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Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima
Authors:Andrey A. Shtyrov  Dmitrii M. Nikolaev  Vladimir N. Mironov  Andrey V. Vasin  Maxim S. Panov  Yuri S. Tveryanovich  Mikhail N. Ryazantsev
Affiliation:1.Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia; (A.A.S.); (D.M.N.); (V.N.M.);2.Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 St. Petersburg, Russia; (M.S.P.); (Y.S.T.);3.Institute of Biomedical Systems and Botechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Street, 195251 St. Petersburg, Russia;
Abstract:A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties.
Keywords:rhodopsins   spectral properties of rhodopsins   spectral tuning in rhodopsins   engineering of red-shifted rhodopsins   photobiology   biological photosensors
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