In-Silico Alanine Scanning Analysis on the Catalytic Residues of a Novel Β-Glucosidase From Trichoderma Asperellum Uc1

Abstract

Currently, the catalytic residue of the highly prolific fungal β-glucosidase (BGL) of Trichoderma asperellum UC1 remains unvalidated. The study used the alanine scanning method to confirm the catalytic residues of the BGL as Glu165, Asp226, and Glu423. This method cancels out all intermolecular hydrogen bonds with substrates, lignin, hemicellulose, and cellulose. Results revealed an overall decline in the stability of the energy-minimized mutant enzymes' compared to the wild-type BGL. The mutant enzyme registered lower PROCHECK (91.0%), ERRAT (93.09%), and Verify-3D (98.92%) values, in comparison to 90.2%, 92.09%, 98.06%, in the wild-type BGL, respectively. The mutant BGL UC1-substrate complexes were less stable than the wild-type enzyme, in which the mutant exhibited higher binding energies for docked lignin (−7.4% kcal mol-1), cellulose (−7.2 kcal mol-1), and hemicellulose (−7.2 kcal mol-1). Binding energies of the wild-type BGL with the corresponding substrates were lower at −7.9 kcal mol-1, −8.1 kcal mol-1, and −7.8 kcal mol-1. An interesting observation was that the alanine scanning changed the substrate preference order based on the calculated binding energies. The mutant BGL bound preferentially to lignin>cellulose=hemicellulose, while the wild-type BGL was selective to cellulose>lignin>hemicellulose. Hence, the findings convey the high likelihood of Glu165, Asp 256, and Glu423 are the catalytic residues of the BGL of T. asperellum UC1.

Bioinformatics analysis and molecular dynamics simulations of azoreductases (AzrBmH2) from Bacillus megaterium H2 for the decolorization of commercial dyes

“…The threshold range for RMSF was between 0.05 -0.3 nm, this determines the significant changes in residue-specific flexibility that gauging an enzyme's substrate specificity (Zhu et al, 2019). Therefore, a high RMSF value represents a higher degree of fluctuation, while a low value implies limited structural movement and a more stable structure (Kumar et al, 2014;Yunus et al, 2021). The AzrBmH2 proteins exhibit low RMSF values for the predicted catalytic or binding site residues, indicating strong molecular interactions with the dyes (ligands).…”