interact with the resin. A recombinant polypeptide with N-terminal cysteine was purified to 90% purity in one step. Polypeptides were eluted from the resin simply by adding a hydroxylamine derivative, which reacts with aldehyde functions to form an oxime. CONCLUSIONS: Polypeptides possessing N-terminal cysteine or threonine can be easily purified using this 'covalent capture' approach.
1074-5521 (Print) 1074-5521 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Department of Medical Biochemistry, University Medical Center, Rue Michel-Servet 1, CH-1211 4, Geneva, Switzerland. number: 7 accession-num: 11451668
Keywords: Chromatography, High Pressure Liquid; Aldehydes/chemistry; Methods; Chemokine CCL5/chemical synthesis/isolation & purification; Chromatography/methods/standards; Peptide Fragments/chemical synthesis/isolation & purification; Peptides/chemical synthesis/*isolation & purification; Recombinant Proteins/isolation & purification; Resins, Plant/*chemistry

Methods and strategies of peptide ligation - Tam, J. P.; Xu, J.; Eom, K. D. (Biopolymers, 2001)
This review focuses on the concept, methods, and strategies of orthogonal peptide ligation. It updates our previous review in 1999 on the same subject matter in Biopolymers (Peptide Science, 1999, Vol. 51, p. 311). Orthogonal peptide ligation is an amino terminal specific method to couple chemically unprotected peptides or proteins derived from synthetic or biosynthetic sources. Unlike conventional chemical methods, peptide ligation methods do not require coupling reagents or protection schemes, but are achieved through a variable chemoselective capture step and then an invariable intramolecular acyl transfer reaction. It is also a convergent method with the fewest steps. More than a dozen orthogonal ligation methods have been developed based on captures by either imine or thioester chemistries to afford native and unusual amino acids at ligation sites of linear, branched, or cyclic peptides. The ligation strategies for multiple segments including sequential and tandem ligations are also discussed.
0006-3525 (Print) 0006-3525 (Linking) Journal Article Review
The following values have no corresponding Zotero field: auth-address: Department of Microbiology and Immunology, Vanderbilt University, A5119 MCN, Nashville, TN 37232, USA. tamjp@ctrvax.vanderbilt.edu number: 3 accession-num: 11774225
Keywords: Cysteine/chemistry; Protein Binding; Amino Acids/chemistry; Peptides/*chemical synthesis/*chemistry; Protein Engineering/methods; Methionine/chemistry; Proline/chemistry

Fmoc-compatible solid-phase peptide synthesis of long C-terminal peptide thioesters - Sewing, Axel; Hilvert, Donald (Angew. Chem. Int. Ed., 2001)
The following values have no corresponding Zotero field: number: 18 publisher: WILEY-VCH Verlag GmbH
Keywords: peptides; solid-phase synthesis; ligation; peptide thioester; peptide fragment condensation

Selenocysteine-mediated native chemical ligation - Quaderer, Richard; Sewing, Axel; Hilvert, Donald (Helv. Chim. Acta, 2001)
C-Terminal peptide thioesters are shown to react efficiently with peptide fragments containing an N-terminal selenocysteine to give selenoproteins. In analogy to the native chemical ligation of thioesters and peptides containing N-terminal cysteines, the selenol presumably attacks the thioester nucleophilically to give a selenoester intermediate that subsequently rearranges to give a native chemical bond. The utility of this procedure was demonstrated by the synthesis of a selenium-containing derivative of bovine pancreatic trypsin inhibitor (BPTI) in which Cys38 is replaced by selenocysteine. The artificial selenoprotein folds into a conformation similar to that of wild-type BPTI and inhibits trypsin and chymotrypsin with unaltered affinity.
The following values have no corresponding Zotero field: number: 5 publisher: Verlag Helvetica Chimica Acta

Improved synthesis of C-terminal peptide thioesters on "safety-catch" resins using LiBr/THF - Quaderer, R.; Hilvert, D. (Org. Lett., 2001)
[reaction: see text] The alkanesulfonamide "safety-catch" resin has proven useful for Fmoc-based synthesis of C-terminal peptide thioesters. We now report that the yield of isolated thioester can increase significantly when the cleavage reaction is carried out in 2 M LiBr/THF rather than DMF or THF. The largest effects are seen with problematic peptides that aggregate or form secondary structures on the resin.
1523-7060 (Print) 1523-7052 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Laboratory of Organic Chemistry, Swiss Federal Institute of Technology (ETH), Universitatstrasse 16, CH-8092 Zurich, Switzerland. number: 20 accession-num: 11574025
Keywords: Amino Acid Sequence; Animals; Molecular Sequence Data; Amino Acids/chemistry; Fluorenes/chemistry; Cattle; Sulfonamides/*chemistry; Furans/chemistry; Peptide Fragments/*chemical synthesis; Resins, Plant/*chemistry; Aprotinin/*chemical synthesis; Bromides/chemistry; Lithium Compounds/chemistry

Guanidine - Palmer, David C. (e-EROS, 2001)
* (acetate) [113-00-8113-00-8] CH5N3 (MW 59.09) InChI = 1S/CH5N3/c2-1(3)4/h(H5,2,3,4) InChIKey = ZRALSGWEFCBTJO-UHFFFAOYSA-N * (carbonate) [593-87-3593-87-3] C3H9N3O2 (MW 119.15) InChI = 1S/C2H4O2.CH5N3/c1-2(3)4;2-1(3)4/h1H3,(H,3,4);(H5,2,3,4) InChIKey = DXTIKTAIYCJTII-UHFFFAOYSA-N * (hydrochloride) [593-85-1593-85-1] C3H12N6O3 (MW 180.21) InChI = 1S/2CH5N3.CH2O3/c3*2-1(3)4/h2*(H5,2,3,4);(H2,2,3,4) InChIKey = STIAPHVBRDNOAJ-UHFFFAOYSA-N * (nitrate) [50-01-150-01-1] CH6ClN3 (MW 95.55) InChI = 1S/CH5N3.ClH/c2-1(3)4;/h(H5,2,3,4);1H InChIKey = PJJJBBJSCAKJQF-UHFFFAOYSA-N * (sulfate) [506-93-4506-93-4] CH6N4O3 (MW 122.11) InChI = 1S/CH5N3.NO3/c2*2-1(3)4/h(H5,2,3,4);/q;-1/p+1 InChIKey = MJFQUUWPZOGYQT-UHFFFAOYSA-O * (thiocyanate) [1184-68-51184-68-5] C2H12N6O4S (MW 216.27) InChI = 1S/2CH5N3.H2O4S/c2*2-1(3)4;1-5(2,3)4/h2*(H5,2,3,4);(H2,1,2,3,4) InChIKey = UYAKTBUPMOOXNW-UHFFFAOYSA-N * [593-84-0593-84-0] C2H6N4S (MW 118.19) InChI = 1S/CH5N3.CHNS/c2-1(3)4;2-1-3/h(H5,2,3,4);3H InChIKey = ZJYYHGLJYGJLLN-UHFFFAOYSA-N (synthesis of heterocycles; selective deacetylating agent; synthesis of primary amines) Physical Data:mp 48–49 °C; pKa 13.6. Solubility:free base readily sol alcohols, water; guanidinium salts of strong acids, e.g. HCl or HNO3, sol water, DMF, alcohol; guanidinium carbonate water sol but virtually insol alcohol; guanidine acetate sl sol ether, while guanidine nitrate moderately sol acetone; guanidinium salts, in general, insol aliphatic or aromatic hydrocarbons. Form Supplied in:commercially available salts include the acetate, carbonate, hydrochloride, nitrate, sulfate, and thiocyanate. Preparative Methods:substituted guanidines can be prepared by several methods. The reaction of an S-alkylisothiourea with an amine is one of the oldest and most useful methods but it suffers from production of noxious side products, namely an alkanethiol. An O-alkylisourea can also function in a similar manner, although these reagents, generally, are not as reactive as the S-alkylisothioureas. Direct oxidation of Thiourea and substituted thioureas to sulfonic acids prior to reaction with amines avoids the problems of thiol production. The intermediate sulfonic acids are at least as reactive as the S-alkylisothioureas. Cyanamide and substituted cyanamides react with amines or ammonium salts to produce guanidines. This approach can be useful to prepare certain hindered guanidines, e.g. derivatives of t-Butylamine. Addition of amines or ammonia to a disubstituted carbodiimide yields guanidines, but this method is limited by the availability of the carbodiimide. Reaction of amines with either 1-guanyl-3,5-dimethylpyrazole nitrate or 1-guanylpyrazole hydrochloride affords good yields of substituted guanidines. Handling, Storage, and Precautions:the free base is very hygroscopic and readily absorbs CO2 from the air. It is liberated from a salt and used in situ. Hydrolysis occurs slowly at room temperature but more rapidly at elevated temperatures or in the presence of alkali to yield urea, then CO2 and NH3. Guanidinium salts of strong acids are stable to boiling water. Toxic fumes of NOx are given off when guanidine is heated to decomposition. Use in a fume hood. Guanidine hydrochloride liberates toxic fumes of HCl and NOx when heated to decomposition. Guanidine nitrate is both a powerful oxidant and high explosive; a warning cautioning against its preparation has been published.
9780470842898
The following values have no corresponding Zotero field: publisher: John Wiley & Sons, Ltd

High-yielding Staudinger ligation of a phosphinothioester and azide to form a peptide - Nilsson, B. L.; Kiessling, L. L.; Raines, R. T. (Org. Lett., 2001)
[figure: see text] The Staudinger ligation can be used to couple a peptide with a C-terminal phosphinothioester to another with an N-terminal alpha-azido group to form a single peptide that contains no residual atoms. Here diphenylphosphinomethanethiol thioesters are shown to give high isolated yields for this transformation. This finding provides precedent for a powerful and versatile new method for the total synthesis of proteins.
1523-7060 (Print) 1523-7052 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. number: 1 accession-num: 11429880
Keywords: Models, Molecular; Molecular Structure; Catalysis; Proteins/*chemical synthesis; Azides/*chemistry; Organothiophosphorus Compounds/*chemistry

SUMO, ubiquitin's mysterious cousin - Muller, S.; Hoege, C.; Pyrowolakis, G.; Jentsch, S. (Nat. Rev. Mol. Cell Biol., 2001)
Covalent modification of cellular proteins by the ubiquitin-like modifier SUMO regulates various cellular processes, such as nuclear transport, signal transduction, stress response and cell-cycle progression. But, in contrast to ubiquitylation, sumoylation does not tag proteins for degradation, but seems to enhance their stability or modulate their subcellular compartmentalization.
Muller, S Hoege, C Pyrowolakis, G Jentsch, S Review England Nature reviews. Molecular cell biology Nat Rev Mol Cell Biol. 2001 Mar;2(3):202-10.
The following values have no corresponding Zotero field: auth-address: Max Planck Institute of Biochemistry, Department of Molecular Cell Biology, Am Klopferspitz 18a, 82152, Martinsried, Germany. stmuelle@biochem.mpg.de number: 3 edition: 2001/03/27 accession-num: 11265250
Keywords: Amino Acid Sequence; Animals; Humans; Sequence Homology, Amino Acid; Molecular Sequence Data; Proteins/metabolism; *Ubiquitin-Conjugating Enzymes; Ligases/metabolism; Saccharomyces cerevisiae/genetics/metabolism; SUMO-1 Protein; Ubiquitins/genetics/*metabolism

Perhydro-1,2,5-dithiazepine - Melnyk, Oleg; Agouridas, Vangelis (Encyclopedia of Reagents for Organic Synthesis, 2001)
[98354-47-398354-47-3] C4H9NS2 (MW 135.25) InChI = 1S/C4H9NS2/c1-3-6-7-4-2-5-1/h5H,1-4H2 InChIKey = LQZPWKIAEIOFEI-UHFFFAOYSA-N (synthesis of thioesters or latent thioesters, synthesis of thioacids, synthesis of amides (peptides), preparation of metal complexes ) Alternate Names:  1,2-dithia-5-azepane, 1,2,5-dithiazepane. Physical Data (Hydrochloride):  mp 178 °C, decomposed at 230 °C, mp 182–185 °C. Solubility:  water (hydrochloride). Analysis of Reagent Purity:  combustion analysis, 1H NMR. Preparative Method:  obtained by reaction of bis(2-chloroethyl)amine with sodium disulfide in water at 0 °C, followed by steam distillation of the resulting perhydro-1,2,5-dithiazepine, which was isolated as the hydrochloride.
The following values have no corresponding Zotero field: electronic-resource-num: 10.1002/047084289X.rn01723

Structure, activity and evolution of the group I thiolactone peptide quorum-sensing system of Staphylococcus aureus - MDowell, P.; Affas, Z.; Reynolds, C.; Holden, M. T.; Wood, S. J.; Saint, S.; Cockayne, A.; Hill, P. J.; Dodd, C. E.; Bycroft, B. W.; Chan, W. C.; Williams, P. (Mol. Microbiol., 2001)
In Staphylococcus aureus, the agr locus is responsible for controlling virulence gene expression via quorum sensing. As the blockade of quorum sensing offers a novel strategy for attenuating infection, we sought to gain novel insights into the structure, activity and turnover of the secreted staphylococcal autoinducing peptide (AIP) signal molecules. A series of analogues (including the L-alanine and D-amino acid scanned peptides) was synthesized to determine the functionally critical residues within the S. aureus group I AIP. As a consequence, we established that (i) the group I AIP is inactivated in culture supernatants by the formation of the corresponding methionyl sulphoxide; and (ii) the group I AIP lactam analogue retains the capacity to activate agr, suggesting that covalent modification of the AgrC receptor is not a necessary prerequisite for agr activation. Although each of the D-amino acid scanned AIP analogues retained activity, replacement of the endocyclic amino acid residue (aspartate) located C-terminally to the central cysteine with alanine converted the group I AIP from an activator to a potent inhibitor. The screening of clinical S. aureus isolates for novel AIP groups revealed a variant that differed from the group I AIP by a single amino acid residue (aspartate to tyrosine) in the same position defined as critical by alanine scanning. Although this AIP inhibits group I S. aureus strains, the producer strains possess a functional agr locus dependent on the endogenous peptide and, as such, constitute a fourth S. aureus AIP pheromone group (group IV). The addition of exogenous synthetic AIPs to S. aureus inhibited the production of toxic shock syndrome toxin (TSST-1) and enterotoxin C3, confirming the potential of quorum-sensing blockade as a therapeutic strategy.
Journal Article Research Support, Non-U.S. Gov't England
The following values have no corresponding Zotero field: auth-address: Institute of Infections and Immunity, School of Pharmaceutical Sciences, and School of BioSciences, University of Nottingham, Nottingham NG7 2RD, UK. alt-title: Molecular microbiology number: 2 accession-num: 11489134
Keywords: Stereoisomerism; Molecular Structure; Molecular Sequence Data; Oxidation-Reduction; *Evolution, Molecular; Cyclization; Structure-Activity Relationship; Electrophoresis, Polyacrylamide Gel; *Gene Expression Regulation, Bacterial/drug effects; *Signal Transduction/drug effects; Bacterial Proteins/*antagonists & inhibitors/metabolism; Colony Count, Microbial; Genes, Bacterial/genetics; Genes, Reporter/genetics; Lactams/chemical synthesis/chemistry/metabolism/pharmacology; Oligopeptides/chemistry/genetics/metabolism/pharmacology; Phenotype; Pheromones/*chemistry/genetics/*metabolism/pharmacology; RNA, Bacterial/genetics/metabolism; Staphylococcus aureus/drug effects/genetics/*metabolism/pathogenicity; Trans-Activators/*antagonists & inhibitors/metabolism; Virulence/genetics

2,2′-Azobis(2-methylpropanimidamide) dihydrochloride (V-50) - Matsugi, Masato; Kita, Yasuyuki (e-EROS, 2001)
[2997-92-42997-92-4] C8H18N6·2ClH (MW 271.19) InChI = 1S/C8H18N6.2ClH/c1-7(2,5(9)10)13-14-8(3,4)6(11)12;;/h1-4H3,(H3,9,10)(H3,11,12);2*1H InChIKey = LXEKPEMOWBOYRF-UHFFFAOYSA-N (reagent used as a water-soluble radical initiator) Alternate Name:V-50. Physical Data:mp 160∼169 °C (decomp.); temperature at which half of the initiator is decomposed after 10 h in H2O: 56 °C. Solubility:soluble in H2O (23.2 g/100 g water); insoluble in benzene, toluene, n-hexane. Form Supplied in:off white powder; widely available. Handling, Storage, and Precautions:to prevent decomposition, store at temperatures under 37 °C. V-50 is a polymerization agent and should be stored without other sources of radical initiation such as oxygen.
9780470842898
The following values have no corresponding Zotero field: publisher: John Wiley & Sons, Ltd

