title: The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin.
abstract: The last phase of the proton transfer cycle of bacteriorhodopsin calls for a passage of a proton from D38 to D96. This reaction utilizes a narrow shaft approximately 10-A long that connects the two carboxylates that cross through a very hydrophobic domain. As the shaft is too narrow to be permanently hydrated, there are two alternatives for the proton propagation into the channel. The proton may propagate through the shaft without solvation at the expense of a high electrostatic barrier; alternatively, the shaft will expand to accommodate some water molecules, thus lowering the Born energy for the insertion of the charge into the protein (B. Schätzler, N. A. Dencher, J. Tittor, D. Oesterhelt, S. Yaniv-Checover, E. Nachliel, and G. Gutman, 2003, BIOPHYS: J. 84:671-686). A comparative study of nine published crystal-structures of bacteriorhodopsin identified, next to the shaft, microcavities in the protein whose position and surrounding atoms are common to the reported structures. Some of the cavities either shrink or expand during the photocycle. It is argued that the plasticity of the cavities provides a working space needed for the transient solvation of the shaft, thus reducing the activation energy necessary for the solvation of the shaft. This suggestion is corroborated by the recent observations of Klink et al. (B. U. Klink, R. Winter, M. Engelhard, and I. Chizhov, 2002, BIOPHYS: J. 83:3490-3498) that the late phases of the photocycle (tau >/=1 ms) are strongly inhibited by external pressure.
authors.affiliation: Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Ran
authors.initials: R
authors.lastname: Friedman
authors.forename: Esther
authors.initials: E
authors.lastname: Nachliel
authors.forename: Menachem
authors.initials: M
authors.lastname: Gutman
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000145:classification / Q000528:radiation effects*; D002384:Catalysis / Q000528:radiation effects; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D004735:Energy Transfer; D008027:Light; D008958:Models, Molecular; D009038:Motion; D016062:Porosity / Q000528:radiation effects; D011487:Protein Conformation / Q000528:radiation effects; D017433:Protein Structure, Secondary; D011522:Protons; D013329:Structure-Activity Relationship
chemical_list: D011522:Protons; D001436:Bacteriorhodopsins