TY - JOUR

T1 - Simple models to study spectral properties of microbial and animal rhodopsins

T2 - Evaluation of the electrostatic effect of charged and polar residues on the first absorption band maxima

AU - Shtyrov, Andrey A.

AU - Nikolaev, Dmitrii M.

AU - Mironov, Vladimir N.

AU - Vasin, Andrey V.

AU - Panov, Maxim S.

AU - Tveryanovich, Yuri S.

AU - Ryazantsev, Mikhail N.

N1 - Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/3/16

Y1 - 2021/3/16

N2 - 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.

AB - 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.

KW - Biological photosensors

KW - Engineering of red-shifted rhodopsins

KW - Photobiology

KW - Rhodopsins

KW - Spectral properties of rhodopsins

KW - Spectral tuning in rhodopsins

UR - http://www.scopus.com/inward/record.url?scp=85102638061&partnerID=8YFLogxK

U2 - 10.3390/ijms22063029

DO - 10.3390/ijms22063029

M3 - Article

AN - SCOPUS:85102638061

VL - 22

SP - 1

EP - 19

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1422-0067

IS - 6

M1 - 3029

ER -