Model of Abnormal Chromophore-Protein Interaction for Е181К Rhodopsin Mutation: Computer Molecular Dynamics Study



Tatyana Feldman1, 2, 3, Mikhail Ostrovsky1, 2, 3, Kholmirzo Kholmurodov*, 2, 4, Kenji Yasuoka5
1 Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 ul. Kosygina, Moscow, 119334 Russia
2 Joint Institute for Nuclear Research, Dubna, Moscow Region, 141980 Russia
3 Moscow State Lomonosov University, Department of Biology, Leninskie Gory, 1, Moscow, 119234 Russia
4 Dubna International University, Department of Chemistry,Dubna, Moscow Region, 119234 Russia
5 Keio University, Department of Mechanical Engineering,3-14-1 Hiyoshi, Yokohama, 223-8522 Japan


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© Feldman et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http: //creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Computer Molecular Modeling Sector, Laboratory of Radiation Biology Joint Institute for Nuclear Research, 141980 Dubna, Moscow region, Russia; Tel: +7 49621 62872;Fax: +7 49621 65948; E-mails: mirzo@jinr.ru, kholmirzo@gmail.com


Abstract

The interaction of the 11-cis-retinal chromophore with the surrounding amino acid residues in the chromophore center of the rhodopsin protein has been investigated for the Е181К mutant form using molecular dynamics simulation. A comparative analysis of the arrangement of the amino acid residues in the chromophore center has been performed for both wild (native) and mutant rhodopsins. It is shown that for the Е181К mutant rhodopsin there is no proper binding of 11-cis-retinal with the surrounding amino acid residues. The distortion of the conformation states in the mutant rhodopsin molecule takes place in both the chromophore center and cytoplasmic domain. Our simulations suggest that a stable covalent linkage of 11-cis-retinal with the protein part (viz. opsin) of the rhodopsin molecule will not form. This, on the other hand, implies that the protein’s active site in the cytoplasmic domain, which is responsible for the G-protein binding (so-called transducin), may not be completely blocked.

Based on our molecular simulation data, we discuss the possible correlation between retinitis pigmentosa pathogenesis and the structural and functional properties of the rhodopsin protein.

Keyword: : Rhodopsin, 11-cis-retinal chromophore, mutant rhodopsin, retinitis pigmentosa, molecular dynamics simulation.