Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins.

Tópicos

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Resumo

Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating transcriptional repression and activation. Histones possess highly conserved sequences and are homologous in most species. However, there is much less sequence conservation among non-histone proteins. Therefore, mechanisms for identifying lysine-methylated sites may greatly differ between histones and non-histone proteins. Nevertheless, this point of view was not considered in previous studies. Here we constructed two support vector machine (SVM) models by using lysine-methylated data from histones and non-histone proteins for predictions of lysine-methylated sites. Numerous features, such as the amino acid composition (AAC) and accessible surface area (ASA), were used in the SVM models, and the predictive performance was evaluated using five-fold cross-validations. For histones, the predictive sensitivity was 85.62% and specificity was 80.32%. For non-histone proteins, the predictive sensitivity was 69.1% and specificity was 88.72%. Results showed that our model significantly improved the predictive accuracy of histones compared to previous approaches. In addition, features of the flanking region of lysine-methylated sites on histones and non-histone proteins were also characterized and are discussed. A gene ontology functional analysis of lysine-methylated proteins and correlations of lysine-methylated sites with other PTMs in histones were also analyzed in detail. Finally, a web server, MethyK, was constructed to identify lysine-methylated sites. MethK now is available at http://csb.cse.yzu.edu.tw/MethK/.

Resumo Limpo

protein methyl kind posttransl modif ptm typic take place lysin arginin amino acid residu protein methyl involv mani import biolog process recent studi focus lysin methyl histon due critic role regul transcript repress activ histon possess high conserv sequenc homolog speci howev much less sequenc conserv among nonhiston protein therefor mechan identifi lysinemethyl site may great differ histon nonhiston protein nevertheless point view consid previous studi construct two support vector machin svm model use lysinemethyl data histon nonhiston protein predict lysinemethyl site numer featur amino acid composit aac access surfac area asa use svm model predict perform evalu use fivefold crossvalid histon predict sensit specif nonhiston protein predict sensit specif result show model signific improv predict accuraci histon compar previous approach addit featur flank region lysinemethyl site histon nonhiston protein also character discuss gene ontolog function analysi lysinemethyl protein correl lysinemethyl site ptms histon also analyz detail final web server methyk construct identifi lysinemethyl site methk now avail httpcsbcseyzuedutwmethk

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