Exploring the Structural Insights of Thermostable Geobacillus esterases by Computational Characterization

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dc.authoridSURMELI, YUSUF/0000-0002-9645-6314
dc.authoridDURMUS, NACIYE/0000-0002-3388-5349
dc.contributor.authorSurmeli, Yusuf
dc.contributor.authorDurmus, Naciye
dc.contributor.authorSanli-Mohamed, Gulsah
dc.date.accessioned2024-10-29T17:58:32Z
dc.date.available2024-10-29T17:58:32Z
dc.date.issued2024
dc.departmentTekirdağ Namık Kemal Üniversitesien_US
dc.description.abstractThis study conducted an in silico analysis of two biochemically characterized thermostable esterases, Est2 and Est3, from Geobacillus strains. To achieve this, the amino acid sequences of Est2 and Est3 were examined to assess their biophysicochemical properties, evolutionary connections, and sequence similarities. Three-dimensional models were constructed and validated through diverse bioinformatics tools. Molecular dynamics (MD) simulation was employed on a pNP-C2 ligand to explore interactions between enzymes and ligand. Biophysicochemical property analysis indicated that aliphatic indices and theoretical T-m values of enzymes were between 82-83 and 55-65 degrees C, respectively. Molecular phylogeny placed Est2 and Est3 within Family XIII, alongside other Geobacillus esterases. DeepMSA2 revealed that Est2, Est3, and homologous sequences shared 12 conserved residues in their core domain (L39, D50, G53, G55, S57, G92, S94, G96, P108, P184, D193, and H223). BAN Delta IT analysis indicated that Est2 and Est3 had a significantly more rigid cap domain compared to Est30. Salt bridge analysis revealed that E150-R136, E124-K165, E137-R141, and E154-K157 salt bridges made Est2 and Est3 more stable compared to Est30. MD simulation indicated that Est3 exhibited greater fluctuations in the N-terminal region including conserved F25, cap domain, and C-terminal region, notably including H223, suggesting that these regions might influence esterase catalysis. The common residues in the ligand-binding sites of Est2-Est3 were determined as F25 and L167. The analysis of root mean square fluctuation (RMSF) revealed that region 1, encompassing F25 within the beta 2-alpha 1 loop of Est3, exhibited higher fluctuations compared to those of Est2. Overall, this study might provide valuable insights for future investigations aimed at improving esterase thermostability and catalytic efficiency, critical industrial traits, through targeted amino acid modifications within the N-terminal region, cap domain, and C-terminal region using rational protein engineering techniques.en_US
dc.description.sponsorshipNumerical calculations reported in this paper were fully performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). Also, the authors thank Tekirdag Namk Kemal University, I.stanbul Technical University, and I.zmir Institute of Technology for their contribution to the access of the full-text articles.en_US
dc.identifier.doi10.1021/acsomega.4c03818
dc.identifier.endpage32941en_US
dc.identifier.issn2470-1343
dc.identifier.issue30en_US
dc.identifier.pmid39100300en_US
dc.identifier.scopus2-s2.0-85199679347en_US
dc.identifier.startpage32931en_US
dc.identifier.urihttps://doi.org/10.1021/acsomega.4c03818
dc.identifier.urihttps://hdl.handle.net/20.500.11776/14376
dc.identifier.volume9en_US
dc.identifier.wosWOS:001274543800001en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherAmer Chemical Socen_US
dc.relation.ispartofAcs Omegaen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectBiochemical-Characterizationen_US
dc.subjectCarboxyl Esterasesen_US
dc.subjectProtein Structuresen_US
dc.subjectStearothermophilusen_US
dc.subjectPurificationen_US
dc.subjectLipaseen_US
dc.subjectIdentificationen_US
dc.subjectKaustophilusen_US
dc.subjectExpressionen_US
dc.subjectSequencesen_US
dc.titleExploring the Structural Insights of Thermostable Geobacillus esterases by Computational Characterizationen_US
dc.typeArticleen_US

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