Analysis of factors that induce cysteine bonding state

Computers in Biology and Medicine

Volumn 39, Issue 4, 2009, Pages 332-339

  Karami, Zahra ^a   Abdolmaleki, Parviz ^a   Rezaei, Mohammad Ali ^a   Jahandideh, Samad ^a   Asadabadi, Ebrahim Barzegari ^a  

^a TARBIAT MODARES UNIVERSITY   (Iran)

Author keywords

Cysteine bonding state; Doublet local propensity (DLP); Sequence analysis; Singlet local propensity (SLP)

Indexed keywords

PROTEINS;

ACID DISTRIBUTION; AMINO ACID SEQUENCE; BONDING STATE; DOUBLET LOCAL PROPENSITY (DLP); ENCODED INFORMATION; PROTEIN STRUCTURES; SEQUENCE ANALYSIS; SINGLET LOCAL PROPENSITY (SLP);

AMINO ACIDS;

CYSTEINE;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; COVALENT BOND; DISULFIDE BOND; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

EID: 62749127195     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2009.01.006     Document Type: Article

References (22)

1. Alberts B., Bray D., Lewis J., Raff M., Roberts K., and Watson J.D. Molecular Biology of the Cell. second ed. (1994), Garland Publishing, New York, London
2. Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
3. T. Creighton, Structures and Molecular Properties in Proteins, second ed., W.H. Freeman, New York, 1993.
4. Huang E.S., Samudrala J., and Ponder W. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J. Mol. Biol. 290 (1999) 267-281
5. Wedemeyer W.J., Welker E., Narayan M., and Scheraga H.A. Disulfide bonds and protein folding. Biochemistry 39 (2000) 4208-4216
6. Fariselli P., Riccobelli P., and Casadio R. Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. Proteins 36 (1999) 340-346
7. Fiser A., and Simon L. Prediction the oxidation state of cysteines by multiple sequence alignment. Bioinformatics 16 3 (2003) 251-256
8. Fiser A., Cserzi M., Tudas E., and Simon I. Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues. FEBS Lett. 302 20 (1992) 117-120
9. Mucchielli-Giorgi M.H., Hazout S., and Tuffèry P. Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins 46 (2002) 243-249
10. Song N., Wang M., Jiang L.W., and Bo X.W. Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition. Biochem. Biophys. Res. Commun. 318 (2004) 142-147
11. Ninga S., Jianga L., and Bo X. Cooperativity of the oxidization of cysteines in globular proteins. J. Theor. Biol. 231 (2004) 85-95
12. Luigi Martelli P., Fariselli P., and Casadio R. Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network. Proteomics 4 (2004) 1665-1671
13. Ching C.Y., Shin L.Y., Jen L.C., and Kang H.J. Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. Proteins 55 (2004) 1036-1042
14. Thangudu R., Vinayagam A., Pugalenthi G., Manonmani A., Offmann B., and Sowdhamini R. Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides. Proteins 58 (2005) 866-879
15. Cheng J., Saigo H., and Baldi P. Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins 62 (2006) 617-629
16. Hobohm U., and Sander C. Enlarged representative set of protein structures. Protein Sci. 3 (1994) 522-524
17. Wang G., Roland L., and Dunbrack J. PISCES: a protein sequence culling server. Bioinformatics 19 12 (2003) 1589-1591
18. Noguchi T., Matsuda T.H., and Akiyama Y. PDB-REPRDB: a database of representative protein chains from the protein data bank (PDB). Nucleic Acids Res. 29 (2001) 219-220
19. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
20. Wayne W.D. Biostatistics: A Foundation for Analysis in the Health Sciences. seventh ed. (1999), Wiley, New York
21. Kumar S., and Bansal M. Dissecting alpha-helices: position-specific analysis of alpha-helices in globular proteins. Proteins Struct. Funct. Genet. 31 (1998) 460-476
22. Donald E.E., and William F.D. Amino acid propensities are position-dependent throughout the length of α-helices. J. Mol. Biol. 337 5 (2004) 1195-1205