Chromophores in a Truly Heterogeneous Environment: Retinal and 13-demethyl-retinal inside the Rhodopsin Binding Pocket - a Qm/mm Study∗

To probe the effect of the protein environment on the retinal chromophore of rhodopsin, we have performed molecular dynamics simulations using combined quantum mechanics / molecular mechanics (QM/MM). The starting geometry of the protein is based on the 2.6Å X-ray structure of bovine rhodopsin by Okada et al. The wild type chromophore of rhodopsin shows a highly twisted conformation around the central region, from C10 to C13, due to nonbonded interaction with the protein pocket. The absolute sense of twist of the C11-C12 and C12-C13 bonds is negative (-19◦±9◦) and positive (170◦±8◦), respectively. The 13-demethyl retinal chromophore, in which the methyl group at C13 position is removed, is less distorted in this region. The C11-C12 bond is twisted less (-15◦±10◦) and the C12-C13 bond is planar (179◦±9◦). The flattened geometry of this artificial chromophore is supported by spectroscopic evidence. ∗Dedicated to Professor Peter Entel on the occasion of his 60th birthday †Corresponding author: Tel.: +49 203 379 1073, fax: +49 203 379 3665, email: [email protected]