The role of a beta-proton transfer donor in the degradation of benzylpenicillin - Llinás, A.; Vilanova, B.; Muñoz, F.; Donoso, J. (J. Mol. Cat. A: Chemical, 2001)
1381-1169 doi: DOI: 10.1016/S1381-1169(01)00203-5
The following values have no corresponding Zotero field: number: 1-2
Keywords: [beta]-Lactam antibiotics; Penicillin; Proton transfer reaction; Thiolysis

Crystal structures of NK1-heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the MET receptor - Lietha, D.; Chirgadze, D. Y.; Mulloy, B.; Blundell, T. L.; Gherardi, E. (EMBO J., 2001)
NK1 is a splice variant of the polypeptide growth factor HGF/SF, which consists of the N-terminal (N) and first kringle (K) domain and requires heparan sulfate or soluble heparin for activity. We describe two X-ray crystal structures of NK1-heparin complexes that define a heparin-binding site in the N domain, in which a major role is played by R73, with further contributions from main chain atoms of T61, K63 and G79 and the side chains of K60, T61, R76, K62 and K58. Mutagenesis experiments demonstrate that heparin binding to this site is essential for dimerization in solution and biological activity of NK1. Heparin also comes into contact with a patch of positively charged residues (K132, R134, K170 and R181) in the K domain. Mutation of these residues yields NK1 variants with increased biological activity. Thus, we uncover a complex role for heparan sulfate in which binding to the primary site in the N domain is essential for biological activity whereas binding to the K domain reduces activity. We exploit the interaction between heparin and the K domain site in order to engineer NK1 as a potent receptor agonist and suggest that dual (positive and negative) control may be a general mechanism of heparan sulfate-dependent regulation of growth factor activity.
0261-4189 (Print) 0261-4189 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Growth Factors Group, MRC Centre, Hills Road, Cambridge CB2 2QH, UK. number: 20 accession-num: 11597998
Keywords: Animals; Humans; Models, Molecular; Protein Conformation; Cell Line; Protein Binding; Crystallography, X-Ray; Protein Structure, Tertiary; Structure-Activity Relationship; Binding Sites; Dimerization; Dogs; Drug Design; Kringles; Macromolecular Substances; effects/*metabolism; Heparin/*chemistry/metabolism; Heparitin Sulfate/metabolism; Hepatocyte Growth Factor/*chemistry/genetics/metabolism/pharmacology; Kidney; Mutagenesis, Site-Directed; Peptide Fragments/*chemistry/metabolism/pharmacology; Proto-Oncogene Proteins c-met/antagonists & inhibitors/drug; Recombinant Fusion Proteins/chemistry; RNA Splicing

Polypeptide synthesis using an expressed peptide as a building block for condensation with a peptide thioester: application to the synthesis of phosphorylated p21Max protein(1-101) - Kawakami, T.; Hasegawa, K.; Teruya, K.; Akaji, K.; Horiuchi, M.; Inagaki, F.; Kurihara, Y.; Uesugi, S.; Aimoto, S. (J. Pept. Sci., 2001)
An expressed peptide proved to be useful as a building block for the synthesis of a polypeptide via the thioester method. A partially protected peptide segment, for use as a C-terminal building block, could be prepared from a recombinant protein; its N-terminal amino acid residue was transaminated to an alpha-oxoacyl group, the side-chain amino groups were then protected with t-butoxycarbonyl (Boc) groups, and. finally, the alpha-oxoacyl group was removed. On the other hand, an O-phosphoserine-containing peptide thioester was synthesized via a solid-phase method using Boc chemistry. These building blocks were then condensed in the presence of silver ions and an active ester component. During the condensation, epimerization at the condensation site could be suppressed by the use of N,N-dimthylformamide (DMF) as a solvent. Using this strategy, a phosphorylated partial peptide of the p21Max protein, [Ser(PO3H2)2.11]-p21Max(1-101), was successfully synthesized.
Kawakami, T Hasegawa, K Teruya, K Akaji, K Horiuchi, M Inagaki, F Kurihara, Y Uesugi, S Aimoto, S England J Pept Sci. 2001 Sep;7(9):474-87.
The following values have no corresponding Zotero field: auth-address: Institute for Protein Research, Osaka University, Japan. alt-title: Journal of peptide science : an official publication of the European Peptide Society number: 9 edition: 2001/10/06 accession-num: 11587186 work-type: Research Support, Non-U.S. Gov't
Keywords: Peptides/*chemistry; Protein Binding; Chromatography, High Pressure Liquid; Phosphorylation; Time Factors; Protein Structure, Tertiary; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Models, Chemical; *Peptide Biosynthesis; *Transcription Factors; Basic-Leucine Zipper Transcription Factors; Dimethylformamide/pharmacology; DNA-Binding Proteins/*chemistry/metabolism; Phosphoserine/chemistry; Solvents/pharmacology

Selenocysteine in native chemical ligation and expressed protein ligation - Hondal, R. J.; Nilsson, B. L.; Raines, R. T. (J. Am. Chem. Soc., 2001)
0002-7863 (Print) 0002-7863 (Linking) Journal Article Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. number: 21 accession-num: 11457362
Keywords: Models, Molecular; Protein Conformation; Hydrogen-Ion Concentration; Selenocysteine/*chemistry; Ribonuclease, Pancreatic/*chemistry

Synthesis of the extracellular Ig domain I of Emmprin carrying a chitobiose unit - Hojo, Hironobu; Watabe, Jun; Nakahara, Yoshiaki; Nakahara, Yuko; Ito, Yukishige; Nabeshima, Kazuki; Toole, Bryan P. (Tetrahedron Lett., 2001)
The following values have no corresponding Zotero field: number: 16
Keywords: thioesters; condensations; glycopeptides

When FT-IR spectroscopy meets X-ray crystallography - Heberle, J.; Gensch, T. (Nat. Struct. Biol., 2001)
Comment News United States
The following values have no corresponding Zotero field: alt-title: Nature structural biology number: 3 accession-num: 11224557
Keywords: Models, Molecular; Hydrogen Bonding; Crystallography, X-Ray; Binding Sites; Protein Structure, Secondary; Photochemistry; Spectrophotometry, Infrared; Vibration; Crystallization; *Photoreceptors, Microbial; Bacterial Proteins/*chemistry/metabolism; Bacteriorhodopsins/chemistry/metabolism; Halorhodospira halophila/*chemistry; Isomerism; Light; Spectroscopy, Fourier Transform Infrared

2,2′-Azobis[2-(2-imidazolin-2-yl)propane] dihydrochloride - Grant, Daniel (e-EROS, 2001)
[27776-21-227776-21-2] C12H22N6·2HCl (MW 323.33) InChI = 1S/C12H22N6.2ClH/c1-11(2,9-13-5-6-14-9)17-18-12(3,4)10-15-7-8-16-10;;/h5-8H2,1-4H3,(H,13,14)(H,15,16);2*1H InChIKey = LBSPZZSGTIBOFG-UHFFFAOYSA-N Alternative Name:VA-044. Physical Data:mp 188–193 °C, half-life in water of 10 h at 44 °C. Solubility:freely soluble in water or methanol (30 g and above/ 100 g solvent); insoluble in toluene or hexanes. Form Supplied in:white-pale yellow crystals or crystalline powder, widely available. Handling, Storage, and Precautions:to prevent decomposition store at less than 30 °C.
9780470842898
The following values have no corresponding Zotero field: publisher: John Wiley & Sons, Ltd

Synthesis of a selenocysteine-containing peptide by native chemical ligation - Gieselman, M. D.; Xie, L.; van Der Donk, W. A. (Org. Lett., 2001)
[reaction in text] A new method for the synthesis of selenocysteine derivatives and selenocysteine-containing peptides is described. Fmoc-Se-p-methoxybenzylselenocysteine (1) was prepared and used for solid-phase synthesis of peptides with an N-terminal unprotected selenocysteine. Subsequent native chemical ligation with a peptide thioester provided a 17-mer that corresponds to the C-terminus of ribonucleotide reductase with selenocysteine in place of cysteine.
1523-7060 (Print) 1523-7052 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, USA. number: 9 accession-num: 11348227
Keywords: Sequence Homology, Amino Acid; Molecular Structure; Peptides/*chemical synthesis/chemistry; Magnetic Resonance Spectroscopy; Structure-Activity Relationship; Ribonucleotide Reductases/chemistry; Selenocysteine/*chemical synthesis/chemistry; Sequence Analysis, Protein

pH corrections and protein ionization in water/guanidinium chloride - Garcia-Mira, M. M.; Sanchez-Ruiz, J. M. (Biophys. J., 2001)
More than 30 years ago, Nozaki and Tanford reported that the pK values for several amino acids and simple substances in 6 M guanidinium chloride differed little from the corresponding values in low salt (Nozaki, Y., and C. Tanford. 1967. J. Am. Chem. Soc. 89:736-742). This puzzling and counter-intuitive result hinders attempts to understand and predict the proton uptake/release behavior of proteins in guanidinium chloride solutions, behavior which may determine whether the DeltaG(N-D) values obtained from guanidinium chloride-induced denaturation data can actually be interpreted as the Gibbs energy difference between the native and denatured states (Bolen, D. W., and M. Yang. 2000. Biochemistry. 39:15208-15216). We show in this work that the Nozaki-Tanford result can be traced back to the fact that glass-electrode pH meter readings in water/guanidinium chloride do not equal true pH values. We determine the correction factors required to convert pH meter readings in water/guanidinium chloride into true pH values and show that, when these corrections are applied, the effect of guanidinium chloride on the pK values of simple substances is found to be significant and similar to that of NaCl. The results reported here allow us to propose plausible guanidinium chloride concentration dependencies for the pK values of carboxylic acids in proteins and, on their basis, to reproduce qualitatively the proton uptake/release behavior for the native and denatured states of several proteins (ribonuclease A, alpha-chymotrypsin, staphylococcal nuclease) in guanidinium chloride solutions. Finally, the implications of the pH correction for the experimental characterization of protein folding energetics are briefly discussed.
Journal Article Research Support, Non-U.S. Gov't United States
The following values have no corresponding Zotero field: auth-address: Facultad de Ciencias, Departamento de Quimica Fisica, Universidad de Granada, 18071 Granada, Spain. alt-title: Biophysical journal number: 6 accession-num: 11721010
Keywords: Temperature; Hydrogen-Ion Concentration; Dose-Response Relationship, Drug; Thermodynamics; Protein Folding; Water/*chemistry; Carboxylic Acids/chemistry; *Ions; Guanidine/*chemistry; Models, Theoretical; Protons

Characterization of aromatic-thiol pi-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses - Duan, Guilin; Smith, Vedene H.; Weaver, Donald F. (Mol. Phys., 2001)
doi: 10.1080/00268970110063917 0026-8976 doi: 10.1080/00268970110063917
The following values have no corresponding Zotero field: number: 19 publisher: Taylor & Francis

Tributylphosphine - Diver, Steven T.; Dermenci, Alpay (e-EROS, 2001)
[998-40-3998-40-3] C12H27P (MW 202.36) InChI = 1S/C12H27P/c1-4-7-10-13(11-8-5-2)12-9-6-3/h4-12H2,1-3H3 InChIKey = TUQOTMZNTHZOKS-UHFFFAOYSA-N (1,4-addition catalyst; used with disulfides for the thioetherification of alcohols; acylation catalyst; used to prepare active esters) Physical Data:bp 240 °C; bp 130 °C/20 mmHg; d 0.812 g cm−3. Solubility:sol most organic solvents; slightly sol MeCN, H2O. Form Supplied in:widely available, neat; usually requires distillation. Analysis of Reagent Purity:31P NMR. Purification:distillation at reduced pressure. Improperly stored bottles of Bu3P are invariably contaminated with tributylphosphine oxide and butyl dibutylphosphinate. Handling, Storage, and Precautions:can be stored at room temperature indefinitely under an inert atmosphere. Oxygen should be rigorously excluded to avoid free radical chain oxidation. Tributylphosphine is pyrophoric and has an unpleasant odor. Toxicity: LD50 (rat) 750 mg kg−1.
The following values have no corresponding Zotero field: publisher: John Wiley & Sons, Ltd

Effects of aromatic thiols on thiol-disulfide interchange reactions that occur during protein folding - DeCollo, Todd V.; Lees, Watson J. (J. Org. Chem., 2001)
doi: 10.1021/jo015600a 0022-3263 doi: 10.1021/jo015600a
The following values have no corresponding Zotero field: number: 12 publisher: American Chemical Society

1,4-Dithiothreitol - Cleland, W. Wallace (e-EROS, 2001)
[27565-41-927565-41-9] C4H10O2S2 (MW 154.28) InChI = 1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2/t3-,4-/m1/s1 InChIKey = VHJLVAABSRFDPM-QWWZWVQMSA-N (reducing agent for disulfides; protection of thiols and proteins containing free SH groups from air oxidation) Alternate Names:DTT; threo-2,3-dihydroxybutane-1,4-dithiol. Physical Data:mp 42–44 °C (racemate); redox potential −0.33 V, pH 7, varying −0.06 V per pH unit; pK 9.2 and 10.1. Solubility:very sol water, alcohols. Form Supplied in:white solid; widely available; normally supplied as the racemate, but chiral 1,4-dithio-L-threitol [16096-97-2], mp 49–51 °C, is also available. The erythro isomer (1,4-dithioerythritol, DTE, [6892-68-8], mp 82–84 °C) has redox properties similar to the threo isomer (E°′ is more positive by 0.004 V) and is also available. The oxidized cyclic form (trans-1,2-dithiane-4,5-diol [14193-38-5], mp 130–132 °C) is available; it has a UV spectrum (λmax 283 nm; ε = 273). DTT and DTE are colorless above 260 nm, but both reduced and oxidized forms absorb below 240 nm. Analysis of Reagent Purity:the presence of monothiols can be detected by addition of arsenite (which forms a tight tridentate complex with DTT), followed by addition of 5,5′-dithiobis(2-nitrobenzoate). Total thiol content is determined by omitting arsenite. Handling, Storage, and Precautions:solid material should be stored under refrigeration in a closed bottle. Solutions will slowly oxidize in the presence of air to the cyclic disulfide, which is inert. The concentration of reduced material can be determined by assay with 5,5′-dithiobis(2-nitrobenzoate).
The following values have no corresponding Zotero field: publisher: John Wiley & Sons, Ltd

Thiophenol - Campopiano, Onorato; Minassian, Frédéric (e-EROS, 2001)
Keywords: #nosource

Total syntheses of thiocoraline and BE-22179 and assessment of their DNA binding and biological properties - Boger, D. L.; Ichikawa, S.; Tse, W. C.; Hedrick, M. P.; Jin, Q. (J. Am. Chem. Soc., 2001)
Full details of the total syntheses of thiocoraline (1) and BE-22179 (2), C(2) symmetric bicyclic octadepsipeptides possessing two pendant 3-hydroxyquinoline chromophores, are described in which their relative and absolute stereochemistry were established. Key elements of the approach include the late-stage introduction of the chromophore, symmetrical tetrapeptide coupling, macrocyclization of the 26-membered octadepsipeptide conducted at the single secondary amide site following disulfide formation, and a convergent assemblage of the tetradepsipeptide with introduction of the labile thiol ester linkage in the final coupling reaction under near racemization free conditions. By virtue of the late-stage introduction of the chromophore and despite the challenges this imposes on the synthesis, this approach provides ready access to a range of key chromophore analogues. Thiocoraline and BE-22179 were shown to bind to DNA by high-affinity bisintercalation analogous to echinomycin, but with little or no perceptible sequence selectivity. Both 1 and 2 were found to exhibit exceptional cytotoxic activity (IC(50) = 200 and 400 pM, respectively, L1210 cell line) comparable to echinomycin and one analogue, which bears the luzopeptin chromophore, was also found to be a potent cytotoxic agent.
Boger, D L Ichikawa, S Tse, W C Hedrick, M P Jin, Q CA41101/CA/NCI NIH HHS/ J Am Chem Soc. 2001 Jan 31;123(4):561-8.
The following values have no corresponding Zotero field: auth-address: Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. alt-title: Journal of the American Chemical Society number: 4 edition: 2001/07/18 accession-num: 11456568 work-type: Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
Keywords: Animals; Cattle; Mice; DNA/*metabolism; Tumor Cells, Cultured; Inhibitory Concentration 50; *Depsipeptides; *Peptides; Anti-Bacterial Agents/*chemical synthesis/metabolism/pharmacology; Antibiotics, Antineoplastic/chemical synthesis/metabolism/pharmacology; Cell Survival/drug effects; Echinomycin/metabolism/pharmacology; HIV-1/enzymology; Reverse Transcriptase Inhibitors

