Water molecules and hydrogen-bonded networks in bacteriorhodopsin—molecular dynamics simulations of the ground state and the M-intermediate

Abstract : 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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Submitted on : Tuesday, May 5, 2015 - 12:57:12 PM
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Sergei Grudinin, Georg Büldt, Valentin Gordeliy, Artur Baumgaertner. Water molecules and hydrogen-bonded networks in bacteriorhodopsin—molecular dynamics simulations of the ground state and the M-intermediate. Biophysical Journal, Biophysical Society, 2005, 88 (5), pp.3252--3261. ⟨http://www.sciencedirect.com/science/article/pii/S0006349505733762⟩. ⟨10.1529/biophysj.104.047993⟩. ⟨hal-01148776⟩

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