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.

Dmitrii M. Nikolaev,Andrey V. Vasin,Andrey A. Shtyrov,Yuri S. Tveryanovich,Maxim S. Panov,Mikhail N. Ryazantsev,Vladimir N. Mironov

doi:10.3390/ijms22063029

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.

Highlights

Introduction iationsRhodopsins are photosensitive membrane proteins that have been discovered in many species across all three life domains
The main goal of this article was to present a simple ab initio-based approach to evaluate ∆λmax caused by substitution of charged or polar amino acids in visual and microbial rhodopsins
If the rhodopsin three-dimensional structure is available, ∆λmax can be obtained from the plots and tables given in the article and Supplementary Materials

Summary

Introduction

Introduction iationsRhodopsins are photosensitive membrane proteins that have been discovered in many species across all three life domains. The same strategy is used in modern technologies to obtain rhodopsin variants with an optimal λmax [3,4,5,6] In this context, it is desirable to develop methodologies for prediction of the λmax change caused by the modifications of the primary protein structure, e.g., single or multiple amino acid substitutions (∆λmax ). Amino acid substitutions are introduced into rhodopsins to measure ∆λmax and, to estimate the substituted residue contribution to the absorption maximum [7,8,9]. The objectives of these studies are to evaluate the correlations

Objectives

Results

Conclusion