The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

• Published in: Biochemical Society transactions Vol. 43; no. 2; p. 162
• Main Authors: Khalid, Syma, Berglund, Nils A, Holdbrook, Daniel A, Leung, Yuk M, Parkin, Jamie
• Format: Journal Article
• Language: English
• Published: England 01.04.2015
• Subjects: Antimicrobial Cationic Peptides - chemistry; Computer Simulation; Gram-Negative Bacteria - chemistry; Lipid Bilayers - chemistry; Membrane Proteins - chemistry; Models, Molecular; Molecular Dynamics Simulation; Peptides - chemistry
• ISSN: 1470-8752
• DOI: 10.1042/BST20140262

Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have been studied using molecular dynamics simulations in simple models of membranes, usually only comprising one lipid species. Thus, traditionally, the simulations have reflected the majority of in vitro membrane experimental setups, enabling observations from the latter to be rationalized at the molecular level. In the last few years, the sophistication and complexity of membrane models have improved considerably, such that the heterogeneity of the lipid and protein composition of the membranes can now be considered both at the atomistic and coarse-grain levels of granularity. Importantly this means relevant biology is now being retained in the models, thereby linking the in silico and in vivo scenarios. We discuss recent progress in simulations of proteins in simple lipid bilayers, more complex membrane models and finally describe some efforts to overcome timescale limitations of atomistic molecular dynamics simulations of bacterial membranes.