A sensitive fluorescence monitor for the detection of activated Ras: total chemical synthesis of site-specifically labeled Ras binding domain of c-Raf1 immobilized on a surface - Becker, C. F.; Hunter, C. L.; Seidel, R. P.; Kent, S. B. H.; Goody, R. S.; Engelhard, M. (Chem. Biol., 2001)
BACKGROUND: The Ras.GDP-Ras.GTP cycle plays a central role in eukaryotic signaling cascades. Mutations in Ras which stabilize activated Ras.GTP lead to a continuous stimulation of downstream effectors and ultimately to cell proliferation. Ras mutants which increase the steady-state concentration of Ras.GTP are involved in about 30% of all human cancers. It is therefore of great interest to develop a biosensor which is sensitive to Ras.GTP but not to Ras.GDP. RESULTS: The Ras binding domain (RBD) of c-Raf1 was synthesized from two unprotected peptide segments by native chemical ligation. Two fluorescent amino acids with structures based on the nitrobenz-2-oxa-1,3-diazole and coumaryl chromophores were incorporated at a site which is close to the RBD/Ras.GTP binding surface. Additionally, a C-terminal tag consisting of His6 was introduced. The Kd values for binding of the site-specifically modified proteins to Ras.GTP are comparable to that of wild-type RBD. Immobilization of C-terminal His6 tag-modified fluorescent RBD onto Ni-NTA-coated surfaces allowed the detection of Ras.GTP in the 100 nM range. Likewise, Ras.GTP/Q61L (an oncogenic mutant of Ras with very low intrinsic GTP hydrolysis activity) can also be detected in this assay system. Ras.GDP does not bind to the immobilized RBD, thus allowing discrimination between inactive and activated Ras. CONCLUSIONS: The site-specific incorporation of a fluorescent group at a strategic position in a Ras effector protein allows the detection of activated Ras with high sensitivity. This example illustrates the fact that the chemical synthesis of proteins or protein domains makes it possible to incorporate any kind of natural or unnatural amino acid at the position of choice, thereby enabling the facile preparation of specific biosensors, enhanced detection systems for drug screening, or the synthesis of activated proteins, e.g. phosphorylated proteins involved in signaling pathways, as defined molecular species.
Journal Article Research Support, Non-U.S. Gov't United States
The following values have no corresponding Zotero field: auth-address: Max-Planck-Institut fur moleculare Physiologie, Dortmund, Germany. alt-title: Chemistry & biology number: 3 accession-num: 11306349
Keywords: Animals; Humans; Binding Sites; Sensitivity and Specificity; Affinity Labels; Biosensing Techniques/*instrumentation/standards; Fluorescent Dyes/chemical synthesis; Guanosine Triphosphate/metabolism; Peptide Fragments/chemical synthesis; Proto-Oncogene Proteins c-raf/chemistry/metabolism; ras Proteins/*metabolism; Spectrometry, Fluorescence/methods

New quinone-amino acid conjugates linked via a vinylic spacer - Alnabari, M.; Bittner, S. (Amino Acids, 2001)
Chloranil and 2,3-dichloro-1,4-naphthoquinone have been linked to different natural and unnatural amino acids via a vinylic spacer. Two routes were developed for the facile preparation of these novel modified amino acids: the direct method, which can only be applied to secondary amines, and the indirect method (transamination reaction), which can be applied to any amino acid or ester.
Alnabari, M Bittner, S Research Support, Non-U.S. Gov't Austria Amino acids Amino Acids. 2001;20(4):381-7.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel. number: 4 edition: 2001/07/17 accession-num: 11452981
Keywords: Magnetic Resonance Spectroscopy; Models, Chemical; Chloranil/chemistry; Naphthoquinones/chemistry; Amino Acids/chemical synthesis/*chemistry; Benzoquinones/chemical synthesis/*chemistry; Indicators and Reagents/chemistry

Ab initio evaluation of the free energy surfaces for the general base/acid catalyzed thiolysis of formamide and the hydrolysis of methyl thiolformate: A reference solution reaction for studies of cysteine proteases - Å trajbl, Marek; FloriÃ¡n, Jan; Warshel, Arieh (J. Phys. Chem. B, 2001)
doi: 10.1021/jp010279l 1520-6106 doi: 10.1021/jp010279l
The following values have no corresponding Zotero field: number: 19 publisher: American Chemical Society

Computational studies of the aminolysis of oxoesters and thioesters in aqueous solution - Yang, Wei; Drueckhammer, Dale G. (Org. Lett., 2000)
doi: 10.1021/ol006691l 1523-7060 doi: 10.1021/ol006691l
The following values have no corresponding Zotero field: number: 26 publisher: American Chemical Society

Domain size distributions can predict domain boundaries - Wheelan, S. J.; Marchler-Bauer, A.; Bryant, S. H. (Bioinformatics, 2000)
MOTIVATION: The sizes of protein domains observed in the 3D-structure database follow a surprisingly narrow distribution. Structural domains are furthermore formed from a single-chain continuous segment in over 80% of instances. These observations imply that some choices of domain boundaries on an otherwise uncharacterized sequence are more likely than others, based solely on the size and segment number of predicted domains. This property might be used to guess the locations of protein domain boundaries. RESULTS: To test this possibility we enumerate putative domain boundaries and calculate their relative likelihood under a probability model that considers only the size and segment number of predicted domains. We ask, in a cross-validated test using sequences with known 3D structure, whether the most likely guesses agree with the observed domain structure. We find that domain boundary predictions are surprisingly successful for sequences up to 400 residues long and that guessing domain boundaries in this way can improve the sensitivity of threading analysis.
Journal Article Research Support, Non-U.S. Gov't England
The following values have no corresponding Zotero field: auth-address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. alt-title: Bioinformatics (Oxford, England) number: 7 accession-num: 11038331
Keywords: *Algorithms; *Models, Molecular; Proteins/*chemistry; Protein Structure, Tertiary; Probability

Facile, Fmoc-compatible solid-phase synthesis of peptide C-terminal thioesters - Swinnen, Dominique; Hilvert, Donald (Org. Lett., 2000)
The following values have no corresponding Zotero field: number: 16 publisher: American Chemical Society

Resolution of conflicting mechanistic observations in ester aminolysis. A warning on the qualitative prediction of isotope effects for reactive intermediates - Singleton, Daniel A.; Merrigan, Steven R. (J. Am. Chem. Soc., 2000)
doi: 10.1021/ja005519+ 0002-7863 doi: 10.1021/ja005519+
The following values have no corresponding Zotero field: number: 44 publisher: American Chemical Society

Cell surface engineering by a modified Staudinger reaction - Saxon, E.; Bertozzi, C. R. (Science, 2000)
Selective chemical reactions enacted within a cellular environment can be powerful tools for elucidating biological processes or engineering novel interactions. A chemical transformation that permits the selective formation of covalent adducts among richly functionalized biopolymers within a cellular context is presented. A ligation modeled after the Staudinger reaction forms an amide bond by coupling of an azide and a specifically engineered triarylphosphine. Both reactive partners are abiotic and chemically orthogonal to native cellular components. Azides installed within cell surface glycoconjugates by metabolism of a synthetic azidosugar were reacted with a biotinylated triarylphosphine to produce stable cell-surface adducts. The tremendous selectivity of the transformation should permit its execution within a cell's interior, offering new possibilities for probing intracellular interactions.
0036-8075 (Print) 0036-8075 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. number: 5460 accession-num: 10720325
Keywords: Humans; Acetylation; Oxidation-Reduction; Jurkat Cells; Biotinylation; Solubility; Azides/chemical synthesis/chemistry/*metabolism; Biotin/*analogs & derivatives/chemical synthesis/chemistry/metabolism; Cell Membrane/*chemistry/*metabolism; Flow Cytometry; Fluorescent Dyes/metabolism; Glycoconjugates/metabolism; Hela Cells; Hexosamines/chemical synthesis/chemistry/*metabolism; Ketones/metabolism; Phosphines/chemical synthesis/chemistry/*metabolism; Sulfhydryl Compounds/metabolism

A "traceless" Staudinger ligation for the chemoselective synthesis of amide bonds - Saxon, E.; Armstrong, J. I.; Bertozzi, C. R. (Org. Lett., 2000)
[reaction: see text] Here we report a novel modification of our previously reported "Staudinger ligation" that generates an amide bond from an azide and a specifically functionalized phosphine. This method for the selective formation of an amide bond, which does not require the orthogonal protection of distal functional groups, should find general utility in synthetic and biological chemistry.
1523-7060 (Print) 1523-7052 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, University of California, Berkeley, California 94720, USA. number: 14 accession-num: 10891251
Keywords: Molecular Conformation; Chromatography, High Pressure Liquid; Amides/*chemical synthesis/chemistry; Indicators and Reagents

Na-2-mercaptobenzylamine-assisted chemical ligation - Offer, John; Dawson, Philip E. (Org. Lett., 2000)
The following values have no corresponding Zotero field: number: 1 publisher: American Chemical Society

Population, acid-base, and redox properties of N-acetylcysteine conformers - Noszal, Béla; Visky, Dora; Kraszni, Marta (J. Med. Chem., 2000)
doi: 10.1021/jm9909600 0022-2623 doi: 10.1021/jm9909600
The following values have no corresponding Zotero field: number: 11 publisher: American Chemical Society

Staudinger ligation: a peptide from a thioester and azide - Nilsson, B. L.; Kiessling, L. L.; Raines, R. T. (Org. Lett., 2000)
[reaction: see text] The technique of native chemical ligation enables the total chemical synthesis of proteins. This method is limited, however, by an absolute requirement for a cysteine residue at the ligation juncture. Here, this restriction is overcome with a new chemical ligation method in which a phosphinobenzenethiol is used to link a thioester and azide. The product is an amide with no residual atoms.
1523-7060 (Print) 1523-7052 (Linking) Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. number: 13 accession-num: 10891196
Keywords: Esters/chemistry; Azides/chemistry; Peptides/*chemical synthesis; Biochemistry/*methods; Cysteine

Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast - Mossessova, E.; Lima, C. D. (Mol. Cell, 2000)
Modification of cellular proteins by the ubiquitin-like protein SUMO is essential for nuclear processes and cell cycle progression in yeast. The Ulp1 protease catalyzes two essential functions in the SUMO pathway: (1) processing of full-length SUMO to its mature form and (2) deconjugation of SUMO from targeted proteins. Selective reduction of the proteolytic reaction produced a covalent thiohemiacetal transition state complex between a Ulp1 C-terminal fragment and its cellular substrate Smt3, the yeast SUMO homolog. The Ulp1-Smt3 crystal structure and functional testing of elements within the conserved interface elucidate determinants of SUMO recognition, processing, and deconjugation. Genetic analysis guided by the structure further reveals a regulatory element N-terminal to the proteolytic domain that is required for cell growth in yeast.
Mossessova, E Lima, C D Research Support, Non-U.S. Gov't United states Molecular cell Mol Cell. 2000 May;5(5):865-76.
The following values have no corresponding Zotero field: auth-address: Biochemistry Department, Weill Medical College of Cornell University, New York, New York 10021, USA. number: 5 edition: 2000/07/06 accession-num: 10882122
Keywords: Amino Acid Sequence; Models, Molecular; Sequence Homology, Amino Acid; Molecular Sequence Data; Substrate Specificity; Catalytic Domain; Crystallography, X-Ray; Saccharomyces cerevisiae; Peptide Fragments/chemistry; *Small Ubiquitin-Related Modifier Proteins; Cysteine Endopeptidases/*chemistry/metabolism; Fungal Proteins/*chemistry; Glycine; Surface Properties; Ubiquitins/*chemistry

Relationship between the occurrence of cysteine in proteins and the complexity of organisms - Miseta, Attila; Csutora, Peter (Mol. Biol. Evol., 2000)
The occurrence and relative positions of cysteine residues were investigated in proteins of various species. Considering random mathematical occurrence for an amino acid coded by two codons (3.28%), cysteine is underrepresented in all organisms investigated. Representation of cysteine appears to correlate positively with the complexity of the organism, ranging between 2.26% in mammals and 0.5% in some members of the Archeabacteria order. This observation, together with the results obtained from comparison of cysteine content of various ribosomal proteins, indicates that evolution takes advantage of increased use of cysteine residues. In all organisms studied except plants, two cysteines are frequently found two amino acid residues apart (C-(X)2-C motif). Such a motif is known to be present in a variety of metal-binding proteins and oxidoreductases. Remarkably, more than 21% of all of cysteines were found within the C-(X)2-C motifs in Archea. This observation may indicate that cysteine appeared in ancient metal-binding proteins first and was introduced into other proteins later.
The following values have no corresponding Zotero field: number: 8

Functionalization of peptides and proteins by aldehyde or keto groups - Melnyk, O.; Fehrentz, J. A.; Martinez, J.; Gras-Masse, H. (Biopolymers, 2000)
The functionalization of peptides and proteins by aldehyde or keto groups has become the subject of intensive research since the discovery of the inhibition properties of peptide aldehydes and the advent of protein engineering. The first part of this review focuses upon the tremendous efforts devoted to the solid-phase synthesis of peptide aldehydes as protease inhibitors. The second part describes the utility of the aldehyde or keto functionalities for the site-specific modification of peptides or proteins.
Melnyk, O Fehrentz, J A Martinez, J Gras-Masse, H Research Support, Non-U.S. Gov't Review United states Biopolymers Biopolymers. 2000;55(2):165-86.
The following values have no corresponding Zotero field: auth-address: UMR 8525 Institut de Biologie et Institut Pasteur de Lille, Universite de Lille 2, 1 rue du Pr Calmette, 59021 Lille, France. Oleg.melnyk@pasteur-lille.fr number: 2 edition: 2000/11/14 accession-num: 11074412
Keywords: Proteins/*chemical synthesis; Aldehydes/chemistry; Peptides/*chemical synthesis; Formic Acid Esters; Ketones/chemistry; Resins, Plant

Expeditious amide-forming reactions using thiol esters - Kurosu, Michio (Tetrahedron Lett., 2000)
0040-4039
The following values have no corresponding Zotero field: number: 5

Synthesis of a molt-inhibiting hormone of the american crayfish, Procambarus clarkii, and determination of the location of its disulfide linkages - Kawakami, T.; Toda, C.; Akaji, K.; Nishimura, T.; Nakatsuji, T.; Ueno, K.; Sonobe, M.; Sonobe, H.; Aimoto, S. (J. Biochem., 2000)
A molt-inhibiting hormone (Prc-MIH) of the American crayfish, Procambarus clarkii, a member of the type II CHH family, was chemically synthesized and the location of its three disulfide linkages was determined. Prc-MIH consists of 75 amino acid residues and was synthesized by a thioester method. Two peptide segments, Boc-[Cys(Acm)(7,24,27), Lys(Boc)(19)]-Prc-MIH(1-39)-SCH(2)CH(2)CO-Nle-NH(2) and H-[Cys(Acm)(40,44,53), Lys(Boc)(42,51,67)]-Prc-MIH(40-75)-NH(2), were prepared using peptides obtained via the Boc solid-phase method. Condensation of the building blocks in the presence of silver chloride, 3,4-dihydro-3-hydroxy-4-oxo-1,2,3-benzotriazine, and N, N-diisopropylethylamine, followed by removal of the protecting groups, gave the reduced form of Prc-MIH(1-75)-NH(2). This product was converted to the native form of Prc-MIH (synthetic Prc-MIH) in a buffer which contained cysteine and cystine. The synthetic Prc-MIH showed the same behavior by RP-HPLC and biological activity assays as the natural Prc-MIH. The disulfide bond between Cys7 and Cys44 was determined by isolation of a fragment from an enzymatic digest of the synthetic Prc-MIH by RP-HPLC, followed by mass analysis. The disulfide bonds between Cys24 and Cys40 and between Cys27 and Cys53 were determined by comparing the elution position of an enzymatic digest of the synthetic Prc-MIH with authentic chemically synthesized samples, which contained three types of possible disulfide linkages.
Kawakami, T Toda, C Akaji, K Nishimura, T Nakatsuji, T Ueno, K Sonobe, M Sonobe, H Aimoto, S England J Biochem. 2000 Sep;128(3):455-61.
The following values have no corresponding Zotero field: auth-address: Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan. aimoto@protein.osaka-u.ac.jp alt-title: Journal of biochemistry number: 3 edition: 2000/08/31 accession-num: 10965045 work-type: Comparative Study Research Support, Non-U.S. Gov't
Keywords: Animals; Dose-Response Relationship, Drug; Esters/chemistry; Chromatography, High Pressure Liquid; Mass Spectrometry; Disulfides/*chemistry; Peptide Fragments/chemistry; Astacoidea/*chemistry; Ecdysterone/metabolism; Neuropeptides/*chemical synthesis/*chemistry/isolation & purification; Serine Endopeptidases/metabolism

