Lipopolysaccharide membrane building and simulation

Methods in Molecular Biology
Sunhwan JoWonpil Im

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.

Citations

Jun 23, 2016·Biophysical Journal·Patrick J FlemingWonpil Im
Feb 6, 2017·Current Opinion in Structural Biology·Dhilon S PatelWonpil Im
Oct 21, 2016·Biophysical Journal·Seonghoon KimWonpil Im
Jan 31, 2016·Biochimica Et Biophysica Acta·Anna PavlovaJames C Gumbart
Jun 18, 2017·Journal of Chemical Theory and Computation·Pin-Kuang Lai, Yiannis N Kaznessis
Feb 20, 2020·Annual Review of Physical Chemistry·Wonpil Im, Syma Khalid
May 27, 2020·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Carlo MartinottiRicardo L Mancera
Dec 13, 2019·Biochimica Et Biophysica Acta. Biomembranes·Jingjing GuoThomas Seviour
Dec 18, 2019·Biochimica Et Biophysica Acta. Biomembranes·Cesar A LópezS Gnanakaran
Feb 19, 2021·The Journal of Physical Chemistry. B·Emanuel LunaWonpil Im
Jan 26, 2017·Biophysical Journal·Joonseong LeeWonpil Im
Jul 10, 2018·Cell Chemical Biology·Mary Sabulski FeigmanMarcos M Pires
Jun 25, 2021·Journal of Chemical Information and Modeling·Pietro G A AronicaChandra S Verma
Aug 5, 2018·The Journal of Physical Chemistry. B·Joonseong LeeWonpil Im
Mar 1, 2016·ACS Infectious Diseases·Helen I ZgurskayaS Gnanakaran
Feb 21, 2019·Chemical Reviews·Alison N LeonardJeffery B Klauda
Mar 28, 2020·ACS Infectious Diseases·George M OngwaeMarcos M Pires
Jul 2, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Pradyumn SharmaJaydeep Kumar Basu
Oct 9, 2019·ACS Infectious Diseases·Ricardo J Ferreira, Peter M Kasson
Jul 2, 2019·The Journal of Physical Chemistry. B·Anusha KesireddyUlrich Kleinekathöfer
Dec 12, 2018·Journal of Chemical Theory and Computation·Jumin LeeWonpil Im
Dec 29, 2021·Langmuir : the ACS Journal of Surfaces and Colloids·Min-Kang HsiehJeffery B Klauda

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