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Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations

Gumbart, James C. and Beeby, Morgan and Jensen, Grant J. and Roux, Benoît (2014) Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLOS Computational Biology, 10 (2). Art. No. e10034. ISSN 1553-7358. PMCID PMC3930494. http://resolver.caltech.edu/CaltechAUTHORS:20140604-091447469

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Abstract

Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003475#abstract0PublisherArticle
http://dx.doi.org/10.1371/journal.pcbi.1003475DOIArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930494/PubMed CentralArticle
ORCID:
AuthorORCID
Beeby, Morgan0000-0001-6413-9835
Jensen, Grant J.0000-0003-1556-4864
Additional Information:© 2014 Gumbart et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. August 8, 2013; Accepted January 5, 2014; Published February 20, 2014. NIH K22-AI100927 to J.C.G. R01 GM062342 to B.R. HHMI to G.J.J. Gordon and Betty Moore Center for Integrative Study of Cell Regulation at Caltech to G.J.J. Computational resources were provided by the Computation Institute and the Biological Sciences Division of the University of Chicago and Argonne National Laboratory, under grant S10 RR029030-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Funders:
Funding AgencyGrant Number
NIHK22-AI100927
NIHR01 GM062342
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Gordon and Betty Moore FoundationUNSPECIFIED
Argonne National Laboratory S10 RR029030-01
PubMed Central ID:PMC3930494
Record Number:CaltechAUTHORS:20140604-091447469
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20140604-091447469
Official Citation:Gumbart JC, Beeby M, Jensen GJ, Roux B (2014) Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLoS Comput Biol 10(2): e1003475. doi:10.1371/journal.pcbi.1003475
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:46069
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:04 Jun 2014 22:30
Last Modified:13 Apr 2017 23:08

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