Inter- and Intra-Chain Disulfide Bond Prediction Based on Optimal Feature Selection

Shen      Niu; Tao      Huang; Kai-Yan      Feng; Zhisong      He; Weiren      Cui; Lei      Gu; Haipeng      Li; Yu-Dong      Cai; Yixue      Li

doi:10.2174/0929866511320030011

Abstract

Protein disulfide bond is formed during post-translational modifications, and has been implicated in various physiological and pathological processes. Proper localization of disulfide bonds also facilitates the prediction of protein three-dimensional (3D) structure. However, it is both time-consuming and labor-intensive using conventional experimental approaches to determine disulfide bonds, especially for large-scale data sets. Since there are also some limitations for disulfide bond prediction based on 3D structure features, developing sequence-based, convenient and fast-speed computational methods for both inter- and intra-chain disulfide bond prediction is necessary. In this study, we developed a computational method for both types of disulfide bond prediction based on maximum relevance and minimum redundancy (mRMR) method followed by incremental feature selection (IFS), with nearest neighbor algorithm as its prediction model. Features of sequence conservation, residual disorder, and amino acid factor are used for inter-chain disulfide bond prediction. And in addition to these features, sequential distance between a pair of cysteines is also used for intra-chain disulfide bond prediction. Our approach achieves a prediction accuracy of 0.8702 for inter-chain disulfide bond prediction using 128 features and 0.9219 for intra-chain disulfide bond prediction using 261 features. Analysis of optimal feature set indicated key features and key sites for the disulfide bond formation. Interestingly, comparison of top features between interand intra-chain disulfide bonds revealed the similarities and differences of the mechanisms of forming these two types of disulfide bonds, which might help understand more of the mechanisms and provide clues to further experimental studies in this research field.

Keywords: Disulfide bond, inter-chain, intra-chain, incremental feature selection, maximum relevance minimum redundancy, nearest neighbor algorithm, post-translational modifications, incremental feature selection (IFS), cysteine, oxidation