In silico study of cox protein from P2 type enteric bacteriophages based on sequence, structure and dynamics to understand its functional integrity

• Published in: Journal of biomolecular structure & dynamics 2022-01, Vol.40 (24), p.14035-14050
• Main Authors: Hazra, Mousumi, Dubey, Ramesh Chandra
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacteriophage P2 - genetics; Bacteriophage P2 - metabolism; Bacteriophages - genetics; Bacteriophages - metabolism; Cox protein; DNA - metabolism; DNA binding protein; enterobacteriophage; free energy landscape; Gromacs; homology modelling; Molecular Dynamics Simulation; normal mode analysis; Phylogeny; principal component analysis
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2021.2000496

Cox protein plays a critical role in deciding the lytic-lysogenic switch of P2 enteric phages. This phenomenon makes Cox protein one of the most important candidates in developing novel phage-based therapeutics against antibacterial resistant pathogens. The principle focus concerning protein and its decision making is a DNA binding event, which helps to regulate differential promoter expression. In the current study, we have attempted to understand the sequence, structural and dynamic features associated with Cox protein and its DNA binding. Unavailability of information was a big burden in further proceedings. We have done an extensive literature search to develop a database of Cox with relevant information. That information coupled with the methods of Sequence-based phylogenetic and conservation studies, Homology Modelling, Atomic-level Docking and Molecular Dynamics (MD) Simulation (50 ns each for 10 systems, i.e. total of 500 ns) were performed in the current study. Analysis of those extensive studies has provided us the required sequence to structure to dynamics to functional understanding. Our present study would indeed be very helpful in understanding the biochemical mechanism of Cox activation as well as designing potential phage therapeutics.