A Computational Structural Biology of SoxR and DNA: A Modelling and Interactive Discern to Express the Sox Operon in Pseudaminobacter salicylatoxidans (KCT001) for Global Sulphur Oxidation

摘要

Computational and microbial molecular-level participation of sox operon and its repressor protein (SoxR) in sulphur oxidation from Pseudaminobacter salicylatoxidans (KCT001) was investigated. Documentation reveals that P. salicylatoxidans (KCT001) has sox TRSVWXYZABCD operon that is regulated by a repressor protein (SoxR). Previously, various experimental procedures such as DMS-mediated DNA methylations and hydroxyl radical footprinting have disclosed that SoxR interacts first with an operator region-sv (present in between soxS and soxV). Detailed computational studies were accomplished in the present study. 3D models of repressor protein and the DNA sequence from operon’s promoter region were demonstrated using molecular modelling techniques. Molecular docking simulation was performed to predict DNA–protein interaction. Amino acid residues and nucleotide bases responsible for interaction were identified by PyMOL and Discovery Studio software suite. This novel residue-level study is paramount for initiating transcription in the operon, thereby leading to sulphur oxidation.