Limited Tendency Of Alpha-Helical Residues To Form Disulfide Bridges: A Structural Explanation(485 views) De Simone A, Berisio R, Zagari A, Vitagliano L
Keywords: Data Mining, Disulfide Bridges, Protein And Peptide Structure, Protein Data Bank, Statistics, Amino Acid, Cysteine, Polypeptide, Alpha Chain, Alpha Helix, Amino Acid Sequence, Article, Beta Chain, Disulfide Bond, Information Processing, Priority Journal, Protein Analysis, Protein Database, Protein Determination, Protein Folding, Protein Localization, Protein Motif, Protein Secondary Structure, Protein Stability, Protein Synthesis, Structural Proteomics, Protein Structure,
Affiliations: *** IBB - CNR ***
Dipartimento delle Scienze Biologiche, Sezione Biostrutture, Università degli Studi di Napoli Federico II, I-80134 Napoli, Italy
Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB), I-80134 Napoli, Italy
References: Bulaj, G., Formation of disulfide bonds in proteins and peptides (2005) Biotechnol Adv., 23, pp. 87-9
Skorko-Glonekv, J., Sobiecka, A., Periplasmatic disulfide oxidoreductases from bacterium escherichia coli-their structure and function (2005) Postepy Biochem., 51, pp. 459-467
Tu, B.P., Weissman, J.S., Oxidative protein folding in eukaryotes: Mechanisms and consequences (2004) J. Cell Biol., 164, pp. 341-346
Craik, D.J., Daly, N.L., Waine, C., The cystine knot motif in toxins and implications for drug design (2001) Toxicon, 39, pp. 43-60
Iqbalsyah, T.M., Moutevelis, E., Warwicker, J., Errington, N., Doig, A.J., The cxxc: Motif at the n terminus of an α-helical peptide (2006) Protein Sci., 15, pp. 1945-1950
Thornton, J., Disulphide bridges in globular proteins (1981) J. Mol. Biol., 151, pp. 261-287
Srinivasan, N., Sowdhamini, R., Ramakrishnan, C., Balaram, P., Conformations of disulfide bridges in proteins (1990) Int. J. Pept. Protein Res., 36, pp. 147-155
Petersen, M.T., Jonson, P.H., Petersen, S.B., Amino acid neighbours and detailed conformational analysis of cysteines in proteins (1999) Protein Eng., 12, pp. 535-548
Carugo, O., Cemazar, M., Zabariev, S., Hudaky, I., Gaspari, Z., Perczel, A., Pongor, S., Vicinal disulfide turns (2003) Protein Eng., 16, pp. 637-639
Esposito, L., De Simone, A., Zagari, A., Vitagliano, L., Correlation between omega and psi dihedral angles in protein structures (2005) J. Mol. Biol., 347, pp. 483-487
Bhattacharyya, R., Pal, D., Chakrabarti, P., Disulfide bonds, their stereospecific environment and conservation in protein structures (2004) Protein Eng. Des. Sel., 17, pp. 795-808
Benham, C.J., Jafri, M.S., Disulfide bonding patterns and protein topologies (1993) Protein Sci., 2, pp. 41-54
Fariselli, P., Casadio, R., Prediction of disulfide connectivity in proteins (2001) Bioinformatics, 17, pp. 957-964
Thornton, J.M., Gardner, S.P., Protein motifs and data-base searching (1989) Trends Biochem. Sci., 14, pp. 300-304
Berman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Feng, Z., Zardecki, C., The protein data bank (2002) Acta Crystallogr., D58, pp. 899-907
Thangudu, R.R., Vinayagam, A., Pugalenthi, G., Manonmani, A., Offmann, B., Sowdhamini, R., Native and modeled disulfide bonds in proteins: Knowledge-based approaches toward structure prediction of disulfide-rich polypeptides (2005) Proteins, 58, pp. 866-879
Mas, J.M., Aloy, P., Marti-Renom, M.A., Oliva, B., Blanco-Aparicio, C., Molina, M.A., de Llorens, R., Aviles, F.X., Protein similarities beyond disulphide bridge topology (1998) J. Mol. Biol., 284, pp. 541-548
van Vlijmen, H.W., Gupta, A., Narasimhan, L.S., Singh, J., A novel database of disulfide patterns and its application to the discovery of distantly related homologs (2004) J. Mol. Biol., 335, pp. 1083-1092
Gupta, A., Van Vlijmen, H.W., Singh, J., A classification of disulfide patterns and its relationship to protein structure and function (2004) Protein Sci., 13, pp. 2045-2058
Cheng, J., Saigo, H., Baldi, P., Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching (2006) Proteins, 62, pp. 617-629
Wang, G., Dunbrack Jr., R.L., Pisces: A protein sequence culling server (2003) Bioinformatics, 19, pp. 1589-1591
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Laskowski, R.A., MacArthur, M.W., Moss, M.D., Thorton, J.M., Procheck: A program to check the stereochemical quality of protein structure (1993) J. Appl. Crystallogr., 26, pp. 283-291
Berisio, R., Loguercio, S., De Simone, A., Zagari, A., Vitagliano, L., Polyproline helices in protein structures: A statistical survey (2006) Prot. Pept. Lett., 13, pp. 847-854
Eisenberg, D., McLachlan, A.D., Solvation energy in protein folding and binding (1986) Nature, 319, pp. 199-203
Mazzarella, L., Capasso, S., Dernasi, D., Di Lorenzo, G., Mattia, C.A., Zagari, A., Bovine seminal ribonuclease: Structure at 1.9 Å resolution (1993) Acta Crystallogr., D49, pp. 389-402
