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Microbiology and Biotechnology Letters

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Microbial Biotechnology (MB)  |  Protein Structure, Function, and Engineering

Microbiol. Biotechnol. Lett. 2021; 49(1): 65-74

https://doi.org/10.48022/mbl.2009.09012

Received: September 28, 2020; Accepted: November 30, 2020

Exploring the Catalytic Significant Residues of Serine Protease Using Substrate-Enriched Residues and a Peptidase Inhibitor

Zahoor Khan1,2, Maryam Shafique2*, Amir Zeb3,4, Nusrat Jabeen1, Sehar Afshan Naz2, and Arif Zubair5

1Department of Microbiology, University of Karachi 75270, Pakistan 2Department of Microbiology, Federal Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan 3Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea 4College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea 5Department of Environmental Sciences, Federal Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan

Correspondence to :
Maryam Shafique,
maryamshafique@yahoo.com

Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively. The three-dimensional structure of the enzyme was modeled using the MODELLER program present in Discovery Studio followed by Molecular Dynamics simulation using GROMACS 5.0.7 package with CHARMM36m force field. The proteolytic potential was measured by performing docking with casein- and keratin-enriched residues, while the effect of the inhibitor was studied using phenylmethylsulfonyl fluoride, (PMSF) applying GOLDv5.2.2. Molecular weight, instability index, aliphatic index, and isoelectric point for serine protease were 39.53 kDa, 27.79, 82.20 and 8.91, respectively. The best model was selected based on the lowest MOLPDF score (1382.82) and DOPE score (-29984.07). The analysis using ProSA-web revealed a Z-score of -9.7, whereas 88.86% of the residues occupied the most favored region in the Ramachandran plot. Ser327, Asp138, Asn261, and Thr326 were found as critical residues involved in ligand binding and execution of biocatalysis. Our findings suggest that bioengineering of these critical residues may enhance the catalytic potential of this enzyme.

Keywords: Catalytic potential, serine protease, caseinolytic, keratinolytic, modelling

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