Polypeptide synthesis using an expressed peptide as a building block via the thioester method - Kawakami, Toru; Hasegawa, Koki; Teruya, Kenta; Akaji, Kenichi; Horiuchi, Masataka; Inagaki, Fuyuhiko; Kurihara, Yasuyuki; Uesugi, Seiichi; Aimoto, Saburo (Tetrahedron Lett., 2000)
The following values have no corresponding Zotero field: number: 15
Keywords: thioesters; condensations; peptide building blocks; peptides and polypeptides

Unconventional origin of metal ion rescue in the Hammerhead ribozyme reaction: Mn2+-assisted redox conversion of 2'-mercaptocytidine to cytidine - Hamm, Michelle L.; Nikolic, Dejan; van Breemen, Richard B.; Piccirilli, Joseph A. (J. Am. Chem. Soc., 2000)
doi: 10.1021/ja000379p 0002-7863 doi: 10.1021/ja000379p
The following values have no corresponding Zotero field: number: 49 publisher: American Chemical Society

The role of ring strain on the ease of ring closure of bifunctional chain molecules - Galli, Carlo; Mandolini, Luigi (Eur. J. Org. Chem., 2000)
The role of ring strain on the ease of ring formation over a wide range of ring sizes is discussed on the basis of a comparison of transition state versus product-ring strain energies. A general procedure is illustrated for the assessment of transition-state strain energies, based on experimental effective molarities (EMs) and an extra-thermodynamic treatment of entropy data for ring closure. It is found that the ring product is a good model of the transition state of cyclisation for all but the shortest chains. Our earlier interpretation of this remarkable lack of correspondence between transition state and product-ring strain energies in intramolecular nucleophilic substitutions of the very short chains, is compared with the results of recent theoretical calculations.
1099-0690
The following values have no corresponding Zotero field: number: 18 publisher: WILEY-VCH Verlag GmbH
Keywords: Macrocycles; Lactones; Ring closure; Strained molecules

Synthesis of native proteins by chemical ligation - Dawson, P. E.; Kent, S. B. H. (Annu. Rev. Biochem., 2000)
In just a few short years, the chemical ligation of unprotected peptide segments in aqueous solution has established itself as the most practical method for the total synthesis of native proteins. A wide range of proteins has been prepared. These synthetic molecules have led to the elucidation of gene function, to the discovery of novel biology, and to the determination of new three-dimensional protein structures by both NMR and X-ray crystallography. The facile access to novel analogs provided by chemical protein synthesis has led to original insights into the molecular basis of protein function in a number of systems. Chemical protein synthesis has also enabled the systematic development of proteins with enhanced potency and specificity as candidate therapeutic agents.
0066-4154 (Print) 0066-4154 (Linking) In Vitro Journal Article Review
The following values have no corresponding Zotero field: auth-address: The Scripps Research Institute, La Jolla, California 92037, USA. dawson@scripps.edu accession-num: 10966479
Keywords: Amino Acid Sequence; Humans; Models, Molecular; Molecular Sequence Data; Protein Folding; Protein Structure, Tertiary; Proteins/*chemical synthesis/chemistry/genetics; Chemistry, Organic/methods; HIV Protease/chemical synthesis/chemistry

Generation of a dual-labeled fluorescence biosensor for Crk-II phosphorylation using solid-phase expressed protein ligation - Cotton, G. J.; Muir, T. W. (Chem. Biol., 2000)
BACKGROUND: The site-specific chemical modification of proteins has proved to be extremely powerful for generating tools for the investigation of biological processes. Although a few elegant methods exist for engineering a recombinant protein at a unique position, these techniques cannot be easily extended to allow several different chemical probes to be specifically introduced into a target sequence. As such multiply labeled proteins could be used to study many biological processes, and in particular biomolecular interactions, we decided to investigate whether such protein reagents could be generated using an extension of the semisynthesis technique known as expressed protein ligation. RESULTS: A solid-phase expressed protein ligation (SPPL) technology is described that enables large semisynthetic proteins to be assembled on a solid support by the controlled sequential ligation of a series of recombinant and synthetic polypeptide building blocks. This modular approach allows multiple, different chemical modifications to be introduced site-specifically into a target protein. This process, which is analogous to solid-phase peptide synthesis, was used to dual-label the amino and carboxyl termini of the Crk-II adapter protein with the fluorescence resonance energy transfer pair tetramethylrhodamine and fluorescein, respectively. The resulting construct reports (through a fluorescence change) the phosphorylation of Crk-II by the nonreceptor protein tyrosine kinase, c-Abl, and was used to probe the protein-protein interactions that regulate this important post-translational process. CONCLUSIONS: SPPL provides a powerful method for specifically modifying proteins at multiple sites, as was demonstrated by generating a protein-based biosensor for Crk-II phosphorylation. Such protein derivatives are extremely useful for investigating protein function in vitro and potentially in vivo. This modular approach should be applicable to many different protein systems.
1074-5521 (Print) 1074-5521 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10021, USA. number: 4 accession-num: 10780925
Keywords: Animals; Phosphorylation; Fluoresceins/chemistry; Rhodamines/chemistry; Mice; Spectrometry, Fluorescence; Fluorescent Dyes/chemistry; Biosensing Techniques/*methods; src Homology Domains; *Proto-Oncogene Proteins; Phosphotyrosine/chemistry; Protein Kinases/*chemistry; Proto-Oncogene Proteins c-abl/chemistry; Proto-Oncogene Proteins c-crk

Peptide segment coupling by prior ligation and proximity-induced intramolecular acyl transfer - Coltart, Don M. (Tetrahedron, 2000)
0040-4020 doi: 10.1016/S0040-4020(00)00147-2
The following values have no corresponding Zotero field: number: 22

Peptide thioester preparation by Fmoc solid phase peptide synthesis for use in native chemical ligation - Clippingdale, A. B.; Barrow, C. J.; Wade, J. D. (J. Pept. Sci., 2000)
Established methodology for the preparation of peptide thioesters requires the use of t-butoxycarbonyl chemistry owing to the lability of thioester linkers to the nucleophilic reagents used in Fmoc solid phase peptide synthesis. Both the greater ease of use and the broad applicability of the method has led to the development of an Fmoc-based methodology for direct peptide thioester synthesis. It was found that successful preparation of a peptide thioester could be achieved when the non-nucleophilic base, 1,8-diazabicyclo[5.4.0]undec-7-ene, together with 1-hydroxybenzotriazole in dimethylformamide, were used as the N(alpha)-Fmoc deprotection reagent. Native chemical ligation of the resulting thioester product to an N-terminal cysteine-containing peptide was successfully performed in aqueous solution to produce a fragment peptide of human alpha-synuclein. The formation of aspartimide (cyclic imide) in a base-sensitive hexapeptide fragment of scorpion toxin II was found to be significant under the deprotection conditions used. However, this could be controlled by the judicious protection of sensitive residues using the 2-hydroxy-4-methoxybenzyl group.
1075-2617 (Print) 1075-2617 (Linking) Journal Article Research Support, Non-U.S. Gov't
The following values have no corresponding Zotero field: auth-address: Howard Florey Institute of Experimental Physiology and Medicine, The University of Melbourne, Victoria, Australia. number: 5 accession-num: 10823491
Keywords: Humans; Chromatography, High Pressure Liquid; Time Factors; Amino Acids/*chemistry; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Peptides/*chemical synthesis/*chemistry; Models, Chemical; Esters/*chemical synthesis; Fluorenes/*chemistry; Dimethylformamide/chemistry; *Peptide Biosynthesis; alpha-Synuclein; Aspartic Acid/analogs & derivatives/biosynthesis; Nerve Tissue Proteins/chemistry; Synucleins; Triazoles/pharmacology

An overview of structural genomics - Burley, S. K. (Nat Struct Biol, 2000)
With access to sequences of entire human genomes plus those of various model organisms and many important microbial pathogens, structural biology is on the verge of a dramatic transformation. Our newfound wealth of sequence information will serve as the foundation for an important initiative in structural genomics. We are poised to embark on a systematic program of high-throughput X-ray crystallography and NMR spectroscopy aimed at developing a comprehensive view of the protein structure universe. Structural genomics will yield a large number of experimental protein structures (tens of thousands) and an even larger number of calculated comparative protein structure models (millions). This enormous body of structural data will be freely available, and promises to accelerate scientific discovery in all areas of biological science, including biodiversity and evolution in natural ecosystems, agricultural plant genetics, breeding of farm and domestic animals, and human health and disease.
Journal Article Research Support, U.S. Gov't, P.H.S. United states
The following values have no corresponding Zotero field: auth-address: Howard Hughes Medical Institute, Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA. burley@rockefeller.edu alt-title: Nature structural biology accession-num: 11103991
Keywords: Animals; Humans; Protein Conformation; Crystallography, X-Ray; Internet; Structure-Activity Relationship; Nuclear Magnetic Resonance, Biomolecular; *Genomics/economics/trends; Computational Biology/economics/trends; Databases as Topic; Pilot Projects; Proteins/*chemistry/genetics/*metabolism

Protein synthesis by solid-phase chemical ligation using a safety catch linker - Brik, A.; Keinan, E.; Dawson, P. E. (J. Org. Chem., 2000)
The native chemical ligation reaction has been used extensively for the synthesis of the large polypeptides that correspond to folded proteins and domains. The efficiency of the synthesis of the target protein is highly dependent on the number of peptide segments in the synthesis. Assembly of proteins from multiple components requires repeated purification and lyophilization steps that give rise to considerable handling losses. In principle, performing the ligation reactions on a solid support would eliminate these inefficient steps and increase the yield of the protein assembly. A new strategy is described for the assembly of large polypeptides on a solid support that utilizes a highly stable safety catch acid-labile linker. This amide generating linker is compatible with a wide range of N-terminal protecting groups and ligation chemistries. The utility of the methodology is demonstrated by a three-segment synthesis of vMIP I, a chemokine that contains all 20 natural amino acids and has two disulfide bonds. The crude polypeptide product was recovered quantitatively from the solid support and purified in 20%-recovered yield. This strategy should facilitate the synthesis of large polypeptides and should find useful applications in the assembly of protein libraries.
0022-3263 (Print) 0022-3263 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Departments of Cell Biology and Chemistry, Deparment of Molecular Biology, and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. number: 12 accession-num: 10864771
Keywords: Amino Acid Sequence; Molecular Sequence Data; Proteins/*chemical synthesis; Indicators and Reagents; Chemistry, Organic/methods; *Viral Proteins; Disulfides; Macrophage Inflammatory Proteins/*chemical synthesis/chemistry; Peptide Fragments/*chemical synthesis/chemistry; Sepharose

The deprotection of Lys(Mtt) revisited - Bourel, L.; Carion, O.; Gras-Masse, H.; Melnyk, O. (J. Pept. Sci., 2000)
The selective deprotection of Lys(Mtt)-containing peptidyl resins was successfully monitored by RP-HPLC using very short linear gradients. RP-HPLC analyses of the acidic filtrates also revealed the partial cleavage of the Trt groups and of the peptide-resin bond. The absorbance of the Mtt carbocation at 470 nm is only twice that of the Trt cation. Thus, the UV monitoring at 470 nm seems to be inappropriate, especially at the end of the deprotection, when the Mtt and the Trt levels are comparable.
Bourel, L Carion, O Gras-Masse, H Melnyk, O Research Support, Non-U.S. Gov't England Journal of peptide science : an official publication of the European Peptide Society J Pept Sci. 2000 Jun;6(6):264-70.
The following values have no corresponding Zotero field: auth-address: UMR 8525 CNRS-Universite de Lille 2, Institut de Biologie et Institut Pasteur de Lille, France. line.bourel@pasteur-lille.fr number: 6 edition: 2000/07/27 accession-num: 10912906
Keywords: Amino Acid Sequence; Molecular Sequence Data; Chromatography, High Pressure Liquid; Ultraviolet Rays; Gas Chromatography-Mass Spectrometry; Lysine/*analogs & derivatives/chemistry/*metabolism; Peptides/chemical synthesis/metabolism; Trityl Compounds/chemistry/*metabolism

Quinonic enaminones; Synthesis of new dialkylaminovinyl and bis(dialkylaminovinyl) derivatives of quinones - Alnabari, M.; Bittner, S. (Synthesis, 2000)
Keywords: #nosource

Lactone and lactam library synthesis by silver ion-assisted orthogonal cyclization of unprotected peptides - Zhang, Lianshan; Tam, James P. (J. Am. Chem. Soc., 1999)
The following values have no corresponding Zotero field: number: 14 publisher: American Chemical Society

A cyclic antimicrobial peptide produced in primate leukocytes by the ligation of two truncated alpha-defensins - Tang, Y. Q.; Yuan, J.; Osapay, G.; Osapay, K.; Tran, D.; Miller, C. J.; Ouellette, A. J.; Selsted, M. E. (Science, 1999)
Analysis of rhesus macaque leukocytes disclosed the presence of an 18-residue macrocyclic, tridisulfide antibiotic peptide in granules of neutrophils and monocytes. The peptide, termed rhesus theta defensin-1 (RTD-1), is microbicidal for bacteria and fungi at low micromolar concentrations. Antibacterial activity of the cyclic peptide was threefold greater than that of an open-chain analog, and the cyclic conformation was required for antimicrobial activity in the presence of 150 millimolar sodium chloride. Biosynthesis of RTD-1 involves the head-to-tail ligation of two alpha-defensin-related nonapeptides, requiring the formation of two new peptide bonds. Thus, host defense cells possess mechanisms for synthesis and granular packaging of macrocyclic antibiotic peptides that are components of the phagocyte antimicrobial armamentarium.
AI22931/AI/NIAID NIH HHS/United States DK33506/DK/NIDDK NIH HHS/United States DK44632/DK/NIDDK NIH HHS/United States etc. Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Pathology, College of Medicine, University of California, Irvine, CA 92697, USA. alt-title: Science (New York, N.Y number: 5439 accession-num: 10521339
Keywords: Amino Acid Sequence; Animals; Humans; Protein Conformation; Molecular Sequence Data; Protein Processing, Post-Translational; Disulfides/chemistry; Cloning, Molecular; *Protein Biosynthesis; Anti-Bacterial Agents; Anti-Infective Agents/chemistry/*metabolism/pharmacology; Bacteria/drug effects; Defensins; Fungi/drug effects; Leukopoiesis; Macaca mulatta; Monocytes/*metabolism; Neutrophils/*metabolism; Oligopeptides/chemistry/genetics/metabolism; Osmolar Concentration; Peptides, Cyclic/*biosynthesis/chemistry/genetics/pharmacology; Protein Precursors/chemistry/genetics/metabolism; Proteins/chemistry/genetics/pharmacology

Orthogonal ligation strategies for peptide and protein - Tam, J. P.; Yu, Q.; Miao, Z. (Biopolymers, 1999)
This review focuses on the concept, criteria, and methods of an orthogonal amide ligating strategy suitable for syntheses of peptides, peptide mimetics, and proteins. Utilizing unprotected peptides or proteins derived from chemical or biosynthetic sources, this ligation strategy has been shown to be general and exceptionally mild. Its orthogonality in ligating two unprotected segments with free N-terminal (NT)-amines at a specific NT-amine is achieved through a chemoselective capture step and then an intramolecular acyl transfer reaction. Both coupling reagents for enthalpic activation and protection schemes therefore become unnecessary. More than a dozen orthogonal ligation methods based on either imine or thioester captures have been developed to afford native and unusual amino acids at ligation sites of linear, branched, or cyclic peptides. Because unprotected peptides and proteins of different sizes and forms can be obtained from either chemical or recombinant sources, orthogonal ligation removes the size limitation imposed on the chemical synthesis of a protein with a native or non-native structure. Furthermore, by using building blocks from biosynthetic sources, orthogonal ligation provides a unifying operational concept for both total and semisynthesis of peptides and proteins.
0006-3525 (Print) 0006-3525 (Linking) Journal Article Research Support, U.S. Gov't, P.H.S. Review
The following values have no corresponding Zotero field: auth-address: Department of Microbiology and Immunology, Vanderbilt University, A5119 MCN, Nashville, TN 37232-2363, USA. tamjp@ctrvax.vanderbilt.edu number: 5 accession-num: 10685043
Keywords: Ligands; Protein Engineering/methods; *Peptide Biosynthesis; *Peptides/chemical synthesis/metabolism; *Proteins/chemical synthesis/metabolism; Amino Acids/metabolism

