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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.

Original publication

DOI

10.1016/j.sbi.2016.06.007

Type

Journal article

Journal

Curr Opin Struct Biol

Publication Date

10/2016

Volume

40

Pages

8 - 16

Keywords

Animals, Cell Membrane, Humans, Lipid Metabolism, Membrane Proteins, Molecular Dynamics Simulation, Protein Binding