Manuscript Title:

COMPUTATIONAL ANALYSIS OF ACTION MECHANISM AND EVOLUTIONARY INSIGHT OF CHITIN DEGRADING ENZYMES IN BACILLUS CEREUS

Author:

AMMARAH FATEEN, MUHAMMAD ZEESHAN AHMED, NAEEM MAHMOOD ASHRAF, MUHAMMAD KHURSHID, MOAZZAM ALI, ZEESHAN MUTAHIR

DOI Number:

DOI:10.5281/zenodo.10686103

Published : 2024-02-10

About the author(s)

1. AMMARAH FATEEN - School of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan.
2. MUHAMMAD ZEESHAN AHMED - Department of Biochemistry, Bahauddin Zakariya University, Multan 60800, Pakistan. School of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan.
3. NAEEM MAHMOOD ASHRAF - School of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan.
4. MUHAMMAD KHURSHID - School of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan.
5. MOAZZAM ALI - School of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan.
6. ZEESHAN MUTAHIR - School of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan.

Full Text : PDF

Abstract

Lytic Polysaccharide Monooxygenases (LPMOs) and chitinases constitute pivotal chitinolytic enzymatic components in Bacillus cereus, exerting significant influence on the degradation of chitin. This investigation used bioinformatics tools to endeavor the evolution and action mechanisms of enzymes (chitinases and BcLPMO10B) influencing chitin and cellulose degradation in B. cereus, employing computational methods for phylogenetic analysis, 3D structure modeling, validation, and molecular dynamics simulations (MDS), offering insights into their potential applications in biofuels, medicine, and agriculture. Phylogenetic analysis of chitinases and BcLPMO10B exhibit strong associations with other bacteria, indicating a potential history of shared genetic material over time. To achieve the objective of analyzing action mechanism, the homology modeling technique was employed to construct three-dimensional structures of BcLPMO10B and chitinases using SwissModel, I-TASSER, and ROBETTA Baker Laboratory. Following the comparative validation of predicted structures utilizing various servers, 3D structures generated by the Swiss Model were chosen for subsequent computational analysis. Subsequently, docking studies elucidated the functional significance of target proteins; through the prediction of ligand binding modes. The research also explored the dynamic behaviors of BcLPMO10B and chitinases by MDS. AutoDock Vina revealed robust binding affinities and unveiled key interacting amino acids of chitinases with N-acetyl-D(+)-glucosamine (GLcNAc) and BcLPMO10B with 2,6-dimethoxyphenol. Furthermore, MDS validated the stability of these complexes by assessing the temporal motion of individual atoms within these complexes, employing Root Mean Square Deviation (RMSD) analysis, recording low RMSF values, and evaluating the extent of hydrogen bonding interactions. The implications of these complexes extend the enzymatic efficiencies, functionalities and substrate binding affinities. In sum, this computational analysis augments our comprehension of these enzymes and highlights their potential applications in biotechnology and pharmaceutical research.


Keywords

Bacillus cereus, Chitin-Degrading Enzymes, In-Silico Characterization, Molecular Docking, Molecular Dynamic Simulation, Phylogenetic Analysis