Torsion Potential Works in Rhodopsin

Authors

  • Atsushi Yamada,

    1. Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
    Search for more papers by this author
    • Current address: Institute for Molecular Science, Myodaiji, Okazaki 444–8585, Japan.

  • Takahisa Yamato,

    1. Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
    Search for more papers by this author
  • Toshiaki Kakitani,

    Corresponding author
    1. Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
      *To whom correspondence should be addressed; Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Fax: 81-52-789-3528; e-mail: kakitani@allegro.phys.nagoya-u.ac.jp
    Search for more papers by this author
  • Shigeyoshi Yamamoto

    1. Chukyo University, Faculty of Liberal Arts, Nagoya, Japan
    Search for more papers by this author

  • Posted on the website on 30 March 2004

*To whom correspondence should be addressed; Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Fax: 81-52-789-3528; e-mail: kakitani@allegro.phys.nagoya-u.ac.jp

ABSTRACT

We investigate the role of protein environment of rhodopsin and the intramolecular interaction of the chromophore in the cis-trans photoisomerization of rhodopsin by means of a newly developed theoretical method. We theoretically produce modified rhodopsins in which a force field of arbitrarily chosen part of the chromophore or the binding pocket of rhodopsin is altered. We compare the equilibrium conformation of the chromophore and the energy stored in the chromophore of modified rhodopsins with those of native rhodopsins. This method is called site-specific force field switch (SFS). We show that this method is most successfully applied to the torsion potential of rhodopsin. Namely, by reducing the twisting force constant of the C11=C12 of 11-cis retinal chromophore of rhodopsin to zero, we found that the equilibrium value of the twisting angle of the C11=C12 bond is twisted in the negative direction down to about −80°. The relaxation energy obtained by this change amounts to an order of 10 kcal/mol. In the case that the twisting force constant of the other double bond is reduced to zero, no such large twisting of the bond happens. From these results we conclude that a certain torsion potential is applied specifically to the C11=C12 bond of the chromophore in the ground state of rhodopsin. This torsion potential facilitates the bond-specific cis-trans photoisomerization of rhodopsin. This kind of the mechanism is consistent with our torsion model proposed by us more than a quarter of century ago. The origin of the torsion potential is analyzed in detail on the basis of the chromophore structure and protein conformation, by applying the SFS method extensively.

Ancillary