Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase

Proteins
Andrew B WardRonald D Hills

Abstract

Coarse-grained (CG) modeling has proven effective for simulating lipid bilayer dynamics on scales of biological interest. Modeling the dynamics of flexible membrane proteins within the bilayer, on the other hand, poses a considerable challenge due to the complexity of the folding or conformational landscape. In the present work, the multiscale coarse-graining method is applied to atomistic peptide-lipid "soup" simulations to develop a general set of CG protein-lipid interaction potentials. The reduced model was constructed to be compatible with recent solvent-free CG models developed for protein-protein folding and lipid-lipid model bilayer interactions. The utility of the force field was demonstrated by molecular dynamics simulation of the MsbA ABC transporter in a mixed DOPC/DOPE bilayer. An elastic network was parameterized to restrain the MsbA dimer in its open, closed and hydrolysis intermediate conformations and its impact on domain flexibility was examined. Conformational stability enabled long-time dynamics simulation of MsbA freely diffusing in a 25 nm membrane patch. Three-dimensional density analysis revealed that a shell of weakly bound "annular lipids" solvate the membrane accessible surface of MsbA and its interna...Continue Reading

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Feb 13, 2016·Journal of Computational Chemistry·Ronald D Hills, Nicholas McGlinchey
Jan 3, 2016·The Journal of Chemical Physics·Ghulam MustafaRebecca C Wade
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Feb 14, 2019·Chemical Reviews·Valentina CorradiD Peter Tieleman

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