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J. Biol. Chem., Vol. 279, Issue 3, 2147-2158, January 16, 2004

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Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin^*

From the ^aDepartment of Chemistry and Bioscience, Chalmers University of Technology, Box 462, S-40530 Gothenburg, Sweden, the ^bInstitut de Biologie Structurale, UMR5075, Commissariat à l'Energie Atomique-CNRS-Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France, the ^cEuropean Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, F-38043 Grenoble Cedex, France, the ^dDepartment of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius vag 12, 106 91 Stockholm, Sweden, the ^eDepartment of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Centre, Box 590, 751 24 Uppsala, Sweden, the ^fDepartment of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala; Sweden, and the ^gMembrane Protein Laboratory, Sealy Center for Structural Biology, and Department of Physiology and Biophysics, The University of Texas Medical Branch, Galveston, Texas 77555-0437

X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed.

Received for publication, January 22, 2003 , and in revised form, October 7, 2003.

The atomic coordinates and structure factors (code 1R3P) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by the Swiss National Science Foundation, the European Union-BIOTECH, the Howard Hughes Medical Institute, The Swedish Science Research Council (VR), SWEGENE, the Swedish Strategic Research Foundation (SSF), and the French Ministry of Education and Research (MENR). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

h To whom correspondence may be addressed. E-mail: emlandau{at}utmb.edu. i To whom correspondence may be addressed. E-mail: pebay{at}godot.ibs.fr. j To whom correspondence may be addressed. E-mail: neutze{at}molbiotech.chalmers.se.

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