Stereospecific pseudoproline ligation of N-terminal serine, threonine, or cysteine-containing unprotected peptides - Tam, James P.; Miao, Zhenwei (J. Am. Chem. Soc., 1999)
The following values have no corresponding Zotero field: number: 39 publisher: American Chemical Society

Fmoc-based synthesis of peptide-athioesters: application to the total chemical synthesis of a glycoprotein by native chemical ligation - Shin, Youngsook; Winans, Katharine A.; Backes, Bradley J.; Kent, Stephen B. H.; Ellman, Jonathan A.; Bertozzi, Carolyn R. (J. Am. Chem. Soc., 2013)
doi: 10.1021/ja992881j
The following values have no corresponding Zotero field: number: 50 publisher: American Chemical Society

The CATH Database provides insights into protein structure/function relationships - Orengo, C. A.; Pearl, F. M.; Bray, J. E.; Todd, A. E.; Martin, A. C.; Lo Conte, L.; Thornton, J. M. (Nucleic Acids Res, 1999)
We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.
Journal Article England
The following values have no corresponding Zotero field: auth-address: Department of Biochemistry and Molecular Biology, Darwin Building, Univeristy College London, Gower Street, London WC1E 6BT, UK. orengo@biochem.ucl.ac.uk alt-title: Nucleic acids research number: 1 accession-num: 9847200
Keywords: Amino Acid Sequence; Computational Biology; Sequence Homology, Amino Acid; Protein Folding; Internet; Structure-Activity Relationship; Protein Structure, Secondary; Algorithms; *Databases, Factual/trends; Enzymes/chemistry/classification/physiology; Evolution, Molecular; Genome; Phylogeny; Proteins/*chemistry/classification/*physiology

Structure-activity analysis of synthetic autoinducing thiolactone peptides from Staphylococcus aureus responsible for virulence - Mayville, P.; Ji, G.; Beavis, R.; Yang, H.; Goger, M.; Novick, R. P.; Muir, T. W. (Proc. Natl. Acad. Sci. U. S. A., 1999)
The synthesis of virulence factors and other extracellular proteins responsible for pathogenicity in Staphylococcus aureus is under the control of the agr locus. A secreted agr-encoded peptide, AgrD, processed from the AgrD gene product, is known to be an effector of self-strain activation and cross-strain inhibition of the agr response. Biochemical analysis of AgrD peptides isolated from culture supernatants has suggested that they contain an unusual thiol ester-linked cyclic structure. In the present work, chemical synthesis is used to confirm that the mature AgrD peptides contain a thiolactone structure and that this feature is absolutely necessary for full biological activity. The AgrD synthetic thiolactone peptides exhibited biological activity in vivo in a mouse protection test. Structure-activity studies have allowed key aspects of the peptide structure involved in the differential activation and inhibition functions to be identified. Accordingly, we propose a model for activation and inhibition of the agr response in which the former, but not the latter, involves specific acylation of the agr transmembrane receptor, AgrC.
A142783/PHS HHS/United States AI30138-09/AI/NIAID NIH HHS/United States R01 GM055843/GM/NIGMS NIH HHS/United States R21 AI030138/AI/NIAID NIH HHS/United States R29 GM055843/GM/NIGMS NIH HHS/United States GM55843-01/GM/NIGMS NIH HHS/United States R01 AI030138/AI/NIAID NIH HHS/United States Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. alt-title: Proceedings of the National Academy of Sciences of the United States of America number: 4 accession-num: 9990004
Keywords: Amino Acid Sequence; Animals; Lactones/chemistry; Mice; Structure-Activity Relationship; Virulence/genetics; *Trans-Activators; Abscess/drug therapy/pathology/prevention & control; Bacterial Proteins/biosynthesis/chemistry/*genetics; Lactams; Oligopeptides/chemical synthesis/chemistry/*pharmacology; Peptides, Cyclic/chemical synthesis/chemistry/*pharmacology; Skin Diseases, Bacterial/drug therapy/pathology/prevention & control; Staphylococcal Infections/*drug therapy/prevention & control; Staphylococcus aureus/drug effects/genetics/*pathogenicity; Transcription Factors/biosynthesis/chemistry/*genetics

A new protease required for cell-cycle progression in yeast - Li, S. J.; Hochstrasser, M. (Nature, 1999)
In eukaryotes, protein function can be modulated by ligation to ubiquitin or to ubiquitin-like proteins (Ubl proteins). The vertebrate Ubl protein SUMO-1 is only 18% identical to ubiquitin but is 48% identical to the yeast protein Smt3. Both SUMO-1 and Smt3 are ligated to cellular proteins, and protein conjugation to SUMO-1/Smt3 is involved in many physiological processes. It remained unknown, however, whether deconjugation of SUMO-1/Smt3 from proteins is also essential. Here we describe a yeast Ubl-specific protease, Ulp1, which cleaves proteins from Smt3 and SUMO-1 but not from ubiquitin. Ulp1 is unrelated to any known deubiquitinating enzyme but shows distant similarity to certain viral proteases, indicating the existence of a widely conserved protease fold. Proteins related to Ulp1 are present in many organisms, including several human pathogens. The pattern of Smt3-coupled proteins in yeast changes markedly throughout the cell cycle, and specific conjugates accumulate in ulp1 mutants. Ulp1 has several functions, including an essential role in the G2/M phase of the cell cycle.
Li, S J Hochstrasser, M Research Support, U.S. Gov't, P.H.S. England Nature Nature. 1999 Mar 18;398(6724):246-51.
The following values have no corresponding Zotero field: auth-address: University of Chicago, Department of Biochemistry & Molecular Biology, Illinois 60637, USA. number: 6724 edition: 1999/03/27 accession-num: 10094048
Keywords: Humans; Sequence Homology, Amino Acid; Molecular Sequence Data; Substrate Specificity; Escherichia coli; Mutagenesis; Ubiquitins/metabolism; Carrier Proteins/metabolism; Cloning, Molecular; SUMO-1 Protein; *Saccharomyces cerevisiae Proteins; Cell Cycle Proteins/genetics/isolation & purification/*metabolism; Cysteine Endopeptidases/genetics/isolation & purification/*metabolism; Fungal Proteins/isolation & purification/metabolism; G2 Phase/physiology; Mitosis/physiology; Recombinant Fusion Proteins/genetics/metabolism; Repressor Proteins/metabolism; Saccharomyces cerevisiae/cytology/*enzymology; Small Ubiquitin-Related Modifier Proteins

Solid phase synthesis of peptide C-terminal thioesters by Fmoc/t-Bu chemistry - Ingenito, Raffaele; Bianchi, Elisabetta; Fattori, Daniela; Pessi, Antonello (J. Am. Chem. Soc., 2013)
doi: 10.1021/ja992668n
The following values have no corresponding Zotero field: number: 49 publisher: American Chemical Society

Protein synthesis by native chemical ligation: expanded scope by using straightforward methodology - Hackeng, T. M.; Griffin, J. H.; Dawson, P. E. (Proc. Natl. Acad. Sci. U. S. A., 1999)
The total chemical synthesis of proteins has great potential for increasing our understanding of the molecular basis of protein function. The introduction of native chemical ligation techniques to join unprotected peptides next to a cysteine residue has greatly facilitated the synthesis of proteins of moderate size. Here, we describe a straightforward methodology that has enabled us to rapidly analyze the compatibility of the native chemical ligation strategy for X-Cys ligation sites, where X is any of the 20 naturally occurring amino acids. The simplified methodology avoids the necessity of specific amino acid thioester linkers or alkylation of C-terminal thioacid peptides. Experiments using matrix-assisted laser-desorption ionization MS analysis of combinatorial ligations of LYRAX-C-terminal thioester peptides to the peptide CRANK show that all 20 amino acids are suitable for ligation, with Val, Ile, and Pro representing less favorable choices because of slow ligation rates. To illustrate the method's utility, two 124-aa proteins were manually synthesized by using a three-step, four-piece ligation to yield a fully active human secretory phospholipase A(2) and a catalytically inactive analog. The combination of flexibility in design with general access because of simplified methodology broadens the applicability and versatility of chemical protein synthesis.
Hackeng, T M Griffin, J H Dawson, P E HL 21544/HL/NHLBI NIH HHS/United States HL 31950/HL/NHLBI NIH HHS/United States Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United states Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10068-73.
The following values have no corresponding Zotero field: auth-address: Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. number: 18 edition: 1999/09/01 accession-num: 10468563
Keywords: Amino Acid Sequence; Humans; Proteins/*chemical synthesis/chemistry; Kinetics; Peptides/*chemical synthesis/chemistry; Molecular Sequence Data; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Peptide Fragments/chemistry; Indicators and Reagents; Chemistry, Organic/methods; Cysteine; Amino Acids, Sulfur; Phospholipases A/*chemical synthesis/chemistry

A comparison between the sulfhydryl reductants tris(2-carboxyethyl)phosphine and dithiothreitol for use in protein biochemistry - Getz, E. B.; Xiao, M.; Chakrabarty, T.; Cooke, R.; Selvin, P. R. (Anal. Biochem., 1999)
The newly introduced sulfhydryl reductant tris(2-carboxyethyl)phosphine (TCEP) is a potentially attractive alternative to commonly used dithiothreitol (DTT). We compare properties of DTT and TCEP important in protein biochemistry, using the motor enzyme myosin as an example protein. The reductants equally preserve myosin's enzymatic activity, which is sensitive to sulfhydryl oxidation. When labeling with extrinsic probes, DTT inhibits maleimide attachment to myosin and must be removed before labeling. In contrast, maleimide attachment to myosin was achieved in the presence of TCEP, although with less efficiency than no reductant. Surprisingly, iodoacetamide attachment to myosin was nearly unaffected by either reductant at low (0.1 mM) concentrations. In electron paramagnetic resonance (EPR) spectroscopy utilizing nitroxide spin labels, TCEP is highly advantageous: spin labels are two to four times more stable in TCEP than DTT, thereby alleviating a long-standing problem in EPR. During protein purification, Ni(2+) concentrations contaminating proteins eluted from Ni(2+) affinity columns cause rapid oxidation of DTT without affecting TCEP. For long-term storage of proteins, TCEP is significantly more stable than DTT without metal chelates such as EGTA in the buffer, whereas DTT is more stable if metal chelates are present. Thus TCEP has advantages over DTT, although the choice of reductant is application specific.
0003-2697 (Print) 0003-2697 (Linking) Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Cardiovascular Research Institute, University of California, San Francisco, California 94143, USA. number: 1 accession-num: 10452801
Keywords: Animals; Hydrolysis; Oxidation-Reduction; Models, Chemical; Rabbits; *Dithiothreitol; *Indicators and Reagents; *Phosphines; *Sulfhydryl Reagents; Adenosine Triphosphatases/metabolism; Cation Transport Proteins; Electron Spin Resonance Spectroscopy; Myosin Subfragments/metabolism

Mode of action of thiocoraline, a natural marine compound with anti-tumour activity - Erba, E.; Bergamaschi, D.; Ronzoni, S.; Faretta, M.; Taverna, S.; Bonfanti, M.; Catapano, C. V.; Faircloth, G.; Jimeno, J.; D'Incalci, M. (Br. J. Cancer, 1999)
Thiocoraline, a new anticancer agent derived from the marine actinomycete Micromonospora marina, was found to induce profound perturbations of the cell cycle. On both LoVo and SW620 human colon cancer cell lines, thiocoraline caused an arrest in G1 phase of the cell cycle and a decrease in the rate of S phase progression towards G2/M phases, as assessed by using bromodeoxyuridine/DNA biparametric flow cytometric analysis. Thiocoraline does not inhibit DNA-topoisomerase II enzymes in vitro, nor does it induce DNA breakage in cells exposed to effective drug concentrations. The cell cycle effects observed after exposure to thiocoraline appear related to the inhibition of DNA replication. By using a primer extension assay it was found that thiocoraline inhibited DNA elongation by DNA polymerase alpha at concentrations that inhibited cell cycle progression and clonogenicity. These studies indicate that the new anticancer drug thiocoraline probably acts by inhibiting DNA polymerase alpha activity.
Erba, E Bergamaschi, D Ronzoni, S Faretta, M Taverna, S Bonfanti, M Catapano, C V Faircloth, G Jimeno, J D'Incalci, M England Br J Cancer. 1999 Jun;80(7):971-80.
The following values have no corresponding Zotero field: auth-address: Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy. alt-title: British journal of cancer number: 7 edition: 1999/06/11 accession-num: 10362104 work-type: Research Support, Non-U.S. Gov't
Keywords: Humans; Time Factors; Cell Cycle/drug effects; Tumor Cells, Cultured; Inhibitory Concentration 50; *Depsipeptides; *Peptides; Flow Cytometry; Anti-Bacterial Agents/*pharmacology; Antibiotics, Antineoplastic/*pharmacology; Bromodeoxyuridine/metabolism; Cell Division/drug effects; DNA-Directed DNA Polymerase/drug effects; DNA/drug effects/metabolism; Tumor Stem Cell Assay

Intramolecular acid-catalyzed amide isomerization in aqueous solution - Cox, Christopher; Lectka, Thomas (Org. Lett., 1999)
doi: 10.1021/ol9901265 1523-7060 doi: 10.1021/ol9901265
The following values have no corresponding Zotero field: number: 5 publisher: American Chemical Society

Insertion of a Synthetic Peptide into a Recombinant Protein Framework: A Protein Biosensor - Cotton, Graham J.; Ayers, Brenda; Xu, Rong; Muir, Tom W. (J. Am. Chem. Soc., 2012)
doi: 10.1021/ja983804b 0002-7863 doi: 10.1021/ja983804b
The following values have no corresponding Zotero field: number: 5 publisher: American Chemical Society

Crystal structure of the NK1 fragment of HGF/SF suggests a novel mode for growth factor dimerization and receptor binding - Chirgadze, D. Y.; Hepple, J. P.; Zhou, H.; Byrd, R. A.; Blundell, T. L.; Gherardi, E. (Nat. Struct. Biol., 1999)
Although ligand-induced receptor dimerization is a common prerequisite for receptor activation, the mode by which different growth factors bind their receptors and cause them to dimerize varies considerably. Here we report the crystal structure at 2.5 A resolution of NK1, a receptor-binding fragment and a natural splice variant of hepatocyte growth factor/scatter factor (HGF/SF). NK1 assembles as a homodimer in the asymmetric unit, revealing a novel mode of growth factor dimerization produced by close packing of the N domain of one subunit and the kringle domain of the other, thus bringing the two linkers in close proximity. The structure suggests the presence of a binding site for heparan sulfate chains and a mechanism by which the NK1 dimer may engage two receptor molecules through clusters of amino acids located on each protomer and on opposite surfaces of the homodimer. We also report that short (14-mer) heparin fragments effectively dimerize NK1 in solution, implying that heparan sulfate chains may stabilize the NK1 dimer. These results provide a basis for the agonistic activity of NK1 and have implications for the mechanism of receptor binding of HGF/SF.
1072-8368 (Print) 1072-8368 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Department of Biochemistry, University of Cambridge, UK. number: 1 accession-num: 9886295
Keywords: Animals; Humans; Molecular Sequence Data; Crystallography, X-Ray; Binding Sites; Dimerization; Proto-Oncogene Proteins c-met/metabolism; *Protein Conformation; Hepatocyte Growth Factor/*chemistry/metabolism; Peptide Fragments/chemistry/metabolism

Kinetics and mechanisms of reactions of thiol, thiono, and dithio analogues of carboxylic esters with nucleophiles - Castro, Enrique A. (Chem. Rev., 1999)
doi: 10.1021/cr990001d 0009-2665 doi: 10.1021/cr990001d
The following values have no corresponding Zotero field: number: 12 publisher: American Chemical Society

Chemical protein synthesis by solid phase ligation of unprotected peptide segments - Canne, Lynne E.; Botti, Paolo; Simon, Reyna J.; Chen, Yijun; Dennis, Edward A.; Kent, Stephen B. H. (J. Am. Chem. Soc., 1999)
In this paper we describe "solid phase chemical ligation" (SPCL), the application of the principles of polymer-supported organic synthesis to the construction of large polypeptide chains for the total chemical synthesis of proteins. In this method, each building block used is an unprotected peptide segment of 20 or more amino acids. These are consecutively reacted by chemical ligation, the chemoselective reaction of the unprotected peptide segments from aqueous solution, to make the polymer-supported target polypeptide. In a final step, the assembled full-length target polypeptide is released from the aqueous-compatible polymer support. Here we report chemistries for the attachment of the first segment to a polymer support, and for the assembly of the target polypeptide chain starting from the polymer-bound peptide segment. In this solid phase protein synthesis method, large target polypeptide chains can be built efficiently and rapidly by SPCL and, after release from the polymer support, folded to give functional protein molecules. Several examples of the application of SPCL are given: model peptides consisting of 27 and 68 amino acids, and polypeptides corresponding to the proteins C5a (74 amino acids) and MIF (115 amino acids), were each made in good yield and purity from the consecutive solid phase ligation of peptide segments. In addition, we report the total synthesis by SPCL of the enzyme "human group V secretory phospholipase A2" (GV-PLA2), which comprises a polypeptide of 118 amino acids containing 6 disulfide bonds. As demonstrated by these examples, SPCL is an important extension of our capabilities for total chemical protein synthesis.
doi: 10.1021/ja9836287 0002-7863 doi: 10.1021/ja9836287
The following values have no corresponding Zotero field: number: 38 publisher: American Chemical Society

