TCB Publications - Abstract

Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus Schulten. Molecular dynamics study of bacteriorhodopsin and the purple membrane. Journal of Physical Chemistry B, 105:905-918, 2001.

BAUD2001 Vectorial proton translocation through membranes is a fundamental energy conversion process in biological cells. Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven, voltage sensitive proton pump in the purple membrane (PM) of Halobacterium salinarium and achieves its biological function by cycling through a reaction sequence that includes ultrafast ($\sim$500 fs) events, intermediate ($\mu$s) as well as slow ($\sim$10 ms) steps. bR is of utmost simplicity in comparison with other proton translocating bioenergetic proteins and, therefore, constitutes an ideal model for the study of this process. The PM involves a highly structured supramolecular organization, and is fundamental for the in vivo functioning of bR. Over the last ten years, crystal structures of bR have become available at increasing resolution. The most recent structures resolve many of the lipids of the PM and provide atomic level detail of bR at below 2 Å resolution. Fundamental for an understanding of the function of bR is internal water that participates in proton pumping. Several water molecules have been resolved now crystallographically in two channels, on the extracellular and on the intracellular side of bR. We show that free energy perturbation theory can place water molecules in bR, with results that compare well with the observed water molecules, and we apply the method to predict water movement during bR's photocycle. We demonstrate that water molecules may indeed be displaced during the photocycle, after retinal undergoes an all-trans $\rightarrow$ 13-cis isomerization, and that this displacement may constitute a mechanism for proton pumping. A key advance reported in this feature article is the integration of the available bR structures into a model for the entire PM. This hexagonally periodic, lamellar model has been hydrated and refined through a constant pressure molecular dynamics simulation. The resulting structure connects extracellular bulk water with water molecules and key side groups in the interior of bR, permitting a seamless overall description of proton path in the PM, from intracellular to extracellular space. For the first time a complex cellular reaction can be accounted for in full atomic detail in its complete native environment.

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