In silico investigation of sequences and predicted three-dimensional homology models of thermoalkaliphilic GH13 ?-amylases
Küçük Resim Yok
Tarih
2023
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Springer
Erişim Hakkı
info:eu-repo/semantics/closedAccess
Özet
Thermoalkaliphilic 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.
Açıklama
Anahtar Kelimeler
Thermoalkaliphilic amylase, Molecular docking, Industrial process, GH13 alpha-amylase
Kaynak
Biologia
WoS Q Değeri
Q3
Scopus Q Değeri
Q3
Cilt
78
Sayı
7
