Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides

Thangudu, Ratna Rajesh ; Vinayagam, A. ; Pugalenthi, G. ; Manonmani, A. ; Offmann, B. ; Sowdhamini, R. (2005) Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides Proteins: Structure, Function, and Bioinformatics, 58 (4). pp. 866-879. ISSN 0887-3585

Full text not available from this repository.

Official URL: http://onlinelibrary.wiley.com/doi/10.1002/prot.20...

Related URL: http://dx.doi.org/10.1002/prot.20369

Abstract

Structure prediction and three-dimensional modeling of disulfide-rich systems are challenging due to the limited number of such folds in the structural databank. We exploit the stereochemical compatibility of substructures in known protein structures to accomodate disulfide bonds in predicting the structures of disulfide-rich polypeptides directly from disulfide connectivity pattern and amino acid sequence in the absence of structural homologs and any other structural information. This knowledge-based approach is illustrated using structure prediction of 40 nonredundant bioactive disulfide-rich polypeptides such as toxins, growth factors, and endothelins available in the structural databank. The polypeptide conformation could be predicted in 35 out of 40 nonredundant entries (87%). Nonhomologous templates could be identified and models could be obtained within 2 Å deviation from the query in 29 peptides (72%). This procedure can be accessed from the World Wide Web (http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html).

Item Type:Article
Source:Copyright of this article belongs to John Wiley and Sons.
Keywords:SS Bonds; Covalent Crosslinks; Fold Recognition; Bioactive Peptides; DSDBASE; Disulfide Database
ID Code:61237
Deposited On:15 Sep 2011 03:58
Last Modified:15 Sep 2011 03:58

Repository Staff Only: item control page