Native chemical ligation of polypeptides - Camarero, J. A.; Muir, T. W. (Curr. Protoc. Prot. Sci., 1999)
The following values have no corresponding Zotero field: auth-address: The Rockefeller University, New York, New York, USA. accession-num: 18429140
Keywords: Protein Engineering/*methods; Models, Biological; Genetic Vectors/genetics; Peptide Fragments/*chemistry/genetics; Proteins/*chemical synthesis/*chemistry/genetics

Biosynthesis of a head-to-tail cyclized protein with improved biological activity - Camarero, Julio A.; Muir, Tom W. (J. Am. Chem. Soc., 2012)
doi: 10.1021/ja990929n 0002-7863 doi: 10.1021/ja990929n
The following values have no corresponding Zotero field: number: 23 publisher: American Chemical Society

Ground state and transition state contributions to the rates of intramolecular and enzymatic reactions - Bruice, Thomas C.; Lightstone, Felice C. (Acc. Chem. Res., 1999)
doi: 10.1021/ar960131y 0001-4842 doi: 10.1021/ar960131y
The following values have no corresponding Zotero field: number: 2 publisher: American Chemical Society

Engineering and chemical synthesis of a transmembrane protein: The HCV protease cofactor protein NS4A - Bianchi, Elisabetta; Ingenito, Raffaele; Simon, Reyna J.; Pessi, Antonello (J. Am. Chem. Soc., 1999)
doi: 10.1021/ja9901617 0002-7863 doi: 10.1021/ja9901617
The following values have no corresponding Zotero field: number: 33 publisher: American Chemical Society

Conformationally assisted protein ligation using C-terminal thioester peptides - Beligere, Gangamani S.; Dawson, Philip E. (J. Am. Chem. Soc., 1999)
doi: 10.1021/ja9907919 0002-7863 doi: 10.1021/ja9907919
The following values have no corresponding Zotero field: number: 26 publisher: American Chemical Society

An alkanesulfonamide "safety-catch" linker for solid-phase synthesis - Backes, Bradley J.; Ellman, Jonathan A. (J. Org. Chem., 2013)
doi: 10.1021/jo981990y
The following values have no corresponding Zotero field: number: 7 publisher: American Chemical Society

Backbone amide linker (BAL) strategy for Na-9-fluorenylmethoxycarbonyl (Fmoc) solid-phase synthesis of unprotected peptide p-nitroanilides and thioesters - Alsina, Jordi; Yokum, T. Scott; Albericio, Fernando; Barany, George (J. Org. Chem., 2013)
doi: 10.1021/jo990629o
The following values have no corresponding Zotero field: number: 24 publisher: American Chemical Society

Polypeptide synthesis by the thioester method - Aimoto, S. (Biopolymers, 1999)
A novel method for polypeptide synthesis, in which partially protected peptide thioesters are used as building blocks, has been developed. Partially protected peptide thioesters are easily prepared by solid-phase methodology. The thioester moiety is converted to an active ester in the presence of a silver compound such as AgNO(3) or AgCl and an active ester component such as 1-hydroxybenzotriazole or 3,4-dihydro-3-hydro-4-oxo-1,2, 3-benzotriazine. Segment condensation can be accomplished using partially protected peptide segments. The consecutive condensation of the partially protected peptide segments is realized by the selective removal of the 9-flourenylmethoxycarbonyl group, for terminal amino protection, after segment condensation has been achieved. In this method, large peptide segments can easily be used. Thus, the products obtained by the thioester method can be separated from by-products by reverse phase high performance liquid chromatography, even when no purification process was performed during the prior segment condensation procedures. This indicates that proteins that have no specific features such as enzymatic or biological activities can be obtained after isolation, solely based on their chromatographic profiles. Thus, the thioester method will provide a new basis for protein studies including phosphorylated and glycosylated polypeptides.
Aimoto, S Biopolymers. 1999;51(4):247-65.
The following values have no corresponding Zotero field: auth-address: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. alt-title: Biopolymers number: 4 edition: 2000/01/05 accession-num: 10618594 work-type: Research Support, Non-U.S. Gov't Review
Keywords: Amino Acid Sequence; Animals; Cysteine/chemistry; Esters/chemistry; Molecular Sequence Data; Sulfhydryl Compounds/*chemistry; Mice; Peptides/*chemical synthesis

Crystal structure of the NK1 fragment of human hepatocyte growth factor at 2.0 A resolution - Ultsch, M.; Lokker, N. A.; Godowski, P. J.; de Vos, A. M. (Structure, 1998)
BACKGROUND: Hepatocyte growth factor (HGF) is a mitogen for hepatocytes and has also been implicated as an epithelial morphogen in tumor invasion. HGF activates its specific cellular receptor, c-met, through an aggregation mechanism potentiated by heparan sulfate glycosaminoglycans. HGF consists of an N-terminal (N) domain, four kringle domains (the first of which carries receptor-binding determinants), and an inactive serine-protease-like domain. NK1, a naturally occurring fragment of HGF, acts as an antagonist of HGF in the absence of heparin. RESULTS: The N domain of NK1 consists of a central five-stranded antiparallel beta sheet flanked by an alpha helix and a two-stranded beta ribbon. The overall N domain structure in the context of the NK1 fragment is similar to the structure of the isolated domain; two lysines and an arginine residue coordinate a bound sulfate ion. The NK1 kringle domain is homologous to kringle 4 from plasminogen, except that the lysine-binding pocket is altered by the insertion of a glycine residue. Here, a HEPES molecule is bound in the pocket. The asymmetric unit of the crystal contains a 'head-to-tail' NK1 dimer. We use this dimer to propose a model of the NK2 fragment of HGF. CONCLUSIONS: A cluster of exposed lysine and arginine residues in or near the hairpin-loop region of the N domain might form part of the NK1 heparin-binding site. In our NK2 model, both kringle domains pack loosely against the N domain, and a long, positively charged groove lines the interface. This groove might be involved in glycosaminoglycan binding. The HGF receptor-binding determinants are clustered near the binding pocket of the first kringle domain, opposite the N domain.
0969-2126 (Print) 0969-2126 (Linking) Journal Article
The following values have no corresponding Zotero field: auth-address: Department of Protein Engineering Genentech, Inc. 460 Point San Bruno Boulevard South San Francisco, CA 94080, USA. number: 11 accession-num: 9817840
Keywords: Amino Acid Sequence; Humans; Protein Conformation; Sequence Homology, Amino Acid; Molecular Sequence Data; Crystallography, X-Ray; Dimerization; Proto-Oncogene Proteins c-met/metabolism; Hepatocyte Growth Factor/*chemistry/metabolism; Kringles

Methionine ligation strategy in the biomimetic synthesis of parathyroid hormones - Tam, J. P.; Yu, Q. (Biopolymers, 1998)
In biological systems, both proteolysis and aminolysis of amide bonds produce activated intermediates through acyl transfer reactions either inter- or intramolecularly. Protein splicing is an illustrative example that proceeds through a series of catalyzed acyl transfer reactions and culminates at an O- or S-acyl intermediate. This intermediate leads to an uncatalyzed acyl migration to form an amide bond in the spliced product. A ligation method mimicking the uncatalyzed final steps in protein splicing has been developed utilizing the acyl transfer amide-bond feature for the blockwise coupling of unprotected, free peptide segments at methionine (Met). The latent thiol moiety of Met can be exploited using homocysteine at the alpha-amino terminal position of a free peptide for transthioesterification with another free peptide containing an alpha-thioester to give an S-acyl intermediate. A subsequent, proximity-driven S- to N-acyl migration of this acyl intermediate spontaneously rearranges to form a homocysteinyl amide bond. S-methylation with excess p-nitrobenezensulfonate yields Met at the ligation site. The methionine ligation is selective and orthogonal, and is usually completed within 4 h when performed at slightly basis pH and under strongly reductive conditions. No side reactions due to acylation were observed with any other alpha-amines of both peptide segments as seen in the synthesis of parathyroid hormone peptides. Furthermore, cyclic peptide can also be obtained through the same strategy by placing both homocysteine at the amino terminus and the thioester at the carboxyl terminus in an unprotected peptide precursor. These biomimetic ligation strategies hold promise for engineering novel peptides and proteins.
AI 37965/AI/NIAID NIH HHS/United States CA 36544/CA/NCI NIH HHS/United States Journal Article Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Department of Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232-2363, USA. alt-title: Biopolymers number: 5 accession-num: 9754028
Keywords: Chromatography, High Pressure Liquid; Mass Spectrometry; Esterification; Methionine/*chemistry; Peptides/*chemical synthesis; Methylation; Protein Engineering/methods; Amides/metabolism; Homocysteine/chemistry; Parathyroid Hormone/*chemistry; Protein Splicing/physiology

A biomimetic strategy in the synthesis and fragmentation of cyclic protein - Tam, J. P.; Lu, Y. A. (Protein Sci., 1998)
This paper describes a simple biomimetic strategy to prepare small cyclic proteins containing multiple disulfide bonds. Our strategy involves intramolecular acyl transfer reactions to assist both the synthesis and fragmentation of these highly constrained cyclic structures in aqueous solution. To illustrate our strategy, we synthesized the naturally occurring circulin B and cyclopsychotride (CPT), both consisting of 31 amino acid residues tightly packed in a cystine-knot motif with three disulfide bonds and an end-to-end cyclic form. The synthesis of these small cyclic proteins can be achieved by orthogonal ligation of free peptide thioester via the thia zip reaction, which involves a series of reversible thiol-thiolactone exchanges to arrive at an alpha-amino thiolactone, which then undergoes an irreversible, spontaneous ring contraction through an S,N-acyl migration to form the cyclic protein. A two-step disulfide formation strategy is employed for obtaining the desired disulfide-paired products. Partial acid hydrolysis through intramolecular acyl transfer of X-Ser, X-Thr, Asp-X, and Glu-X sequences is used to obtain the assignment of the circulins disulfide bond connectives. Both synthetic circulin B and CPT are identical to the natural products and, thus, the total synthesis confirms the disulfide connectivity of circulin B and CPT contain a cystine-knot motif of 1-4, 2-5, and 3-6. In general, our strategy, based on the convergence of chemical proteolysis and aminolysis of peptide bonds through acyl transfer, is biomimetic and provides a useful approach for the synthesis and characterization of large end-to-end cyclic peptides and small proteins.
AI 37965/AI/NIAID NIH HHS/United States CA36544/CA/NCI NIH HHS/United States Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S. United States a publication of the Protein Society
The following values have no corresponding Zotero field: auth-address: Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232, USA. Tamjp@ctrvax.vanderbilt.edu number: 7 accession-num: 9684891
Keywords: Amino Acid Sequence; Cysteine/chemistry; Molecular Sequence Data; Chromatography, High Pressure Liquid; Hydrolysis; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Cyclization; Peptides, Cyclic/*chemical synthesis/chemistry; *Cyclotides; Anti-HIV Agents/chemical synthesis/chemistry; Cystine; Dimethyl Sulfoxide; Disulfides/*chemical synthesis/chemistry; Oxalates; Oxalic Acid; Peptide Mapping; Urea

Oxidative damage to and by cysteine in proteins: An ab Initio study of the radical structures, C-H, S-H, and C-C bond dissociation energies, and transition structures for H abstraction by thiyl radicals - Rauk, A.; Yu, D.; Armstrong, D. A. (J. Am. Chem. Soc., 1998)
doi: 10.1021/ja9807789 0002-7863 doi: 10.1021/ja9807789
The following values have no corresponding Zotero field: number: 34 publisher: American Chemical Society

Effect of added dimethylsulfoxide on pKa values of uncharged organic acids and pH values of aqueous buffers - Mukerjee, P.; Ostrow, J. D. (Tetrahedron Letters, 1998)
Keywords: #nosource

Expressed protein ligation: a general method for protein engineering - Muir, T. W.; Sondhi, D.; Cole, P. A. (Proc. Natl. Acad. Sci. U. S. A., 1998)
A protein semisynthesis method-expressed protein ligation-is described that involves the chemoselective addition of a peptide to a recombinant protein. This method was used to ligate a phosphotyrosine peptide to the C terminus of the protein tyrosine kinase C-terminal Src kinase (Csk). By intercepting a thioester generated in the recombinant protein with an N-terminal cysteine containing synthetic peptide, near quantitative chemical ligation of the peptide to the protein was achieved. The semisynthetic tail-phosphorylated Csk showed evidence of an intramolecular phosphotyrosine-Src homology 2 interaction and an unexpected increase in catalytic phosphoryl transfer efficiency toward a physiologically relevant substrate compared with the non-tail-phosphorylated control. This work illustrates that expressed protein ligation is a simple and powerful new method in protein engineering to introduce sequences of unnatural amino acids, posttranslational modifications, and biophysical probes into proteins of any size.
0027-8424 (Print) 0027-8424 (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Laboratory of Synthetic Protein Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. muirt@rockvax.rockefeller.edu number: 12 accession-num: 9618476
Keywords: Animals; Humans; Protein Engineering/*methods; Proteins/*chemistry/genetics; Recombinant Proteins/chemistry/genetics

Aryl hydrazides as linkers for solid phase synthesis which are cleavable under mild oxidative conditions - Millington, Christopher R.; Quarrell, Rachel; Lowe, Gordon (Tetrahedron Lett., 1998)
We have developed and acid/base stable aryl hydrazide linker which is readily coupled to solid phase resins. Cleavage is specific and facile, requiring a copper (II) catalyst, base and a nucleophile to proceed. The conditions are compatible with all 20 proteinogenic amino acids and quantitative cleavage is achieved within 2 hours at 20°C to give peptides with C-terminal acid, amide or ester functionalities. Aryl hydrazides also offer scope as simple “traceless” linkers.
The following values have no corresponding Zotero field: number: 39
Keywords: peptide synthesis; linkers; oxidative cleavage; solid phase synthesis

Enthalpy and entropy in ring closure reactions - Lightstone, Felice C.; Bruice, Thomas C. (Bioorg. Chem., 1998)
The strain and entropy effects of the lactone formation from ω-bromoalkane-carboxylate ions in ring sizes 3 to 23 is reevaluated. We find that ΔH‡is the largest contributor to the observed rates (ΔG‡) for ring sizes 3 to 6, while −TΔS‡has little influence, −TΔS‡has more effect on the observed rates for ring sizes 8 and larger.
0045-2068
The following values have no corresponding Zotero field: number: 4

Direct preparation of peptide thioesters using an Fmoc solid-phase method - Li, X.; Kawakami, T.; Aimoto, S. (Tetrahedron Lett., 1998)
Aiming at the direct preparation of peptide thioesters by an Fmoc solid-phase method, we searched a new deblocking reagent, which efficiently removed Fmoc groups while keeping the thioester intact. The deblocking reagent, which contains 1-methylpyrrolidine, hexamethyleneimine and HOBt in a one to one mixture of NMP and DMSO, realized the preparation of peptide thioesters by an Fmoc solid-phase method in a yield equivalent to that obtained by a Boc solid-phase method.
0040-4039 doi: DOI: 10.1016/S0040-4039(98)01868-1
The following values have no corresponding Zotero field: number: 47
Keywords: Thioesters; Deblocking; Peptides and polypeptides; Solid-phase synthesis

Strengths of chemical bonds - Kerr, J. A. (CRC Handbook of Chemistry and Physics, 1998)
The following values have no corresponding Zotero field: section: 9
Keywords: #nosource

A novel on-resin synthesis of C-terminally amidated peptides - Kaljuste, Kalle; Tam, James P. (Tetrahedron Lett., 1998)
The following values have no corresponding Zotero field: number: 51

Solution calorimetric investigation of oxidative addition of HEAr (E = O, S, Se; Ar = C6H4X, X = CH3, H, Cl, NO2) to (PMe3)4Ru(C2H4): Relationship between HEAr acidity and enthalpy of reaction - Huang, Jinkun; Li, Chunbang; Nolan, Steven P.; Petersen, Jeffrey L. (Organometallics, 1998)
doi: 10.1021/om980253p 0276-7333 doi: 10.1021/om980253p
The following values have no corresponding Zotero field: number: 16 publisher: American Chemical Society

