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

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  • Yan Xu
  • Jun Ding
  • Ling-Yun Wu

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/.

Suggested Citation

  • Yan Xu & Jun Ding & Ling-Yun Wu, 2016. "iSulf-Cys: Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-9, April.
    • Handle: RePEc:plo:pone00:0154237
    DOI: 10.1371/journal.pone.0154237
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    References listed on IDEAS

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    1. Jing Yang & Vinayak Gupta & Kate S. Carroll & Daniel C. Liebler, 2014. "Site-specific mapping and quantification of protein S-sulphenylation in cells," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    2. Eranthie Weerapana & Chu Wang & Gabriel M. Simon & Florian Richter & Sagar Khare & Myles B. D. Dillon & Daniel A. Bachovchin & Kerri Mowen & David Baker & Benjamin F. Cravatt, 2010. "Quantitative reactivity profiling predicts functional cysteines in proteomes," Nature, Nature, vol. 468(7325), pages 790-795, December.
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