Amino acid patterns around disulfide bonds

International Journal of Molecular Sciences

Volumn 11, Issue 11, 2010, Pages 4673-4686

  Marques, José R F ^a   da Fonseca, Rute R ^b   Drury, Brett ^c   Melo, André ^a  

^a Faculdade de Farmácia da Universidade do Porto   (Portugal)

^b UNIVERSITY OF PORTO   (Portugal)

^c UNIVERSITY OF PORTO   (Portugal)

Author keywords

Classification; Disulfide bond; Diversity; Frequency; Neighborhood

Indexed keywords

AMINO ACID; AROMATIC AMINO ACID;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; ARTICLE; BIOLOGICAL ACTIVITY; CLASSIFICATION; DISULFIDE BOND; HYDROPHILICITY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CLASSIFICATION; DISULFIDE BOND; DIVERSITY; FREQUENCY; NEIGHBORHOOD;

AMINO ACID SEQUENCE; AMINO ACIDS, SULFUR; MOLECULAR SEQUENCE DATA; PROTEINS; SULFUR;

EID: 78650971596     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms11114673     Document Type: Article

References (32)

1. Bhattacharyya, R.; Pal, D.; Chakrabarti, P. Disulfide bonds, their stereospecific environment and conservation in protein structures. Prot. Eng. Des. Sel. 2004, 17, 795-808.
2. Hogg, P.J. Disulfide bonds as switches for protein function. Trends Biochem. Sci. 2003, 28, 210-214.
3. Klink, T.A.; Woycechowsky, K.J.; Taylor, K.M.; Raines, R.T. Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A. Eur. J. Biochem. 2000, 267, 566-572.
4. Sardiu, M.E.; Cheung, M.S.; Yi-Kuo, Y. Cysteine-cysteine contact preference leads to target-focusing in protein folding. Biophys. J. 2007, 93, 938-951.
5. Wedemeyer, W.J.; Welker, E.; Narayan, M.; Scheraga, H.A. Disulfide bonds and protein folding. Biochemistry 2000, 39, 4208-4216.
6. Marques, J.R.; da Fonseca, R.R.; Drury, B.; Melo, A. Conformational characterization of disulfide bonds: A tool for protein classification. J. Theor. Biol. 2010, 267, 388-395.
7. Benham, C.J.; Jafri, M.S. Disulfide bonding patterns and protein topologies. Protein Sci. 1993, 2, 41-54.
8. Gupta, A.; van Vlijmen, H.W.T.; Singh, J.A. Classification of disulfide patterns and its relationship to protein structure and function. Protein Sci. 2004, 13, 2045-2058.
9. Mas, J.M.; Aloy, P.; Marti-Renom, M.A.; Oliva, B.; Blanco-Aparicio, C.; Molina, M.A.; Llorens, R.; Querol, E.; Aviles, F.X. Protein similarities beyond disulphide bridge topology. J. Mol. Biol. 1998, 284, 541-548.
10. Mas, J.M.; Aloy, P.; Marti-Renom, M.A.; Oliva, B.; Llorens, R.; Aviles, F.X.; Querol, E. Classification of protein disulphide-bridge topologies. J. Comput.-Aided Mol. Des. 2001, 15, 477-487.
11. van Vlijmen, H.W.T.; Gupta, A.; Singh, J. A Novel base of disulfide patterns and its application to the discovery of distantly related homologs. J. Mol. Biol. 2004, 335, 1083-1092.
12. Cheek, S.; Krishna, S.S.; Grishin, N.V. Structural classification of small, disulfide-rich protein domains. J. Mol. Biol. 2006, 359, 215-237.
13. Chuang, C.C.; Chen, C.Y.; Yang, J.M.; Lyu, P.C.; Hwang, J.K. Relationship between protein structures and disulfide bonding patterns. Proteins 2003, 53, 1-5.
14. Creighton, T.E. Disulphide bonds and protein stability. BioEssays 2005, 8, 57-63.
15. Harrison, P.M.; Sternberg, J.E. The disulphide-cross: From cystine geometry and clustering to classification of small disulphide-rich protein folds. J. Mol. Biol. 1996, 264, 603-623.
16. Kartik, V.J.; Lavanya, T.; Guruprasad, K. Analysis of disulphide bond connectivity patterns in protein tertiary structure. Int. J. Biol. Macromol. 2006, 38, 174-179.
17. Lenffer, J.; Lai, P.; El Mejaber, W.; Khan, A.M.; Koh, J.L.Y.; Tan, P.T.J.; Seah, S.H.; Brusic, V. CysView: Protein classification based on cysteine pairing patterns. Nucleic Acids Res. 2004, 32, W350-W355.
18. Thangudu, R.R.; Sharma, P.; Srinivasan, N.; Offmann, B. Analycys: A database for conservation and conformation of disulphide bonds in homologous protein domains. Proteins 2007, 67, 255-261.
19. Thornton, J.M. Disulphide bridges in globular proteins. J. Mol. Biol. 1981, 151, 261-287.
20. Jahandideh, S.; Hoseini, S.; Jahandideh, M.; Hoseini, A.; Yazdi, A.S. Analysis of factors that induce cysteine bonding state. Comput. Biol. Med. 2009, 39, 332-339.
21. Petersen, M.T.N.; Jonson, P.H.; Petersen, S.B. Amino acid neighbours and detailed conformational analysis of cysteines in proteins. Protein Eng. Des. Sel. 1999, 12, 535-548.
22. Dani, V.S.; Ramakrishnan, C.; Varadarajan, R. MODIP revisited: Re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Eng. Des. Sel. 2003, 16, 187-193.
23. Inaba, K.; Murakami, S.; Suzuki, M.; Nakagawa, A.; Yamashita, E.; Okada, K.; Ito, K. Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation. Cell 2006, 127, 789-201.
24. Ito, K. Editing disulphide bonds: error correction using redox currencies. Mol. Microbiol. 2010, 75, 1-5.
25. Sevier, C.S.; Kaiser, C.A. Ero1 and redox homeostasis in the endoplasmic reticulum. BBA 2008, 1783, 549-556.
26. Schmidt, B.; Ho, L.; Hogg, P.J. Allosteric disulphide bonds. Biochemistry 2006, 45, 7429-7433.
27. Schmidt, B.; Hogg, P.J. Search for allosteric disulfide bonds in NMR structures. BMC Struct. Biol. 2007, 7, 49.
28. Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C. SCOP: A structural classification of proteins database for investigation of sequences and structures. J. Mol. Biol. 1995, 247, 536-540.
29. Andreeva, A.; Howorth, D.; Brenner, S.E.; Hubbard, T.J.P.; Chothia, C.; Murzin, A.G. SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res. 2004, 32, D222-D229.
30. Andreeva, A.; Howorth, D.; Chandonia, J.-M.; Brenner, S.E.; Hubbard, T.J.P.; Chothia, C.; Murzin, A.G. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008, 36, D419-D425.
31. Xia, X.; Xie, Z. Protein structure, neighbor effect, and a new index of amino acid dissimilarities. Mol. Biol. Evol. 2002, 19, 58-67.
32. Xie, D.; Tropsha, A.; Schlick, T. An efficient projection protocol for chemical databases: Singular value decomposition combined with truncated-Newton minimization. J. Chem. Inf. Comput. Sci. 2000, 40, 167-177.