Dataset Information

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides.

ABSTRACT:

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 leave-one-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 α-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.

SUBMITTER: Vasylenko T

PROVIDER: S-EPMC5260027 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides.

Vasylenko Tamara T Liou Yi-Fan YF Chiou Po-Chin PC Chu Hsiao-Wei HW Lai Yung-Sung YS Chou Yu-Ling YL Huang Hui-Ling HL Ho Shinn-Ying SY

BMC bioinformatics 20161222 Suppl 19

<h4>Background</h4>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 interpreta ...[more]

PMID: 28155663

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Dataset Information

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides.

Background

Results

Conclusions

Publications

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides.

Similar Datasets

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