標題: SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides
作者: Vasylenko, Tamara
Liou, Yi-Fan
Chiou, Po-Chin
Chu, Hsiao-Wei
Lai, Yung-Sung
Chou, Yu-Ling
Huang, Hui-Ling
Ho, Shinn-Ying
生物科技學院
生物資訊及系統生物研究所
生物資訊研究中心
College of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
Center for Bioinformatics Research
關鍵字: BY-kinase;Scoring card method;Drug repurposing;Propensity scores;Dipeptide
公開日期: 22-Dec-2016
摘要: Background: Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular processes, are characterized as a separate class of enzymes and share no structural similarity with their eukaryotic counterparts. However, in silico methods for predicting BY-kinases have not been developed yet. Since these enzymes are involved in key regulatory processes, and are promising targets for anti-bacterial drug design, it is desirable to develop a simple and easily interpretable predictor to gain new insights into bacterial tyrosine phosphorylation. This study proposes a novel SCMBYK method for predicting and characterizing BY-kinases. Results: A dataset consisting of 797 BY-kinases and 783 non-BY-kinases was established to design the SCMBYK predictor, which achieved training and test accuracies of 97.55 and 96.73%, respectively. Furthermore, the leaveone-phylum-out method was used to predict specific bacterial phyla hosts of target sequences, gaining 97.39% average test accuracy. After analyzing SCMBYK-derived propensity scores, four characteristics of BY-kinases were determined: 1) BY-kinases tend to be composed of a-helices; 2) the amino-acid content of extracellular regions of BY-kinases is expected to be dominated by residues such as Val, Ile, Phe and Tyr; 3) BY-kinases structurally resemble nuclear proteins; 4) different domains play different roles in triggering BY-kinase activity. Conclusions: The SCMBYK predictor is an effective method for identification of possible BY-kinases. Furthermore, it can be used as a part of a novel drug repurposing method, which recognizes putative BY-kinases and matches them to approved drugs. Among other results, our analysis revealed that azathioprine could suppress the virulence of M. tuberculosis, and thus be considered as a potential antibiotic for tuberculosis treatment.
URI: http://dx.doi.org/10.1186/s12859-016-1371-4
http://hdl.handle.net/11536/145961
ISSN: 1471-2105
DOI: 10.1186/s12859-016-1371-4
期刊: BMC BIOINFORMATICS
Volume: 17
起始頁: 0
結束頁: 0
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