Homology Modeling And Molecular Docking Studies Of Xylanase Enzyme From Bacillus. Substilis
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Abstract
The purpose of this study was To find the interaction between xylan with xylanase in Bacillus subtilis by performing homology modelling and in-silico based molecular docking analysis.The model of the xylanase protein was constructed with SWISS-MODEL Server. The xylanase gene of the sample was sequenced using Sanger Sequencing Method which was then used for homology modelling and further analysis. The sequence was submitted (Accession No.OM986475) in National Center for Biotechnology Information (NCBI)’The Qualitative Model Energy Analysis (QMEAN Z) and Global Model Quality Estimation (GMQE) scores were used to assess the reliability of the modelled 3D structure, GMQE was found to be 0.90+/-0.05 for the modelled protein structure. Local model per residue score was accessed using the QMEANDisCo scoring function,which is a composite score for a single model quality estimation. The SWISS-MODEL Server was also used to provide the structural validation of the modelled target protein (CTX-M) for stereochemical quality and a Ramachandran plot. The ligand Xylan was obtained from PubChem available at https://pubchem.ncbi.nlm.nih.gov/ and was prepared using the Energy Minimisation tool in UCSF Chimera v.1.16. Molecular docking was performed using Autodock Vina. Visualization of this was done with the help of PyMOL v.2.5.2 and LigPlot+. Effect of xylanase on different substrates like xylan, xyloglucan, glucomannan, galactoglucomannan and arabinogalactan was tested using molecular docking., The xylan showed optimum binding affinity with the binding energy of -6.3 kcal/mol. Further interaction analysis, two H-bonds were hydrogen bonding (H-bonding) and five hydrophobic interactions were found for docking with xylan. Through molecular docking study using AutoDock Vina, amino acid residues relevant in protein-ligand interaction were identified
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