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dc.contributor.authorLiou, Yi-Fanen_US
dc.contributor.authorHuang, Hui-Lingen_US
dc.contributor.authorHo, Shinn-Yingen_US
dc.date.accessioned2019-04-03T06:37:03Z-
dc.date.available2019-04-03T06:37:03Z-
dc.date.issued2016-12-22en_US
dc.identifier.issn1471-2105en_US
dc.identifier.urihttp://dx.doi.org/10.1186/s12859-016-1368-zen_US
dc.identifier.urihttp://hdl.handle.net/11536/145950-
dc.description.abstractBackground: Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein structures, in this study, our aim was to design predictors for estimating relative solvent accessibility (RSA) of amino acid residues to discover protein folding characteristics from sequences. Methods: The proposed 20 real-value RSA predictors were designed on the basis of the support vector regression method with a set of informative physicochemical properties (PCPs) obtained by means of an optimal feature selection algorithm. Then, molecular dynamics simulations were performed for validating the knowledge discovered by analysis of the selected PCPs. Results: The RSA predictors had the mean absolute error of 14.11% and a correlation coefficient of 0.69, better than the existing predictors. The hydrophilic-residue predictors preferred PCPs of buried amino acid residues to PCPs of exposed ones as prediction features. A hydrophobic spine composed of exposed hydrophobic residues of an a-helix was discovered by analyzing the PCPs of RSA predictors corresponding to hydrophobic residues. For example, the results of a molecular dynamics simulation of wild-type sequences and their mutants showed that proteins 1MOF and 2WRP_H16I (Protein Data Bank IDs), which have a perfectly hydrophobic spine, have more stable structures than 1MOF_I54D and 2WRP do (which do not have a perfectly hydrophobic spine). Conclusions: We identified informative PCPs to design high-performance RSA predictors and to analyze these PCPs for identification of novel protein folding characteristics. A hydrophobic spine in a protein can help to stabilize exposed alpha-helices.en_US
dc.language.isoen_USen_US
dc.subjectHydrophobic spineen_US
dc.subjectMolecular dynamics simulationen_US
dc.subjectPhysicochemical propertiesen_US
dc.subjectProtein foldingen_US
dc.subjectSolvent-accessible surface areaen_US
dc.subjectSupport vector regressionen_US
dc.subjectKnowledge discoveryen_US
dc.titleA hydrophobic spine stabilizes a surface-exposed alpha-helix according to analysis of the solvent-accessible surface areaen_US
dc.typeArticleen_US
dc.identifier.doi10.1186/s12859-016-1368-zen_US
dc.identifier.journalBMC BIOINFORMATICSen_US
dc.citation.volume17en_US
dc.citation.spage0en_US
dc.citation.epage0en_US
dc.contributor.department生物科技學系zh_TW
dc.contributor.department生物資訊及系統生物研究所zh_TW
dc.contributor.departmentDepartment of Biological Science and Technologyen_US
dc.contributor.departmentInstitude of Bioinformatics and Systems Biologyen_US
dc.identifier.wosnumberWOS:000392533100008en_US
dc.citation.woscount1en_US
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