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Cooperativity of the oxidization of cysteines in globular proteins.

Authors
  • Jiang-Ning, Song
  • Wei-Jiang, Li
  • Wen-Bo, Xu
Type
Published Article
Journal
Journal of theoretical biology
Publication Date
Nov 07, 2004
Volume
231
Issue
1
Pages
85–95
Identifiers
PMID: 15363931
Source
Medline
License
Unknown

Abstract

Based on the 639 non-homologous proteins with 2910 cysteine-containing segments of well-resolved three-dimensional structures, a novel approach has been proposed to predict the disulfide-bonding state of cysteines in proteins by constructing a two-stage classifier combining a first global linear discriminator based on their amino acid composition and a second local support vector machine classifier. The overall prediction accuracy of this hybrid classifier for the disulfide-bonding state of cysteines in proteins has scored 84.1% and 80.1%, when measured on cysteine and protein basis using the rigorous jack-knife procedure, respectively. It shows that whether cysteines should form disulfide bonds depends not only on the global structural features of proteins but also on the local sequence environment of proteins. The result demonstrates the applicability of this novel method and provides comparable prediction performance compared with existing methods for the prediction of the oxidation states of cysteines in proteins.

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