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Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers

Vaiwala, R and Sharma, P and Puranik, M and Ayappa, KG (2020) Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers. In: Journal of Chemical Theory and Computation, 16 (8). pp. 5369-5384.

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Official URL: https://doi.org/10.1021/acs.jctc.0c00539


The bacterial cell envelope of Gram-negative bacteria is a complex biological barrier with multiple layers consisting of the inner membrane, periplasm of peptidoglycan, and the outer membrane with lipopolysaccharides (LPS). With rising antimicrobial resistance there is increasing interest in understanding interactions of small molecules with the cell membrane to aid in the development of novel drug molecules. Hence suitable representations of the bacterial membrane are required to carry out meaningful molecular dynamics simulations. Given the complexity of the cell envelope, fully atomistic descriptions of the cell membrane with explicit solvent are computationally prohibitive, allowing limited sampling with small system sizes. However, coarse-grained (CG) models such as MARTINI allow one to study phenomena at physiologically relevant length and time scales. Although MARTINI models for lipids and the LPS are available in literature, a suitable CG model of peptidoglycan is lacking. Using an all-atom model described by Gumbart et al. PLoS Comput. Biol. 2014, 10, e1003475, we develop a CG model of the peptidoglycan network within the MARTINI framework. The model is parametrized to reproduce the end-to-end distance of glycan strands. The structural properties such as the equilibrium angle between adjacent peptides along the strands, area per disaccharide, and cavity size distributions agree well with the atomistic simulation results. Mechanical properties such as the area compressibility and the bending modulus are accurately reproduced. While developing novel antibiotics it is important to assess barrier properties of the peptidogylcan network. We evaluate and compare the free energy of insertion for a thymol molecule using umbrella sampling on both the MARTINI and all-atom peptidoglycan models. The insertion free energy was found to be less than kBT for both the MARTINI and all-atom models. Additional restraint free simulations reveal rapid translocation of thymol across peptidogylcan. We expect that the proposed MARTINI model for peptidoglycan will be useful in understanding phenomena associated with bacterial cell walls at larger length and time scales, thereby overcoming the current limitations of all-atom models. Copyright © 2020 American Chemical Society.

Item Type: Journal Article
Publication: Journal of Chemical Theory and Computation
Publisher: American Chemical Society
Additional Information: The copyright for this article belongs to The Author(s).
Keywords: lipopolysaccharide; peptidoglycan, biological model; cell wall; chemistry; conformation; cytology; Gram negative bacterium; metabolism; molecular dynamics; thermodynamics, Cell Wall; Gram-Negative Bacteria; Lipopolysaccharides; Models, Biological; Molecular Conformation; Molecular Dynamics Simulation; Peptidoglycan; Thermodynamics
Department/Centre: Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
Division of Mechanical Sciences > Chemical Engineering
Date Deposited: 13 Jan 2023 06:38
Last Modified: 13 Jan 2023 06:38
URI: https://eprints.iisc.ac.in/id/eprint/79103

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