Dresden 2006 – wissenschaftliches Programm
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AKB: Biologische Physik
AKB 40: Poster Session II
AKB 40.39: Poster
Mittwoch, 29. März 2006, 16:30–19:30, P3
Molecular Dynamics Study of the Chromophore Binding pocket in Rhodopsin — •Minoru Sugihara1,2, Markus Gruner2, Peter Entel2, and Volker Buss1 — 1Theoretical Low-Temperature Physics — 2Theoretical Chemistry, University of Duisburg-Essen
The 11-cis retinal protonated Schiff base (pSb) is the chromophore in rhodopsin, the black/white photoreceptor in the vertebrate eye. The chromophore is covalently attached to Lys296 via a pSb and has a salt-bridge with the negatively charged counterion, Glu113. The first crystal structure of bovine rhodopsin[1] has revealed that the chromophore is fixed in the pocket by hydrophobic interaction at the β-ionone ring and polar interaction, in paticular by a salt-bridge. Upon illumination with light, the chromophore photoisomerizes from 11-cis to all-trans. The first intermediate, bathorhodopsin, stores 32-35 kcal/mol of the photon energy in the twisted all-trans form. The starting model of the chromophore binding pocket (534 atoms) was taken from the crystal structure[2]. In this study, the chromophore conformation inside the pocket, the origin of the twisted conformation, and the stability of the protonation state[3] will be discussed. For molecular dynamics study, the plane wave code, VASP[4] was used. The calculations were carried out on the IBM BlueGene/L at the Reseach Center Jülich. [1] Palczewski, K., Okada, T. et al. Science 289 (200 739.[2] Okada, T., Sugihara, M. et al. J. Mol. Biolog. 342 (2004) 571. [3] Buss, V. Chilarity 13 (2001) 13. Sugihara, M., Buss, V. et al. Biochemistry 41 (2002) 15259. Sugiahra, M., Buss, V. et al. J. Phys. Chem. B 108 (2004) 3673. Sugihara, M., Hufen, J. Biochemistry in press. [4] Kresse, G., Furhermüller J. Phys. Rev. B 54 (1996) 11169.