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Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin—Molecular Dynamics Simulations of the Ground State and the M-Intermediate

Sergei Grudinin ^* , Georg Büldt ^*, Valentin Gordeliy ^*  and Artur Baumgaertner 

^* Institute for Structural Biology (IBI-2), Forschungszentrum Jülich, Jülich, Germany; Center for Biophysic and Physical Chemistry of Supramolecular Structures, MIPT, Moscow, Russia; and Institute for Solid State Research, Forschungszentrum Jülich, Jülich, Germany

Correspondence: Address reprint requests to Prof. A. Baumgaertner, Tel.: 49-2461-614074, 613142; E-mail: a.baumgaertner{at}fz-juelich.de.

Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is 95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR.

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