Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition

In this paper, a novel approach has been introduced to predict the disulfide-bonding state of cysteines in proteins by means of a linear discriminator based on their dipeptide composition. The prediction is performed with a newly enlarged dataset with 8114 cysteine-containing segments extracted from...

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Bibliographic Details
Published in:Biochemical and biophysical research communications 2004-05, Vol.318 (1), p.142-147
Main Authors: Song, Jiang-Ning, Wang, Ming-Lei, Li, Wei-Jiang, Xu, Wen-Bo
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Bioinformatics
Cooperativity
Cysteine
Cysteine - chemistry
Databases, Protein
Dipeptide composition
Dipeptides - chemistry
Disulfide-bonding state
Disulfides - chemistry
Models, Chemical
Oxidation-Reduction
Protein folding
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Summary:In this paper, a novel approach has been introduced to predict the disulfide-bonding state of cysteines in proteins by means of a linear discriminator based on their dipeptide composition. The prediction is performed with a newly enlarged dataset with 8114 cysteine-containing segments extracted from 1856 non-homologous proteins of well-resolved three-dimensional structures. The oxidation of cysteines exhibits obvious cooperativity: almost all cysteines in disulfide-bond-containing proteins are in the oxidized form. This cooperativity can be well described by protein’s dipeptide composition, based on which the prediction accuracy of the oxidation form of cysteines scores as high as 89.1% and 85.2%, when measured on cysteine and protein basis using the rigorous jack-knife procedure, respectively. The result demonstrates the applicability of this new relatively simple method and provides superior prediction performance compared with existing methods for the prediction of the oxidation states of cysteines in proteins.
ISSN:0006-291X
1090-2104
DOI:10.1016/j.bbrc.2004.03.189