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

Pin-Chia Hsu, Bart M H Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S Patel, Siewert J Marrink, Yifei Qi, Syma Khalid, Wonpil Im

Research output: Contribution to journalArticleAcademicpeer-review

47 Citations (Scopus)

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. (c) 2017 Wiley Periodicals, Inc.

Original languageEnglish
Pages (from-to)2354-2363
Number of pages10
JournalJournal of Computational Chemistry
Volume38
Issue number27
Early online date3-Aug-2017
DOIs
Publication statusPublished - 15-Oct-2017

Keywords

  • coarse-grained simulation
  • outer membrane vesicles
  • bilayers
  • nanodiscs
  • micelles
  • MOLECULAR-DYNAMICS SIMULATIONS
  • GRAM-NEGATIVE BACTERIA
  • COARSE-GRAINED MODEL
  • COLI OUTER-MEMBRANE
  • ESCHERICHIA-COLI
  • FORCE-FIELD
  • E.-COLI
  • MD SIMULATIONS
  • SOFTWARE NEWS
  • PROTEINS

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