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Cited by 202Lipid Membrane Structure and BehaviorProtein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

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Hsu, Pin‐Chia, Bruininks, Bart M. H., Jefferies, Damien, Cesar Telles de Souza, Paulo, Lee, Jumin, Patel, Dhilon S., Marrink, Siewert J., Qi, Yifei +2 more·2017·Journal of Computational Chemistry
DOI 10.1002/jcc.24895PMC PMC5939954
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Abstract

A complex cell envelope, composed of a mixture of lipid types including lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM‐GUI Martini Maker for coarse‐grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user‐friendly manner. © 2017 Wiley Periodicals, Inc.

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  • Electropores may form under external electric fields and can also arise spontaneously in naturally occurring systems due to transient transmembrane potentials arising from bilayer-surface charge fluctuations.

    “Electropores may form under external electric fields 9 and can also arise spontaneously in naturallyoccuring (particularly biological) systems due to transient transmembrane potentials arising from bilayer-surface charge flucuations 8,12,[22][23][24][25][26][27][28][29][30] .”

    From Fusion of lipid membranes: an alternative pathway (2026) · cites this paper as [23]

    The Methods section (Vesicle Systems; page unavailable) says two pores were built into simulated vesicles to let water move during equilibration. Neither that passage nor the Bilayer Systems passages addresses electropore formation under external electric fields or spontaneous formation caused by charge fluctuations. Searches for electropores, transient transmembrane potentials, electric fields, and charge fluctuations found no supporting passage in our copy. (LLM, conf=0.76)

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Authors
Hsu, P., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., Marrink, S. J., Qi, Y., Khalid, S., & Im, W.
Affiliations
  • University of Southampton (GB)
  • University of Groningen (NL)
  • Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 7 Groningen AG 9747 The Netherlands
  • Lehigh University (US)
  • East China Normal University (CN)
Corresponding author
  • Qi, Yifei
  • Khalid, Syma
  • Im, Wonpil
ORCID
Venue
Journal of Computational Chemistry
Publisher
Wiley
Published
2017-08-03
Volume
38
Issue
27
Pages
2354-2363
ISSN
  • 0192-8651 (ISSN-L)
  • 1096-987X
DOI
10.1002/jcc.24895
PMC
PMC5939954
OpenAlex
W2743526077
Cited by
202
References
1
Citations by year
2026: 23 · 2025: 24 · 2024: 26 · 2023: 27 · 2022: 32 · 2021: 25 · 2020: 21 · 2019: 14 · 2018: 8 · 2017: 2
FWCI
4.90
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Computational Chemistry (publishedVersion)
  • PubMed (publishedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • ePrints Soton (University of Southampton) (submittedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
Funders
  • NSF (MCB‐1727508)
  • NIH (GM087519, GM103695)
  • European Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords
Martini force field, bacterial outer membrane, lipopolysaccharide, outer membrane proteins, cell envelope, nanodiscs, vesicles, micelles, bilayer membranes, membrane protein simulation
MeSH terms
Bacteria, Bacterial Outer Membrane Proteins, Cell Membrane, Lipid Bilayers, Lipopolysaccharides, Micelles, Models, Chemical, Phospholipids, Software Design, Molecular Dynamics Simulation

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