iSulf-Cys: Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids

PLoS One. 2016 Apr 22;11(4):e0154237. doi: 10.1371/journal.pone.0154237. eCollection 2016.

Abstract

Cysteine S-sulfenylation is an important post-translational modification (PTM) in proteins, and provides redox regulation of protein functions. Bioinformatics and structural analyses indicated that S-sulfenylation could impact many biological and functional categories and had distinct structural features. However, major limitations for identifying cysteine S-sulfenylation were expensive and low-throughout. In view of this situation, the establishment of a useful computational method and the development of an efficient predictor are highly desired. In this study, a predictor iSulf-Cys which incorporated 14 kinds of physicochemical properties of amino acids was proposed. With the 10-fold cross-validation, the value of area under the curve (AUC) was 0.7155 ± 0.0085, MCC 0.3122 ± 0.0144 on the training dataset for 20 times. iSulf-Cys also showed satisfying performance in the independent testing dataset with AUC 0.7343 and MCC 0.3315. Features which were constructed from physicochemical properties and position were carefully analyzed. Meanwhile, a user-friendly web-server for iSulf-Cys is accessible at http://app.aporc.org/iSulf-Cys/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Amino Acids / chemistry
  • Amino Acids / genetics
  • Amino Acids / metabolism*
  • Binding Sites / genetics
  • Chemical Phenomena
  • Computational Biology / methods*
  • Cysteine / chemistry
  • Cysteine / genetics
  • Cysteine / metabolism
  • Internet
  • Peptides / chemistry
  • Peptides / genetics
  • Peptides / metabolism
  • Protein Processing, Post-Translational*
  • Proteins / chemistry
  • Proteins / genetics
  • Proteins / metabolism*
  • Reproducibility of Results
  • Software*
  • Sulfenic Acids / chemistry
  • Sulfenic Acids / metabolism*

Substances

  • Amino Acids
  • Peptides
  • Proteins
  • Sulfenic Acids
  • Cysteine

Grant support

This work was supported by grants from the Natural Science Foundation of China (11301024, 31171263, 81272578, and J1103514) and the Fundamental Research Funds for the Central Universities (No. FRF-BR-15-075A). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.