Tu, B. P., Weissman, J. S., Oxidative protein folding in eukaryotes: Mechanisms and consequences (2004) J. Cell Biol., 164, pp. 341-346
Craik, D. J., Daly, N. L., Waine, C., The cystine knot motif in toxins and implications for drug design (2001) Toxicon, 39, pp. 43-60
Iqbalsyah, T. M., Moutevelis, E., Warwicker, J., Errington, N., Doig, A. J., The cxxc: Motif at the n terminus of an -helical peptide (2006) Protein Sci., 15, pp. 1945-1950
Petersen, M. T., Jonson, P. H., Petersen, S. B., Amino acid neighbours and detailed conformational analysis of cysteines in proteins (1999) Protein Eng., 12, pp. 535-548
Benham, C. J., Jafri, M. S., Disulfide bonding patterns and protein topologies (1993) Protein Sci., 2, pp. 41-54
Thornton, J. M., Gardner, S. P., Protein motifs and data-base searching (1989) Trends Biochem. Sci., 14, pp. 300-304
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Zardecki, C., The protein data bank (2002) Acta Crystallogr., D58, pp. 899-907
Thangudu, R. R., Vinayagam, A., Pugalenthi, G., Manonmani, A., Offmann, B., Sowdhamini, R., Native and modeled disulfide bonds in proteins: Knowledge-based approaches toward structure prediction of disulfide-rich polypeptides (2005) Proteins, 58, pp. 866-879
Mas, J. M., Aloy, P., Marti-Renom, M. A., Oliva, B., Blanco-Aparicio, C., Molina, M. A., de Llorens, R., Aviles, F. X., Protein similarities beyond disulphide bridge topology (1998) J. Mol. Biol., 284, pp. 541-548
van Vlijmen, H. W., Gupta, A., Narasimhan, L. S., Singh, J., A novel database of disulfide patterns and its application to the discovery of distantly related homologs (2004) J. Mol. Biol., 335, pp. 1083-1092
Laskowski, R. A., MacArthur, M. W., Moss, M. D., Thorton, J. M., Procheck: A program to check the stereochemical quality of protein structure (1993) J. Appl. Crystallogr., 26, pp. 283-291
Limited Tendency Of Alpha-Helical Residues To Form Disulfide Bridges: A Structural Explanation
Disulfide bridges have an enormous impact on the structure of a large number of proteins and polypeptides. Understanding the structural basis that regulates their formation may be important for the design of novel peptide-based molecules with a specific fold and stability. Here we report a statistical analysis of the relationships between secondary structure and disulfide bond formation, carried out using a large database of protein structures. Our analyses confirm the observation sporadically reported in previous investigations that cysteine residues located in a-helices display a limited tendency to form disulfide bridges. The very low occurrence of the disulfide bond in all a-chains compared to all beta-chains indicates that this property is also evident when proteins with different topologies are investigated. Taking advantage of the large database that endorsed the analysis on relatively rare motifs, we demonstrate that cysteine residues embedded in 3 (10) helices present a good tendency to form disulfide bonds. This result is somewhat surprising since 3 (10) helices are commonly assimilated into a-helices. A plausible structural explanation for the observed data has been derived combining analyses of disulfide bond sequence separation and of the length of the different secondary structure elements. Copyright (c) 2006 European Peptide Society and John Wiley & Sons, Ltd
Limited Tendency Of Alpha-Helical Residues To Form Disulfide Bridges: A Structural Explanation
Kim YH, Shin SW, Pellicano R, Fagoonee S, Choi IJ, Kim YI, Park B, Choi JM, Kim SG, Choi J, Park JY, Oh S, Yang HJ, Lim JH, Im JP, Kim JS, Jung HC, Ponzetto A, Figura N, Malfertheiner P, Choi IJ, Kook MC, Kim YI, Cho SJ, Lee JY, Kim CG, Park B, Nam BH, Bae SE, Choi KD, Choe J, Kim SO, Na HK, Choi JY, Ahn JY, Jung KW, Lee J, Kim DH, Chang HS, Song HJ, Lee GH, Jung HY, Seta T, Takahashi Y, Noguchi Y, Shikata S, Sakai T, Sakai K, Yamashita Y, Nakayama T, Leja M, Park JY, Murillo R, Liepniece-karele I, Isajevs S, Kikuste I, Rudzite D, Krike P, Parshutin S, Polaka I, Kirsners A, Santare D, Folkmanis V, Daugule I, Plummer M, Herrero R, Tsukamoto T, Nakagawa M, Kiriyama Y, Toyoda T, Cao X, Corral JE, Mera R, Dye CW, Morgan DR, Lee YC, Lin JT, Garcia Martin R, Matia Cubillo A, Lee SH, Park JM, Han YM, Ko WJ, Hahm KB, Leontiadis GI, Ford AC, Ichinose M, Sugano K, Jeong M, Park JM, Han YM, Park KY, Lee DH, Yoo JH, Cho JY, Hahm KB, Bang CS, Baik GH, Shin IS, Kim JB, Suk KT, Yoon JH, Kim YS, Kim DJ * Helicobacter pylori Eradication for Prevention of Metachronous Recurrence after Endoscopic Resection of Early Gastric Cancer(307 views) N Engl J Med (ISSN: 0028-4793, 0028-4793linking, 1533-4406electronic), 2015 Jun; 30642104201566393291: 749-756. Impact Factor:59.558 ViewExport to BibTeXExport to EndNote