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Homology modeling, substrate docking, and molecular simulation studies of mycobacteriophage Che12 lysin A
Shainaba A Saadhali1, Sameer Hassan2, Luke Elizabeth Hanna3
1Department of Bacteriology, National Institute for Research in Tuberculosis, Chetpet, Chennai, 600031, India.
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.
Insights
Mycobacteriophage Che12 lysin A, an enzyme targeting Mycobacterium tuberculosis cell walls, shows potential for therapeutic applications. Molecular dynamics simulations confirm its stability and binding affinity to peptidoglycan components.
Area of Science:
- Microbiology and Virology
- Structural Biology
- Biochemistry
Background:
- Mycobacteriophages are viruses that infect bacteria, and their lysins are crucial for releasing progeny.
- Lysins that degrade mycobacterial cell walls are of significant interest for therapeutic development.
- Mycobacteriophage Che12 is a unique temperate phage capable of lysogenizing Mycobacterium tuberculosis.
Purpose of the Study:
- To characterize Che12 lysin A (gp11) as a potential antimicrobial agent against Mycobacterium tuberculosis.
- To investigate the structural integrity and binding interactions of Che12 lysin A with its target molecules.
Main Methods:
- Structural modeling and Ramachandran plot analysis of Che12 lysin A (gp11).
- In silico generation of NAG-NAM-NAG peptidoglycan tautomers.
- Molecular docking of lysin A with peptidoglycan tautomers.
- Molecular dynamics simulations to assess stability and binding affinity.
Main Results:
- The structure of Che12 lysin A showed high stereochemical quality, with 98% of residues in favored/allowed regions.
- Che12 lysin A was predicted to target NAG-NAM-NAG units within the mycobacterial peptidoglycan.
- Molecular dynamics simulations demonstrated the stability and binding affinity of lysin A to these peptidoglycan components.
Conclusions:
- Che12 lysin A possesses a stable structure and effectively binds to its peptidoglycan target.
- This endolysin represents a promising candidate for developing novel therapeutic strategies against Mycobacterium tuberculosis infections.
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