Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale aimulations
Author(s)
Gumbart, JC
Beeby, M
Jensen, GJ
Roux, B
Type
Journal Article
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 allatom
simulations to reproduce a range of macroscopic observables for extended polymer meshes.
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 allatom
simulations to reproduce a range of macroscopic observables for extended polymer meshes.
Date Issued
2014-02-20
Date Acceptance
2014-01-05
Citation
PLOS Computational Biology, 2014, 10 (2)
ISSN
1553-734X
Publisher
Public Library of Science
Journal / Book Title
PLOS Computational Biology
Volume
10
Issue
2
Copyright Statement
© 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.
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Mathematical & Computational Biology
Biochemistry & Molecular Biology
BIOCHEMICAL RESEARCH METHODS
MATHEMATICAL & COMPUTATIONAL BIOLOGY
GRAM-NEGATIVE BACTERIA
MOLECULAR-DYNAMICS SIMULATION
CELL-WALL PEPTIDOGLYCAN
FORCE-FIELD
BACILLUS-SUBTILIS
MUREIN SACCULUS
ARCHITECTURE
ELASTICITY
FILAMENTS
GROWTH
Biophysical Phenomena
Cell Wall
Computational Biology
Computer Simulation
Escherichia coli
Models, Molecular
Molecular Conformation
Molecular Dynamics Simulation
Molecular Structure
Peptidoglycan
Bioinformatics
Biological Sciences
Information And Computing Sciences
Mathematical Sciences
Publication Status
Published