Isotope effects on enzyme-catalyzed acyl transfer from p-nitrophenyl acetate: Concerted mechanisms and increased hyperconjugation in the transition state - Hess, Robert A.; Hengge, Alvan C.; Cleland, W. W. (J. Am. Chem. Soc., 1998)
doi: 10.1021/ja973413h 0002-7863 doi: 10.1021/ja973413h
The following values have no corresponding Zotero field: number: 12 publisher: American Chemical Society

Kinetics of diketopiperazine formation using model peptides - Goolcharran, C.; Borchardt, R. T. (J. Pharm. Sci., 1998)
The intramolecular aminolysis of Phe-Pro-p-nitroaniline (Phe-Pro-pNA) to Phe-Pro-diketopiperazine (Phe-Pro-DKP) was studied as a function of pH, temperature, buffer concentration, and buffer species using an HPLC assay that permits simultaneous analysis of the disappearance of the starting material and the appearance of degradation products. The degradation followed pseudo-first-order kinetics and showed significant dependence on pH. Phosphate (pH 5-8) and glycine (pH 9-10) buffers exhibit general base catalysis. The pH-rate profile suggested that the rate of Phe-Pro-DKP formation depends on the degree of ionization of the N-terminal amino group, with the unprotonated reactant being more reactive than the protonated form. The pKa value of 6.1, determined kinetically, and three microscopic rate constants were adequate to describe the shape of the pH-rate profile. In the pH range studied, Phe-Pro-DKP was the only product generated upon degradation of Phe-Pro-pNA. At pH values between 3 and 8, Phe-Pro-DKP was stable, while at pH less than 3 and greater than 8 it undergoes hydrolysis to the dipeptide, Phe-Pro-OH. Sequence inversion, a reaction normally associated with DKP formation, was not observed. The influence of primary sequence on the formation of DKP was also investigated using X-Pro-pNA analogues, where X = Gly, Ala, Val, Phe, beta-cyclohexylalanine, and Arg. Changing the amino acid preceding the proline residue had a significant effect on the rate of DKP formation at pH 7.0.
Goolcharran, C Borchardt, R T GM-088359/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov't, P.H.S. United states Journal of pharmaceutical sciences J Pharm Sci. 1998 Mar;87(3):283-8.
The following values have no corresponding Zotero field: auth-address: The Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence 66047, USA. number: 3 edition: 1998/04/02 accession-num: 9523979
Keywords: Amino Acid Sequence; Temperature; Kinetics; Hydrogen-Ion Concentration; Peptides/*chemistry; Chromatography, High Pressure Liquid; Models, Chemical; Buffers; Diketopiperazines; Osmolar Concentration; Piperazines/*chemical synthesis

Structure at 0.85 Å resolution of an early protein photocycle intermediate - Genick, U. K.; Soltis, S. M.; Kuhn, P.; Canestrelli, I. L.; Getzoff, E. D. (Nature, 1998)
Protein photosensors from all kingdoms of life use bound organic molecules, known as chromophores, to detect light. A specific double bond within each chromophore is isomerized by light, triggering slower changes in the protein as a whole. The initial movements of the chromophore, which can occur in femtoseconds, are tightly constrained by the surrounding protein, making it difficult to see how isomerization can occur, be recognized, and be appropriately converted into a protein-wide structural change and biological signal. Here we report how this dilemma is resolved in the photoactive yellow protein (PYP). We trapped a key early intermediate in the light cycle of PYP at temperatures below -100 degrees C, and determined its structure at better than 1 A resolution. The 4-hydroxycinnamoyl chromophore isomerizes by flipping its thioester linkage with the protein, thus avoiding collisions resulting from large-scale movement of its aromatic ring during the initial light reaction. A protein-to-chromophore hydrogen bond that is present in both the preceding dark state and the subsequent signalling state of the photosensor breaks, forcing one of the hydrogen-bonding partners into a hydrophobic pocket. The isomerized bond is distorted into a conformation resembling that in the transition state. The resultant stored energy is used to drive the PYP light cycle. These results suggest a model for phototransduction, with implications for bacteriorhodopsin, photoactive proteins, PAS domains, and signalling proteins.
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. England
The following values have no corresponding Zotero field: auth-address: Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. alt-title: Nature number: 6672 accession-num: 9515969
Keywords: Protein Conformation; Crystallography, X-Ray; Binding Sites; Bacterial Proteins/*chemistry; *Photoreceptors, Microbial; Light; Bacteria; Light Signal Transduction

Semisynthesis of cytotoxic proteins using a modified protein splicing element - Evans, T. C.; Benner, J.; Xu, M. Q. (Protein Sci., 1998)
Two cytotoxic proteins, bovine pancreatic ribonuclease A (RNase A), and a restriction endonuclease from Haemophilus parainfluenzae (HpaI), were produced using a novel semisynthetic approach that utilizes a protein splicing element, an intein, to generate a reactive thioester at the C-terminus of a recombinant protein. Nucleophilic attack on this thioester by the N-terminal cysteine of a synthetic peptide ultimately leads to the ligation of the two reactants through a native peptide bond. This strategy was used to produce RNase A and HpaI by isolating inactive truncated forms of these proteins, the first 109 and 223 amino acids of RNase A and HpaI, respectively, as fusion proteins consisting of the target protein, an intein, and a chitin binding domain. Thiol-induced cleavage of the precursor led to the liberation of the target protein with a C-terminal thioester-tag. Addition of synthetic peptides representing the amino acids missing from the truncated forms led to the generation of full-length products that displayed catalytic activity indicative of the wild-type enzymes. The turnover numbers and Km for ligated and renatured RNase A were 8.2 s(-1) and 1.5 mM, in good agreement with reported values of 8.3 s(-1) and 1.2 mM (Hodges & Merrifield, 1975). Ligated HpaI had a specific activity of 0.5-1.5 x 10(6) U/mg, which compared favorably with the expected value of 1-2 x 10(6) U/mg (J. Benner, unpubl. obs.). Besides assisting in the production of cytotoxic proteins, this technique could allow the easy insertion of unnatural amino acids into a protein sequence.
Journal Article United States a publication of the Protein Society
The following values have no corresponding Zotero field: auth-address: New England Biolabs Inc., Beverly, Massachusetts 01915, USA. number: 11 accession-num: 9827992
Keywords: Amino Acid Sequence; Animals; Catalysis; Molecular Sequence Data; Protein Engineering/*methods; Cattle; Esterification; Binding Sites; *Protein Splicing; Sulfhydryl Compounds/metabolism; Chitin/metabolism; Deoxyribonucleases, Type II Site-Specific/*biosynthesis/chemistry/genetics; Recombinant Fusion Proteins; Ribonuclease, Pancreatic/*biosynthesis/chemistry/genetics

Chemical synthesis of a circular protein domain: Evidence for folding-assisted cyclization - Camarero, Julio A.; Pavel, Joanna; Muir, Tom W. (Angew. Chem. Int. Ed., 1998)
Extremely fast cyclization of the linear polypeptide precursor 1 takes place to form 2. The reaction appears to be assisted by the native fold of 1, which positions the reactive ends in close proximity. The circular topology has no influence on the folding or function of 2.
1521-3773
The following values have no corresponding Zotero field: number: 3 publisher: WILEY-VCH Verlag GmbH
Keywords: Peptides; Solid-phase synthesis; Cyclizations; Protein structures

Chemical ligation of unprotected peptides directly from a solid support - Camarero, J. A.; Cotton, G. J.; Adeva, A.; Muir, T. W. (J. Pept. Res., 1998)
In this article we describe a new, convenient procedure to carry out intramolecular (cyclization) and intermolecular native chemical ligations of unprotected peptides directly from a solid support. Our solid-phase ligation approach eliminates the need to manipulate peptide (alpha)thioacid and peptide (alpha)thioester intermediates in aqueous solution before the ligation step, thereby leading to a reduction in handling losses and significantly increasing the overall efficiency of the chemical ligation strategy. A key step in our ligation scheme is the ability to generate fully unprotected peptides tethered to a solid support through an (alpha)thioester linkage. This can be achieved efficiently using optimized Boc-solid-phase peptide synthesis on a 3-mercaptopropionamide-polyethylene glycol-poly-(N,N-dimethylacrylamide) copolymer support (HS-PEGA). Once the synthesis is complete, the fully protected peptide (alpha)thioester resin is treated with HF to give the corresponding fully unprotected peptide (alpha)thioester resin. Using this procedure several polypeptides ranging from 15 to 47 residues were synthesized successfully. These peptide-resins were then used to perform both intramolecular (head-to-tail cyclizations) and intermolecular solid-phase ligations. The intramolecular solid-phase ligations proceeded much faster than their intermolecular counterparts, but in both cases the reactions were observed to be remarkably clean. The presence of aromatic thiol cofactors significantly accelerated the relatively slow intermolecular ligations. This novel methodology was then extended to provide a general method for performing sequential intermolecular ligations, allowing easy access to much larger polypeptide and protein systems.
1397-002X (Print) 1397-002X (Linking) Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
The following values have no corresponding Zotero field: auth-address: Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, New York 10021, USA. number: 4 accession-num: 9560006
Keywords: Amino Acid Sequence; Protein Conformation; Peptides/*chemistry; Molecular Sequence Data; *Protein Engineering

Studying receptor-ligand interactions using encoded amino acid scanning - Camarero, J. A.; Ayers, B.; Muir, T. W. (Biochemistry, 1998)
A novel technique is described that allows the synthesis, functional analysis, and quantitative readout of defined arrays of polypeptide analogues in aqueous solution. Key to this approach is the use of a simple encoding-decoding system in which a unique Fmoc-amino acid tag is covalently attached to the C terminus of each member of a molecular array through a selectively cleavable bond. These tags can be cleanly removed from the molecules they encode, allowing single-step characterization and quantification of the entire mixture by HPLC. The utility of this technique is illustrated through the preparation of an array of proline-rich sequences based on the exchange factor C3G, one of the natural ligands of the N-terminal SH3 domain from the proto-oncogene, c-Crk. The array was designed to systematically modify those residues within the C3G peptide ligand thought to make key interactions with the c-Crk SH3 domain. Using competition binding experiments, it was possible to determine the relative ED50 values for the entire array of molecules simultaneously. These studies revealed that in order to maintain optimal binding to the SH3 domain, the P-3 side chain of the ligand must be positively charged and the P-0 side chain must be hydrophobic and extend beyond the gamma-carbon. The excellent correlation between these relative ED50 values and a series of relative Kd values determined from individual peptides suggests that this approach may be useful in determining, in a parallel fashion, the relative biological activities of arrays of polypeptides.
Camarero, J A Ayers, B Muir, T W GM55843-01/GM/NIGMS NIH HHS/ Biochemistry. 1998 May 19;37(20):7487-95.
The following values have no corresponding Zotero field: auth-address: Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York 10021, USA. alt-title: Biochemistry number: 20 edition: 1998/06/04 accession-num: 9585562 work-type: Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.
Keywords: Fluorenes/chemistry; Protein Engineering/*methods; Ligands; Proteins/chemical synthesis/chemistry; src Homology Domains; Proto-Oncogene Proteins c-crk; Amino Acids/*chemistry/metabolism; Guanine Nucleotide Exchange Factors; MAP Kinase Kinase Kinases; Peptide Library; Peptides/chemical synthesis/chemistry/metabolism; Protein-Serine-Threonine Kinases/chemistry/metabolism; Protein-Tyrosine Kinases/chemistry/metabolism; Proto-Oncogene Proteins/chemistry/metabolism

Ionization−reactivity relationships for cysteine thiols in polypeptides - Bulaj, Grzegorz; Kortemme, Tanja; Goldenberg, David P. (Biochemistry, 1998)
The following values have no corresponding Zotero field: number: 25 publisher: American Chemical Society

Structure determination of the small ubiquitin-related modifier SUMO-1 - Bayer, P.; Arndt, A.; Metzger, S.; Mahajan, R.; Melchior, F.; Jaenicke, R.; Becker, J. (J. Mol. Biol., 1998)
The recently discovered small ubiquitin-related modifier SUMO-1 belongs to the growing family of ubiquitin-related proteins involved in postranslational protein modification. Unlike ubiquitin, SUMO-1 does not appear to target proteins for degradation but seems to be involved in the modulation of protein-protein interactions. Independent studies demonstrate an essential function of SUMO-1 in the regulation of nucleo-cytoplasmic transport, and suggest a role in cell-cycle regulation and apoptosis. Here, we present the first three-dimensional structure of SUMO-1 solved by NMR. Although having only 18% amino acid sequence identity with ubiquitin, the overall structure closely resembles that of ubiquitin, featuring the betabetaalphabetabetaalphabeta fold of the ubiquitin protein family. In addition, the position of the two C-terminal Gly residues required for isopeptide bond formation is conserved between ubiquitin and SUMO-1. The most prominent feature of SUMO-1 is a long and highly flexible N terminus, which protrudes from the core of the protein and which is absent in ubiquitin. Furthermore, ubiquitin Lys48, required to generate ubiquitin polymers, is substituted in SUMO-1 by Gln69 at the same position, which provides an explanation of why SUMO-1 has not been observed to form polymers. Moreover, the hydrophobic core of SUMO-1 and ubiquitin is maintained by conserved hydrophobic residues, whereas the overall charge topology of SUMO-1 and ubiquitin differs significantly, suggesting specific modifying enzymes and target proteins for both proteins.
Bayer, P Arndt, A Metzger, S Mahajan, R Melchior, F Jaenicke, R Becker, J Research Support, Non-U.S. Gov't England Journal of molecular biology J Mol Biol. 1998 Jul 10;280(2):275-86.
The following values have no corresponding Zotero field: auth-address: Abteilung Physikalische Biochemie, Max-Planck-Institut fur molekulare Physiologie, Dortmund, Germany. number: 2 edition: 1998/07/09 accession-num: 9654451
Keywords: Amino Acid Sequence; Animals; Humans; Protein Conformation; Sequence Homology, Amino Acid; Molecular Sequence Data; Protein Folding; Magnetic Resonance Spectroscopy; SUMO-1 Protein; Ubiquitins/*chemistry; Recombinant Proteins/chemistry

Dictionary of environmentaly important chemicals - Ayres, D.; Hellier, D. (Chapman & Hall, 1998)
Keywords: #nosource

Dissociation constants of organic acids and bases - Lide, D. R. (CRC Handbook of Chemistry and Physics, 1998)
The following values have no corresponding Zotero field: section: 8
Keywords: #nosource

Metal ion-assisted peptide cyclization - Zhang, Lianshan; Tam, James P. (Tetrahedron Lett., 1997)
The following values have no corresponding Zotero field: number: 25

Orthogonal coupling of unprotected peptide segments through histidyl amino terminus - Zhang, Lianshan; Tam, James P. (Tetrahedron Lett., 1997)
We report a new scheme for orthogonal coupling of unprotected peptide segments through the anchimeric assistance of a proximally located histidine at the amino terminus.
0040-4039
The following values have no corresponding Zotero field: number: 1

A pH-modulated, self-replicating peptide - Yao, Shao; Ghosh, Indraneel; Zutshi, Reena; Chmielewski, Jean (J. Am. Chem. Soc., 1997)
The following values have no corresponding Zotero field: number: 43 publisher: American Chemical Society

Synthesis of large cyclic cystine-knot peptide by orthogonal coupling strategy using unprotected peptide precursor - Tam, James P.; Lu, Yi-An (Tetrahedron Lett., 1997)
A simple and direct method for the synthesis of large end-to-end, disulfide rich cyclic peptide using orthogonal coupling of unprotected NÎ±-cysteinyl thioester peptide is described.
0040-4039
The following values have no corresponding Zotero field: number: 32

