Coarse-grained molecular dynamics simulations of membrane proteins and peptides

Bond, Peter J., Holyoake, John, Ivetac, Anthony, Khalid, Syma and Sansom, Mark S.P. (2007) Coarse-grained molecular dynamics simulations of membrane proteins and peptides. Journal of Structural Biology, 157 (3), 593-605. (doi:10.1016/j.jsb.2006.10.004).

Abstract

Molecular dynamics (MD) simulations provide a valuable approach to the dynamics, structure, and stability of membrane–protein systems. Coarse-grained (CG) models, in which small groups of atoms are treated as single particles, enable extended (>100 ns) timescales to be addressed. In this study, we explore how CG–MD methods that have been developed for detergents and lipids may be extended to membrane proteins. In particular, CG–MD simulations of a number of membrane peptides and proteins are used to characterize their interactions with lipid bilayers. CG–MD is used to simulate the insertion of synthetic model membrane peptides (WALPs and LS3) into a lipid (PC) bilayer. WALP peptides insert in a transmembrane orientation, whilst the LS3 peptide adopts an interfacial location, both in agreement with experimental biophysical data. This approach is extended to a transmembrane fragment of the Vpu protein from HIV-1, and to the coat protein from fd phage. Again, simulated protein/membrane interactions are in good agreement with solid state NMR data for these proteins. CG–MD has also been applied to an M3–M4 fragment from the CFTR protein. Simulations of CFTR M3–M4 in a detergent micelle reveal formation of an -helical hairpin, consistent with a variety of biophysical data. In an I231D mutant, the M3–M4 hairpin is additionally stabilized via an inter-helix Q207/D231 interaction. Finally, CG–MD simulations are extended to a more complex membrane protein, the bacterial sugar transporter LacY. Comparison of a 200 ns CG–MD simulation of LacY in a DPPC bilayer with a 50 ns atomistic simulation of the same protein in a DMPC bilayer shows that the two methods yield comparable predictions of lipid–protein interactions. Taken together, these results demonstrate the utility of CG–MD simulations for studies of membrane/protein interactions.

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Contributors

Author: Syma Khalid

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