Shedding light on the spectral tuning mechanisms in Rhodopsin and its analogs using QM/MM methods

BIOL 54

Orr Ravitz, ravitz@chem.rochester.edu, Chemistry Department, University of Rochester, 120 Trustee Rd., Rochester, NY 14627-0216 and Harry A Stern, hstern@chem.rochester.edu, Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627.
We predict optimized conformations and excitation energies of native rhodopsin and several of its analogues using ONIOM(B3LYP/6-31G*:AMBER). We establish excellent structural integrity and demonstrate semiquantitative agreement of vertical excitation energies with experimental data. We identify three structural elements of the retinal that modify its spectral properties, and the opsin interactions that govern them: The twist of the beta-ionone ring relative to the retinal backbone which is determined by steric interactions of the ring with its environment, the planarity of two sections of the backbone that is governed by steric interactions mediated by the methyl groups on C9 and C13, and the configuration of the Schiff base linkage. The polarity of side chains adjacent to the Schiff base governs the latter element by modifying the configuration of a complex involving the Glu-113 counterion and two water molecules, and by perturbing a stable hydrogen bond network that encompasses the chromophore pocket.
 

Protein Structure and Folding
4:30 PM-6:30 PM, Sunday, 10 September 2006 Moscone Center -- Hall D, Poster

Division of Biological Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006