Predicting protein oxidation sites with feature selection and analysis approach

Abstract

Protein oxidation is a ubiquitous post-translational modification that plays important roles in various physiological and pathological processes. Owing to the fact that protein oxidation can also take place as an experimental artifact or caused by oxygen in the air during the process of sample collection and analysis, and that it is both time-consuming and expensive to determine the protein oxidation sites purely by biochemical experiments, it would be of great benefit to develop in silico methods for rapidly and effectively identifying protein oxidation sites. In this study, we developed a computational method to address this problem. Our method was based on the nearest neighbor algorithm in which, however, the maximum relevance minimum redundancy and incremental feature selection approaches were incorporated. From the initial 735 features, 16 features were selected as the optimal feature set. Of such 16 optimized features, 10 features were associated with the position-specific scoring matrix conservation scores, three with the amino acid factors, one with the propensity of conservation of residues on protein surface, one with the side chain count of carbon atom deviation from mean, and one with the solvent accessibility. It was observed that our prediction model achieved an overall success rate of 75.82%, indicating that it is quite encouraging and promising for practical applications. Also, the 16 optimal features obtained through this study may provide useful clues and insights for in-depth understanding the action mechanism of protein oxidation.

Keywords:

• protein oxidation sites
• mRMR
• feature selection
• PSSM score
• disorder

Acknowledgment

This work was supported by the State Key Basic Research Program (973) (2011CB910204, 2011CB510102 and 2011CB510101), Innovation Program of Shanghai Municipal Education Commission (12ZZ087), Research Program of CAS (KSCX2-EW-R-04), and National Natural Science Foundation of China (30900272).

Notes

These authors contributed equally to this work