Thiocoraline, a new depsipeptide with antitumor activity produced by a marine Micromonospora. I. Taxonomy, fermentation, isolation, and biological activities - Romero, F.; Espliego, F.; Perez Baz, J.; Garcia de Quesada, T.; Gravalos, D.; de la Calle, F.; Fernandez-Puentes, J. L. (J. Antibiot., 1997)
A novel bioactive depsipeptide, thiocoraline, was isolated from the mycelial cake of a marine actinomycete strain L-13-ACM2-092. Based on morphological, cultural, physiological, and chemical characteristics, strain L-13-ACM2-092 was ascribed to the genus Micromonospora. Thiocoraline showed a potent cytotoxic activity against P-388, A-549 and MEL-28 cell lines, and also a strong antimicrobial activity against Gram-positive microorganisms. This compound binds to supercoiled DNA and inhibits RNA synthesis.
Romero, F Espliego, F Perez Baz, J Garcia de Quesada, T Gravalos, D de la Calle, F Fernandez-Puentes, J L Japan J Antibiot (Tokyo). 1997 Sep;50(9):734-7.
The following values have no corresponding Zotero field: auth-address: Drug Discovery Division, PharmaMar, S.A., Spain. alt-title: The Journal of antibiotics number: 9 edition: 1997/11/14 accession-num: 9360617
Keywords: Animals; *Depsipeptides; *Peptides; Anti-Bacterial Agents/*isolation & purification/pharmacology; Antibiotics, Antineoplastic/*isolation & purification/pharmacology; Fermentation; Leukemia P388/drug therapy; Microbial Sensitivity Tests; Micromonospora; Tumor Cells, Cultured/drug effects

Intramolecular assistance of cis/trans isomerization of the histidine-proline moiety - Reimer, U.; el Mokdad, N.; Schutkowski, M.; Fischer, G. (Biochemistry, 1997)
Peptidyl-prolyl cis/trans isomerization is a slow conformational interconversion in the polypeptide backbone that is frequently rate-limiting in refolding of proteins and is thought to play a role in cellular restructuring of proteins. In order to probe the influence of positively charged amino acids located in sequence segments adjacent to proline, the rotational barriers of Arg-Pro- and His-Pro-containing peptides were determined by isomer-specific proteolysis and dynamic NMR spectroscopy for Suc-Ala-His-Pro-Phe-NH-Np, Ac-Ala-Arg-Pro-Ala-Lys-NH2, Ac-Ala-His-Pro-Ala-Lys-NH2, angiotensin III, thyrotropin-releasing hormone (TRH), and [His(3-Me)2]TRH in aqueous solution. In contrast to the guanidinium group of arginine, the protonated side chain of histidine preceding proline led to an acceleration of the prolyl isomerization up to 10-fold relative to the unprotonated state. Both arginine and histidine residues succeeding proline in an amino acid sequence proved to be ineffective. Under basic and acidic conditions the kinetic solvent deuterium isotope effects Kc-->tH20/Kc-->tD20 for angiotensin III were 1.0 +/- 0.1 and 2.0 +/- 0.1, respectively. The results are interpreted in terms of intramolecular general acid catalysis of prolyl bond rotation by the imidazolium group that is without precedent in intermolecular catalysis.
Journal Article Research Support, Non-U.S. Gov't United States
The following values have no corresponding Zotero field: auth-address: Research Unit, Max-Planck-Gesellschaft, Halle/Saale, Germany. alt-title: Biochemistry number: 45 accession-num: 9374856
Keywords: Protein Conformation; Stereoisomerism; Catalysis; Protein Folding; Magnetic Resonance Spectroscopy; Solvents; Deuterium; Angiotensin III/metabolism; Histidine/*metabolism; Oligopeptides/*metabolism; Proline/*metabolism; Thyrotropin-Releasing Hormone/metabolism

Thiocoraline, a novel depsipeptide with antitumor activity produced by a marine Micromonospora. II. Physico-chemical properties and structure determination - Perez Baz, J.; Canedo, L. M.; Fernandez Puentes, J. L.; Silva Elipe, M. V. (J. Antibiot., 1997)
Thiocoraline (1) is a new antitumor antibiotic isolated from the mycelium of Micromonospora sp. L-13-ACM2-092. Its structure was elucidated to be a novel cyclic thiodepsipeptide on the basis of spectroscopic methods.
Perez Baz, J Canedo, L M Fernandez Puentes, J L Silva Elipe, M V Japan J Antibiot (Tokyo). 1997 Sep;50(9):738-41.
The following values have no corresponding Zotero field: auth-address: Drug Discovery Division, PharmaMar S.A., Spain. alt-title: The Journal of antibiotics number: 9 edition: 1997/11/14 accession-num: 9360618
Keywords: Molecular Structure; *Depsipeptides; *Peptides; Anti-Bacterial Agents/*chemistry; Antibiotics, Antineoplastic/*chemistry

Granulysin, a new human cytolytic granule-associated protein with possible involvement in cell-mediated cytotoxicity - Pena, S. V.; Krensky, A. M. (Semin. Immunol., 1997)
A primary process by which cytotoxic T lymphocytes (CTL) and natural killer (NK) cells lyse target cells involves the regulated exocytosis of granules present in the cytoplasm of the effector. These granules contain proteins, such as perforin and the granzymes, that play a direct role in the killing process. The localization of a human T and NK cell-specific protein, granulysin (formerly 519), to cytolytic granules suggests that additional mechanisms may be involved in granule-mediated cytolysis. This protein shares homology with small, granule-associated molecules and is a member of a larger family of proteins known as saposin-like proteins (SAPLIP). SAPLIP share common structural features allowing for association with lipids while retaining the ability to mediate a variety of different functions. Expression of granulysin is induced late after T-cell activation, similar to perforin and the granzymes. Two prominent protein products of 15 and 9kDa were identified in CTL. The 9kDa form localizes to dense, highly cytolytic granules and contains the SAPLIP homology domain. A recombinant granulysin protein, corresponding to the 9kDa form, is cytolytic against tumor cell targets.
CA 09302/CA/NCI NIH HHS/United States R01 DK35008/DK/NIDDK NIH HHS/United States Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Review England
The following values have no corresponding Zotero field: auth-address: Department of Pediatrics, Stanford University School of Medicine, CA 94305, USA. alt-title: Seminars in immunology number: 2 accession-num: 9194222
Keywords: Amino Acid Sequence; Animals; Humans; Sequence Homology, Amino Acid; Molecular Sequence Data; Sequence Alignment; Protein Structure, Tertiary; Protein Processing, Post-Translational; *Cytotoxicity, Immunologic; Antigens, Differentiation, T-Lymphocyte/*physiology; Cell Compartmentation; Cell Degranulation; Cytoplasmic Granules/enzymology; Killer Cells, Natural/*physiology; Protein Precursors/metabolism; Proteolipids/*physiology; Pulmonary Surfactants/*physiology; T-Lymphocytes, Cytotoxic/*physiology

Processing, subcellular localization, and function of 519 (granulysin), a human late T cell activation molecule with homology to small, lytic, granule proteins - Pena, S. V.; Hanson, D. A.; Carr, B. A.; Goralski, T. J.; Krensky, A. M. (J. Immunol., 1997)
CTL and NK cells share a common cytolytic mechanism that involves regulated exocytosis of lytic molecules stored within cytoplasmic granules. Here we describe the processing, subcellular localization, and function of a T and NK cell-specific granule protein that shares homology with small, lytic granule-associated molecules. The gene coding for this protein, 519, is expressed late after T cell activation. Antisera raised against a 519/glutathione-S-transferase fusion protein and a series of peptides derived from the 519 protein sequence permitted the identification of two small CTL protein products of 15 and 9 kDa that are exocytosed after stimulation through the TCR. The 9-kDa product is a processed form of 519 and differs from the 15-kDa product in both its amino and carboxyl terminus. While both 519 proteins are found in cytoplasmic granules, the 9-kDa form is also present in dense, highly cytolytic granules. Functional studies indicate that this protein is lytic against tumor cell targets. The cell type- and stage-specific expression pattern of 519 along with its subcellular localization are reminiscent of molecules that play a vital role in granule-mediated cytolysis by CTL and NK cells. Its lytic activity suggests the involvement of 519 in CTL effector function.
CA09302/CA/NCI NIH HHS/United States R01OK35008/PHS HHS/United States Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. United States 1950)
The following values have no corresponding Zotero field: auth-address: Department of Pediatrics, Stanford University School of Medicine, CA 94305, USA. number: 6 accession-num: 9058801
Keywords: Amino Acid Sequence; Humans; Sequence Homology, Amino Acid; Molecular Sequence Data; Protein Processing, Post-Translational; *Cytotoxicity, Immunologic; Molecular Weight; *Lymphocyte Activation; Antigens, Differentiation, T-Lymphocyte/biosynthesis/*metabolism/*physiology; Cytoplasmic Granules/*metabolism/secretion; Cytotoxicity Tests, Immunologic; Exocytosis/immunology; Microscopy, Fluorescence; Receptors, Antigen, T-Cell/physiology; Subcellular Fractions/metabolism; T-Lymphocytes/*metabolism

General acid catalysis of the reversible addition of thiolate anions to cyanamide - N. Dalby, N. Kevin; Jencks, P. William (J. Chem. Soc., Perkin Trans. 2, 1997)
The addition of aromatic thiols (pK = 2.6-6.5) to cyanamide to give the isothiourea is subject to general-acid catalysis of the addition of thiolate anions by tertiary ammonium ions, with [small alpha] = 0.26 and 0.31 (+/-0.07) for the addition of thiophenol and 4-nitrothiophenol, respectively. The Bronsted coefficients and a small solvent isotope effect of k/k = 1.6 for catalysis by 4-morpholinoethanesulfonic acid (MES) buffer and for the uncatalysed addition of thiophenol are consistent with significant movement of a hydron in the transition state. The conclusion that the reaction proceeds through a basic asymmetric intermediate in the absence of catalysis is supported by the similar rate constants for the addition of thiophenolate anion to cyanamide and to N,N-dimethylcyanamide, which cannot tautomerize to the carbodiimide. The reaction has a central transition state in which S-C bond formation takes place with [small beta] = 0.55. It is concluded that the mechanism of catalysis involves partial transfer of a hydron to the cyano nitrogen atom in the transition state.
0300-9580 10.1039/A700205J
The following values have no corresponding Zotero field: number: 8 publisher: The Royal Society of Chemistry

Heavy-atom isotope effects on the hydrazinolysis of methyl formate - Marlier, John F.; Haptonstall, Brandy A.; Johnson, Amanda J.; Sacksteder, Katherine A. (J. Am. Chem. Soc., 1997)
doi: 10.1021/ja970993+ 0002-7863 doi: 10.1021/ja970993+
The following values have no corresponding Zotero field: number: 38 publisher: American Chemical Society

Separation of ground state and transition state effects in intramolecular and enzymatic reactions. 2. A theoretical study of the formation of transition states in cyclic anhydride formation - Lightstone, Felice C.; Bruice, Thomas C. (J. Am. Chem. Soc., 1997)
doi: 10.1021/ja970982g 0002-7863 doi: 10.1021/ja970982g
The following values have no corresponding Zotero field: number: 39 publisher: American Chemical Society

The internal thioester and the covalent binding properties of the complement proteins C3 and C4 - Law, S. K.; Dodds, A. W. (Protein Sci., 1997)
The covalent binding of complement components C3 and C4 is critical for their activities. This reaction is made possible by the presence of an internal thioester in the native protein. Upon activation, which involves a conformational change initiated by the cleavage of a single peptide bond, the thioester becomes available to react with molecules with nucleophilic groups. This description is probably sufficient to account for the binding of the C4A isotype of human C4 to amino nucleophiles. The binding of the C4B isotype, and most likely C3, to hydroxyl nucleophiles, however, involves a histidine residue, which attacks the thioester to form an intramolecular acyl-imidazole bond. The released thiolate anion then acts as a base to catalyze the binding of hydroxyl nucleophiles, including water, to the acyl function. This mechanism allows the complement proteins to bind to the hydroxyl groups of carbohydrates found on all biological surfaces, including the components of bacterial cell walls. In addition, the fast hydrolysis of the thioester provides a means to contain this very damaging reaction to the immediate proximity of the site of activation.
Journal Article ReviewThe covalent binding of complement components C3 and C4 is critical for their activities. United states a publication of the Protein Society
The following values have no corresponding Zotero field: auth-address: Department of Biochemistry, University of Oxford, United Kingdom. alaw@molbiol.ox.ac.uk number: 2 accession-num: 9041627
Keywords: Humans; Protein Binding; Complement C3/*metabolism; Complement C4/*metabolism; Esters/*metabolism; Sulfhydryl Compounds/*metabolism

Bacterial interference caused by autoinducing peptide variants - Ji, G.; Beavis, R.; Novick, R. P. (Science, 1997)
The synthesis of virulence factors and other extracellular proteins by Staphylococcus aureus is globally controlled by the agr locus, which encodes a two-component signaling pathway whose activating ligand is an agr-encoded autoinducing peptide. The cognate peptides produced by some strains inhibit the expression of agr in other strains, and the amino acid sequences of peptide and receptor are markedly different between such strains, suggesting a hypervariability-generating mechanism. Cross-inhibition of gene expression represents a type of bacterial interference that could be correlated with the ability of one strain to exclude others from infection or colonization sites, or both.
R01-AI30138/AI/NIAID NIH HHS/United States Journal Article Research Support, U.S. Gov't, P.H.S. United States
The following values have no corresponding Zotero field: auth-address: Skirball Institute of Biomolecular Medicine, New York University Medical Center, New York, NY 10016, USA. alt-title: Science (New York, N.Y number: 5321 accession-num: 9197262
Keywords: Amino Acid Sequence; Molecular Sequence Data; Mass Spectrometry; Dimerization; Signal Transduction; Cloning, Molecular; *Trans-Activators; *Antibiosis; *Gene Expression Regulation, Bacterial; Bacterial Proteins/chemistry/*genetics/metabolism; Peptides/chemistry/*genetics/metabolism; Promoter Regions, Genetic; Staphylococcus aureus/*genetics/metabolism/pathogenicity; Transcription Factors/chemistry/*genetics/metabolism; Virulence

Synthesis and structural characterization of triple-helical peptides which mimic the ligand binding site of the human macrophage scavenger receptor - Hojo, Hironobu; Akamatsu, Yoshiko; Yamauchi, Kiyoshi; Kinoshita, Masayoshi; Miki, Shunji; Nakamura, Yu (Tetrahedron, 1997)
The following values have no corresponding Zotero field: number: 42

Trifluoroacetic acid cleavage and deprotection of resin-bound peptides following synthesis by Fmoc chemistry - Guy, C. A.; Fields, G. B. (Methods Enzymol., 1997)
0076-6879 (Print) 0076-6879 (Linking) Journal Article Review
The following values have no corresponding Zotero field: auth-address: Department of Laboratory Medicine, University of Minnesota, Minneapolis 55455-0392, USA. accession-num: 9353718
Keywords: Peptides/*chemical synthesis/*chemistry; Resins, Plant; Carbonic Acid; Trifluoroacetic Acid

Dissection of nucleophilic and general base roles for the reaction of phosphate with p-nitrophenyl thiolacetate, p-nitrophenyl thiolformate, and phenyl thiolacetate - Gill, Manjinder S.; Neverov, Alexei A.; Brown, R. S. (J. Org. Chem., 1997)
doi: 10.1021/jo970904b 0022-3263 doi: 10.1021/jo970904b
The following values have no corresponding Zotero field: number: 21 publisher: American Chemical Society

The mechanism of oxidation of 3-mercaptopropionic acid - Forlano, A.; Olabe, J. A.; Magallanes, J. F.; Blesa, M. A. (Can. J. Chem., 1997)
The following values have no corresponding Zotero field: number: 1

Modulation of reactivity in native chemical ligation through the use of thiol additives - Dawson, Philip E.; Churchill, Michael J.; Ghadiri, M. Reza; Kent, Stephen B. H. (J. Am. Chem. Soc., 1997)
null
doi: 10.1021/ja962656r 0002-7863 doi: 10.1021/ja962656r
The following values have no corresponding Zotero field: number: 19 publisher: American Chemical Society

The total chemical synthesis of L- and D-superoxide dismutase - Canne, L. E.; Figliozzi, G. M.; Robson, B.; Siani, M. A.; Thompson, D. A.; Koike, C.; Tainer, J. A.; Kent, S. B. H.; Simon, R. J. (Protein Eng., 1997)
ISI Document Delivery No.: XD832 Times Cited: 1 Cited Reference Count: 6 S
The following values have no corresponding Zotero field: auth-address: Gryphon sci, s san francisco, ca 94080 usa scripps res inst, la jolla, ca 92037 usa alt-title: Protein Eng. accession-num: WOS:A1997XD83200030 work-type: Meeting Abstract
Keywords: #nosource

Intramolecular catalysis of thiol ester hydrolysis by a tertiary amine and a carboxylate - Brown, R. S.; Aman, Ahmed (J. Org. Chem., 1997)
doi: 10.1021/jo9623954 0022-3263 doi: 10.1021/jo9623954
The following values have no corresponding Zotero field: number: 14 publisher: American Chemical Society

The vitamin C and its reactions - Bors, W.; Buettner, G. R. (Vitamin C in Health and Disease, 1997)
The following values have no corresponding Zotero field: section: 4
Keywords: #nosource