Abstract—S-nitrosylation (SNO) is a sulfur atom occurring in cysteine amino acid in the protein connected to nitric oxide (NO), and it is one of the most important and universal Post-translational modifications. Nitroso modification will affect regulating cell function and information transfer. In recent years, there were many studies have developed the method of indentify S-nitrosylation substrate site in silicon. Unfortunately, people did not find significant characteristics for identification in protein sequence. Therefore, this study aims to explore structural characteristics on tertiary structures of S-nitrosylated proteins. As the number of the crystal structure in the PDB increases, also many SNO sites have been experimentally verified, we characterized these substrate sites containing 3D structures by structural analysis methods, such as Spatial amino acid composition, side chain orientation, and DSSP relative solvent accessible area. Besides, the support vector machine (SVM) was employed to generate the predictive model with the consideration of both sequential and spatial features. According to the evaluation of five-fold cross-validation, the spatial model could obtain a higher accuracy than the sequential model. Additionally, this work revealed that the model concerning multiple spatial features could achieve best performance in the prediction of SNO sites.

Index Terms—S-nitrosylation, SNO, nitric oxide, tertiary structure, side chain orientation, support vector machine.

Tzong-Yi Lee is with School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China. He is also with Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China (email: leetzongyi@cuhk.edu.cn).
Justin Bo-Kai Hsu is with Department of Medical Research, Taipei Medical University Hospital, Taipei 110, Taiwan.
Tzu-Hao Chang is with Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan.

Cite: Tzong-Yi Lee, Justin Bo-Kai Hsu, Tzu-Hao Chang, "Characterization and Identification of Protein S-Nitrosylation Sites Based on Tertiary Structures," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 10, no. 1, pp. 15-25, 2020.
 

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