title: Homology modeling, substrate docking, and molecular simulation studies of mycobacteriophage Che12 lysin A.
abstract: Mycobacteriophages produce lysins that break down the host cell wall at the end of lytic cycle to release their progenies. The ability to lyse mycobacterial cells makes the lysins significant. Mycobacteriophage Che12 is the first reported temperate phage capable of infecting and lysogenising Mycobacterium tuberculosis. Gp11 of Che12 was found to have Chitinase domain that serves as endolysin (lysin A) for Che12. Structure of gp11 was modeled and evaluated using Ramachandran plot in which 98 % of the residues are in the favored and allowed regions. Che12 lysin A was predicted to act on NAG-NAM-NAG molecules in the peptidoglycan of cell wall. The tautomers of NAG-NAM-NAG molecule were generated and docked with lysin A. The stability and binding affinity of lysin A - NAG-NAM-NAG tautomers were studied using molecular dynamics simulations.
authors.affiliation: Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India.
authors.forename: Shainaba A
authors.initials: SA
authors.lastname: Saadhali
authors.affiliation: Department of Biomedical Informatics, National Institute for Research in Tuberculosis, Chennai, 600031, India.
authors.forename: Sameer
authors.initials: S
authors.lastname: Hassan
authors.affiliation: Department of Clinical Research, National Institute for Research in Tuberculosis, Chennai, 600031, India.
authors.forename: Luke Elizabeth
authors.initials: LE
authors.lastname: Hanna
authors.affiliation: Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India.
authors.forename: Uma Devi
authors.initials: UD
authors.lastname: Ranganathan
authors.affiliation: Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India. vanaja_kumar51@yahoo.co.in.
authors.forename: Vanaja
authors.initials: V
authors.lastname: Kumar
mesh_terms: D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009160:Mycobacteriophages / Q000201:enzymology*; D009169:Mycobacterium tuberculosis / Q000821:virology*; D010457:Peptidoglycan / Q000737:chemistry*; D040681:Structural Homology, Protein; D014764:Viral Proteins / Q000737:chemistry*
chemical_list: D010457:Peptidoglycan; D014764:Viral Proteins
keywords: Homology modeling; Lysin A; Molecular dynamics simulation; Mycobacteriophage; Mycobacterium tuberculosis; Peptidoglycan