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Russian Chemical Bulletin

, Volume 56, Issue 1, pp 20–27 | Cite as

Interaction of chromophore, 11-cis-retinal, with amino acid residues of the visual pigment rhodopsin in the region of protonated Schiff base: A molecular dynamics study

  • Kh. T. Kholmurodov
  • T. B. Fel’dman
  • M. A. Ostrovsky
Article

Abstract

A molecular dynamics study of the dark adapted visual pigment rhodopsin molecule was carried out. The interaction of the chromophore group, 11-cis-retinal, with the nearest amino acid residues in the chromophore center of the molecule, namely, in the region of the protonated Schiff base linkage, was analyzed. Most likely, the interaction of the CH=NH bond with the negatively charged amino acid residue Glu113 cannot be described as a simple electrostatic interaction of two oppositely charged groups. One can propose that not only Glu113 but also Glu181 and Ser186 are involved in stabilization of the protonated Schiff base linkage. Accord-ing to calculations, Glu181 interacts, as the counter-ion, with the Schiff base indirectly via Ser186. The intramolecular mechanisms of protonated Schiff base stabilization in rhodopsin are discussed.

Key words

visual pigments rhodopsin 11-cis-retinal amino acid residues molecular modeling 

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Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Kh. T. Kholmurodov
    • 1
  • T. B. Fel’dman
    • 2
  • M. A. Ostrovsky
    • 2
  1. 1.Joint Institute for Nuclear ResearchDubna, Moscow RegionRussian Federation
  2. 2.N. M. Emanuel’ Institute of Biochemical PhysicsRussian Academy of SciencesMoscowRussian Federation

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