Regensburg 2002 – scientific programme
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SYBM: Physik biologischer Materie
SYBM 401: Physics of biological matter: Poster
SYBM 401.37: Poster
Tuesday, March 12, 2002, 18:00–19:30, H37
11-cis-Retinal Protonated Schiff Base: The effect of environment and solvent on the chromophore of rhodopsin — •Minoru Sugihara1, Peter Entel1, Volker Buß2, Marcus Elstner3, and Thomas Frauenheim3 — 1Theoretische Tieftemperaturphysik, Gerhard-Mercator-Universität, 47048 Duisburg, Germany — 2Institut für Physikalische und Theoretische Chemie, Gerhard-Mercator-Universität, 47048 Duisburg, Germany — 3Theoretische Physik, Universität Paderborn, 33095 Paderborn, Germany
Recently the structure of rhodopsin was determined from the diffraction date extending to the resolution 2.8 Å [1]. The X-ray model, however, has shown that Glu113 is positioned somewhat close to the protonated Schiff base nitrogen. The distances between the carboxylate oxygen atoms of Glu113 and the Schiff base nitrogen are too short to insert a water molecule, which means that the proton on the Schiff base is not stable. We have studied the effects of amino acid and of water using the density functional based tight-binding code. A model retinal binding pocket was employed containing 27 residues within 4.5 Å distance from the retinal molecule and 7 water molecules. Our results show that water molecules surrounding Glu131 play an important role in stabilizing the protonated state of the Schiff base. We also discuss the structure of 11-cis-retinal PSB, which is highly twisted in the protein pocket due to the nonbonding interaction between the C10-H and C13-methyl group.
[1] K. Palczewski et al. Science286, 739 (2000).