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Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein

The proton transfer pathway in a heptahelical membrane protein, the light‐driven proton pump bacteriorhodopsin (BR), is probed by a combined approach of structural analysis of recent X‐ray models and molecular dynamics (MD) simulations that provide the diffusion pathways of internal and external water molecules. Analyzing the hydrogen‐bond contact frequencies of the water molecules with protein groups, the complete proton pathway through the protein is probed. Beside the well‐known proton binding sites in the protein interior—the protonated Schiff base, Asp85 and Asp96, and the H5O  2+ complex stabilized by Glu204 and Glu194—the proton release and uptake pathways to the protein surfaces are described in great detail. Further residues were identified, by mutation of which the proposed pathways can be verified. In addition the diffusion pathway of water 502 from Lys216 to Asp96 is shown to cover the positions of the intruding waters 503 and 504 in the N‐intermediate. The transiently established water chain in the N‐state provides a proton pathway from Asp96 to the Schiff base in the M‐ to N‐transition in a Grotthus‐like mechanism, as concluded earlier from time‐resolved Fourier transform infrared experiments [le Coutre et al., Proc Nat Acad Sci USA 1995;92:4962–4966]. Proteins 2005. © 2004 Wiley‐Liss, Inc.