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Lipopolysaccharide Membrane Building and Simulation

  • Sunhwan Jo
  • Emilia L. Wu
  • Danielle Stuhlsatz
  • Jeffery B. Klauda
  • Alexander D. MacKerellJr.
  • Göran Widmalm
  • Wonpil Im
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1273)

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.

Key words

Lipid A R1 core O6 antigen Bilayer E. coli Glycan Molecular dynamics simulation 

Notes

Acknowledgements

This work was supported by the University of Kansas General Research Fund allocation #2301388-003, Kansas-COBRE NIH P20 RR-17708, TeraGrid resources provided by Purdue University (NSF OCI-0503992) (to W.I.) and grants from the NIH (GM070855) (to A.D.M.), and from the Swedish Research Council and the Stockholm Center for Biomembrane Research/Swedish Foundation for Strategic Research (to G.W.).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Sunhwan Jo
    • 1
  • Emilia L. Wu
    • 1
  • Danielle Stuhlsatz
    • 1
  • Jeffery B. Klauda
    • 2
  • Alexander D. MacKerellJr.
    • 3
  • Göran Widmalm
    • 4
  • Wonpil Im
    • 1
  1. 1.Department of Molecular Biosciences and Center for Computational BiologyThe University of KansasLawrenceUSA
  2. 2.Department of Chemical and Biomolecular Engineering and Biophysics ProgramThe University of MarylandCollege ParkUSA
  3. 3.Department of Pharmaceutical Sciences, School of PharmacyUniversity of MarylandBaltimoreUSA
  4. 4.Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius LaboratoryStockholm UniversityStockholmSweden

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