How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation

Biophysical Journal
Hyunbum JangThomas B Woolf

Abstract

The light-driven proton pump bacteriorhodopsin (bR) is a transmembrane protein that uses large conformational changes for proton transfer from the cytoplasmic to the extracellular regions. Crystal structures, due to their solvent conditions, do not resolve the effect of lipid molecules on these protein conformational changes. To begin to understand the molecular details behind such large conformational changes, we simulated two conformations of wild-type bacteriorhodopsin, one of the dark-adapted state and the second of an intermediate (M(O)) state, each within an explicit dimyristoyl-phosphatidylcholine (DMPC) lipid bilayer. The simulations included all-hydrogen and all-atom representations of protein, lipid, and water and were performed for 20 ns. We investigate the equilibrium properties and the dynamic motions of the two conformations in the lipid setting. We note that the conformational state of the M(O) intermediate bR remains markedly different from the dark-adapted bR state in that the M(O) intermediate shows rearrangement of the cytoplasmic portions of helices C, F, and G, and nearby loops. This difference in the states remained throughout the simulations, and the results are stable on the molecular dynamics timescale ...Continue Reading

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Citations

Jul 26, 2011·Evidence-based Complementary and Alternative Medicine : ECAM·Lin-Hua WuHong Yu
Aug 16, 2008·Proteins·Tsjerk A WassenaarAlan E Mark
Feb 12, 2013·Structure·Ting WangMarc T Facciotti
Jul 25, 2006·Biophysical Journal·Hyunbum JangRuth Nussinov
Jan 1, 2016·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Hyunbum JangRuth Nussinov
Aug 2, 2006·Molecular BioSystems·Anthony G Lee
Aug 28, 2020·European Biophysics Journal : EBJ·Anna K Manukyan
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Apr 9, 2016·The Biochemical Journal·Hyunbum JangRuth Nussinov
Feb 26, 2015·The Journal of Biological Chemistry·Hyunbum JangVadim Gaponenko
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Jun 15, 2017·Journal of the American Chemical Society·Daryl GoodVladimir Ladizhansky
Mar 16, 2011·Journal of the American Chemical Society·Jun YangClemens Glaubitz
Feb 14, 2006·The Journal of Physical Chemistry. B·Seiichiro Tanizaki, Michael Feig

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