title: Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins.
abstract: The excited states of the three retinal proteins, bovine rhodopsin (Rh), bacteriorhodopsin (bR), and sensory rhodopsin II (sRII) were studied using the symmetry-adapted cluster-configuration interaction (SAC-CI) and combined quantum mechanical and molecular mechanical (QM/MM) methods. The computed absorption energies are in good agreement with the experimental ones for all three proteins. The spectral tuning mechanism was analyzed in terms of three contributions:  molecular structures of the chromophore in the binding pockets, electrostatic (ES) interaction of the chromophore with the surrounding protein environment, and quantum-mechanical effect between the chromophore and the counterion group. This analysis provided an insight into the mechanism of the large blue-shifts in the absorption peak position of Rh and sRII from that of bR. Protein ES effect is primarily important both in Rh and in sRII, and the structure effect is secondary important in Rh. The quantum-mechanical interaction between the chromophore and the counterion is very important for quantitative reproduction of the excitation energy. These results indicate that the present approach is useful for studying the absorption spectra and the mechanism of the color tuning in the retinal proteins.
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Fujimoto
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Hayashi
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan.
authors.forename: Jun-Ya
authors.initials: JY
authors.lastname: Hasegawa
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Nakatsuji