In silico investigation of sequences and predicted three-dimensional homology models of thermoalkaliphilic GH13 ?-amylases

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dc.authoridTutuncu, Havva Esra/0000-0003-3951-399X
dc.contributor.authorTutuncu, Havva Esra
dc.contributor.authorSurmeli, Yusuf
dc.date.accessioned2024-10-29T17:58:21Z
dc.date.available2024-10-29T17:58:21Z
dc.date.issued2023
dc.departmentTekirdağ Namık Kemal Üniversitesi
dc.description.abstractThermoalkaliphilic GH13 alpha-amylases are extensively used in various industrial processes, especially detergent formulations, saccharification of starch, production of bioethanol, and textile industry. This study purposed the comparative analysis of the evolutionary relationships, enzyme sequence similarities, three-dimensional structures, and protein-ligand interactions of three thermoalkaliphilic GH13 alpha-amylases of various bacterial sources (Caldicellulosiruptor changbaiensis = CcAmy, Caldicellulosiruptor saccharolyticus = CsAmy, Streptomyces mobaraensis = SmAmy). To do this, six thermoalkaliphilic amylase candidate sequences obtained from unreviewed protein entries of UniProt/TrEMBL database were investigated for their evolutionary relationships and sequence similarities by MEGA11 and Clustal Omega, respectively. The 3D homology models of the three a-amylases were built and cross-validated by various bioinformatics programs. Protein-ligand interactions were analyzed via molecular docking utilizing three ligands (maltobiose, maltotriose, and maltotetraose). The alignment analysis showed that six amylase candidates possessed highly conserved seven CSRs, three catalytic residues and seven Ca2+-binding site residues. Molecular phylogeny indicated that SmAmy belonged to GH13_32 subfamily, indicating that it could be a-amylase, whereas CcAmy and CsAmy belonged to GH13_36, indicating that they could be intermediary a-amylase having additional specificities like cyclomaltodextrinase and neopullulanase. Analysis of 3D models indicated that three a-amylases were structurally similar to each other containing three main domains (A, B, and C). BAN Delta IT analysis showed that all a-amylases might exhibit higher thermostability than the BlAmy. Docking analysis showed that active site residues including catalytic triad residues were involved in the polar interactions between each ligand and enzyme. Therefore, this work suggested that three alpha-amylases might stand out as candidates for the industrial processes that require thermoalkaliphilicity properties.
dc.identifier.doi10.1007/s11756-023-01432-4
dc.identifier.endpage1845
dc.identifier.issn0006-3088
dc.identifier.issn1336-9563
dc.identifier.issue7en_US
dc.identifier.scopus2-s2.0-85159703793
dc.identifier.scopusqualityQ3
dc.identifier.startpage1833
dc.identifier.urihttps://doi.org/10.1007/s11756-023-01432-4
dc.identifier.urihttps://hdl.handle.net/20.500.11776/14248
dc.identifier.volume78
dc.identifier.wosWOS:000992737900001
dc.identifier.wosqualityQ3
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherSpringer
dc.relation.ispartofBiologia
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectThermoalkaliphilic amylase
dc.subjectMolecular docking
dc.subjectIndustrial process
dc.subjectGH13 alpha-amylase
dc.titleIn silico investigation of sequences and predicted three-dimensional homology models of thermoalkaliphilic GH13 ?-amylases
dc.typeArticle

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