Novel Thermostable α-Amylase from Bacillus subtilis: Molecular Characterization, Optimization, and Docking-Based Substrate Profiling

Abstract

Bacterial alpha-amylases have diverse industrial applications in food, fermentation, and pharmaceuticals. This study focuses on the isolation and characterization of a novel alpha-amylase-producing bacterium through molecular and in silico analyses, including molecular docking to determine enzyme-substrate specificity and binding interactions. Among nine bacterial isolates, S4 demonstrated the highest amylolytic activity of 63.68 U/ml. Molecular identification revealed isolate (S4) identity as Bacillus subtilis (OM278386). Enzyme charcterization revealed that maximum enzyme activity was observed at 40 °C and pH 7.0, after 24 h. The full-length novel alpha-amylase gene from B. subtilis (S4) was amplified, sequenced, and translated into a protein sequence. A putative protein was subjected to BLASTp, phylogenetic analysis, and physicochemical characterization. A 3D model was generated and validated through homology modeling. Molecular docking was performed using six substrates: amylopectin, maltotetraose, glycogen, starch, amylose, and cyclodextrin to determine substrate specificity. The putative AmyE protein comprised 488 amino acids. Phylogenetic analysis confirmed its close association with alpha-amylases of other Bacillus species. The enzymes exhibited industrially desirable traits, including high stability, thermotolerance, and hydrophilicity. In contrast, 3D model investigation showed excellent stereochemical quality, with 95.2% of amino acids in the favored region of the Ramachandran plot. Docking studies revealed the highest affinity for amylopectin (binding energy: – 7.2 kcal/mol). Two essential amino acid residues, Asp and Glu-318, were identified as crucial for active-site substrate interactions and enzyme catalysis across various substrates. In conclusion, the analysis presents alpha-amylase from B. subtilis stain S4 as a promising candidate for diverse industrial applications, offering cost-effective alternatives for starch processing, food preservation, and other biotechnological processes.

Graphical abstract

Schematic presentation of the study workflow illustrates the screening and isolation of a novel alpha-amylase producing isolate (S4) from soil, followed by molecular identification using 16S rDNA sequence. Full-length novel gene is amplified, sequenced, and translated to protein sequence. The three-dimensional model was validated by homology modelling for subsequent docking and substrate binding affinity analysis.

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