title: Discriminating between lysine sumoylation and lysine acetylation using mRMR feature selection and analysis.
abstract: Post-translational modifications (PTMs) are crucial steps in protein synthesis and are important factors contributing to protein diversity. PTMs play important roles in the regulation of gene expression, protein stability and metabolism. Lysine residues in protein sequences have been found to be targeted for both types of PTMs: sumoylations and acetylations; however, each PTM has a different cellular role. As experimental approaches are often laborious and time consuming, it is challenging to distinguish the two types of PTMs on lysine residues using computational methods. In this study, we developed a method to discriminate between sumoylated lysine residues and acetylated residues. The method incorporated several features: PSSM conservation scores, amino acid factors, secondary structures, solvent accessibilities and disorder scores. By using the mRMR (Maximum Relevance Minimum Redundancy) method and the IFS (Incremental Feature Selection) method, an optimal feature set was selected from all of the incorporated features, with which the classifier achieved 92.14% accuracy with an MCC value of 0.7322. Analysis of the optimal feature set revealed some differences between acetylation and sumoylation. The results from our study also supported the previous finding that there exist different consensus motifs for the two types of PTMs. The results could suggest possible dominant factors governing the acetylation and sumoylation of lysine residues, shedding some light on the modification dynamics and molecular mechanisms of the two types of PTMs, and provide guidelines for experimental validations.
authors.affiliation: Department of Biomedical Engineering, Tianjin Key Lab of Biomedical Engineering Measurement, Tianjin University, Tianjin, P.R. China.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China.
authors.forename: You
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China.
authors.forename: Yu-Chao
authors.initials: YC
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China.
authors.forename: Bi-Qing
authors.initials: BQ
authors.lastname: Li
authors.affiliation: College of Information Engineering, Shanghai Maritime University, Shanghai, P.R. China.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: Institute of Systems Biology, Shanghai University, Shanghai, P.R. China.
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
mesh_terms: D000107:Acetylation; D008239:Lysine / Q000378:metabolism*; D058207:Sumoylation
chemical_list: D008239:Lysine