An in-Silico Approach to Understanding the Structure-Function: A Molecular Dynamics Simulation Study of Rand Serine Protease Properties from Bacillus Subtilis in Aqueous Solvents

The protein's 3D structure is important for designing a novel biocatalyst that suits industrial applications.Moreover, the data from the 3D structure may increase enzyme production and help to analyse and provide an understanding of the structure of the thermostable, organic-solventtolerant Rand serine protease.A structural prediction for the Rand serine protease was built using the Yet Another Scientific Artificial Reality Application (YASARA) structure employing a known 3D structure (subtilisin E-propeptide complex; PDB ID: 1SCJ) as a template, which has the highest sequence identity (96%) to the Rand serine protease.In silico study of docking, the substrate N-succinyl-alanyl-alanyl-prolyl-phenylalanine-4-nitroanilide in Rand protease resulted in 25 clusters whereby 4 clusters observed to involve the catalytic triad of rand protease -.Molecular dynamics (MD) simulations were performed in two organic solvents with different logP values, such as pyridine (logP 0.71), benzene (logP 2.0) and pure water, for 10 ns to investigate their effect on the Rand protease structure.The predicted 3D structure of the Rand protease revealed that the topological organization of the α/β-hydrolase fold consisted of 6 α-helices and 13 β-strands.The active site of the enzyme predicted to be consisted of three amino acids residues Asp32, His64 and Ser221.This docking result was in good agreement with the active site prediction -study, which showed the same conserved catalytic triad.In conclusion, the structure analysis confirmed the unique characteristics of this enzyme and explained the organic solvent stability of the enzyme.