Lipopolysaccharide membrane building and simulation.

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TitleLipopolysaccharide membrane building and simulation.
Publication TypeJournal Article
Year of Publication2015
AuthorsJo, S, Wu, EL, Stuhlsatz, D, Klauda, JB, Mackerell, AD, Widmalm, G, Im, W
JournalMethods Mol Biol
Volume1273
Pagination391-406
Date Published2015
ISSN1940-6029
KeywordsCell Membrane, Escherichia coli, Glycosides, Lipid Bilayers, Lipopolysaccharides, Molecular Dynamics Simulation, Time Factors
Abstract

While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to their structural complexity, difficulties in building LPS-membrane systems, and lack of the appropriate molecular force fields. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli R1.O6 LPS and the presentation of preliminary simulation results in terms of per-LPS area and density distributions of various components along the membrane normal.

DOI10.1007/978-1-4939-2343-4_24
Alternate JournalMethods Mol. Biol.
PubMed ID25753722
PubMed Central IDPMC4484582
Grant ListP20 GM103420 / GM / NIGMS NIH HHS / United States
P20 RR017708 / RR / NCRR NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States
P20 RR-17708 / RR / NCRR NIH HHS / United States