Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. (October 2016)

• Record Type: Journal Article
• Authors: Chavent, Matthieu; Duncan, Anna L; Sansom, Mark SP
• Is Part Of: Current opinion in structural biology. Volume 40(2016)
• Page Start: 8
• Page End: 16
• Publication Date: 2016-10
• Subjects: Molecular biology -- Periodicals; 570
• DOI: 10.1016/j.sbi.2016.06.007
• Languages: English
• ISSNs: 0959-440X

Abstract

Graphical abstract: Highlights: Simulations provide a computational tool to probe membrane structure and dynamics. Simulations can successfully predict lipid binding sites on membrane proteins. Large scale simulations reveal crowding and clustering of proteins in membranes. Near atomic resolution models of organelles and enveloped viruses are now possible. Abstract : Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein–lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics.