Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition
Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition
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DOI：
10.1016/j.bbrc.2004.03.189
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发表时间：
2004-05-21
影响因子：
3.1
通讯作者：
Xu, WB
中科院分区：
文献类型：
--
作者：
Song, JN;Wang, ML;Xu, WB
本文介绍了一种基于二肽组成的线性鉴别器来预测蛋白质中半胱氨酸的二硫键状态的新方法。预测是用一个新扩大的数据集进行的，该数据集从1856个非同源蛋白中提取了8114个含半胱氨酸的片段，这些片段具有良好的三维结构。半胱氨酸的氧化表现出明显的协同性：含二硫键的蛋白质中几乎所有的半胱氨酸都以氧化形式存在。蛋白质的二肽组成可以很好地描述这种协同性，在此基础上，半胱氨酸和蛋白质的氧化形式预测精度分别高达89.1%和85.2%。结果表明，相对于现有的半胱氨酸氧化态预测方法，该方法具有较好的适用性和较好的预测性能。(C) 2004爱思唯尔公司版权所有。
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. (C) 2004 Elsevier Inc. All rights reserved.