Perspective Tools for Optogenetics and Photopharmacology: From Design to Implementation

Nikolaev, Dmitrii M.; Panov, Maxim S.; Shtyrov, Andrey A.; Бойцов, В. М.; Vyazmin, Sergey Yu.; Chakchir, Oleg B.; Yakovlev, I. P.; Ryazantsev, Mikhail N.

doi:10.1007/978-3-030-05974-3_8

Cited by 9 publications

(6 citation statements)

References 208 publications

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“…The natural diversity of the rhodopsins’ first absorption band maxima (

) is achieved via the variation of the proteins’ amino acid compositions during evolutionary processes [ 1 , 2 ]. The same strategy is used in modern technologies to obtain rhodopsin variants with an optimal

[ 3 , 4 , 5 , 6 ]. In this context, it is desirable to develop methodologies for prediction of the

change caused by the modifications of the primary protein structure, e.g., single or multiple amino acid substitutions (

).…”

Section: Introductionmentioning

confidence: 99%

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

Shtyrov

Nikolaev

Mironov

et al. 2021

IJMS

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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.

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“…The natural diversity of the rhodopsins’ first absorption band maxima (

[ 3 , 4 , 5 , 6 ]. In this context, it is desirable to develop methodologies for prediction of the

change caused by the modifications of the primary protein structure, e.g., single or multiple amino acid substitutions (

).…”

Section: Introductionmentioning

confidence: 99%

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

Shtyrov

Nikolaev

Mironov

et al. 2021

IJMS

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“…Fluorescence and photoisomerization of the chromophore in opsin-based photosensitive proteins have been investigated for decades [7,8,98,99]. Recently, the research in this area has been facilitated by application of rhodopsins as tools for optogenetics [100][101][102], which is, along with photopharmacology [103][104][105][106], a widely used approach to control and monitor biological cell activity using light. Although high fluorescence and, accordingly, inefficient photoisomerization of the chromophore in rhodopsins is an impediment for application of these proteins as actuators, intense fluorescence is a desirable feature for their applications as genetically encoded voltage indicators.…”

Section: Discussionmentioning

confidence: 99%

Fluorescence of the Retinal Chromophore in Microbial and Animal Rhodopsins

Nikolaev,

Shtyrov,

Vyazmin

et al. 2023

IJMS

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Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low, in accordance with their functions that depend on efficient transduction of absorbed light energy. However, several recently proposed classes of engineered rhodopsins with enhanced fluorescence, along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsin property. Here, we review the available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates, as well as different isomers of the protonated retinal Schiff base in various solvents and the gas phase.

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“…Recently, the research in this 10/24 https://doi.org/10.26434/chemrxiv-2023-3n1d0 ORCID: https://orcid.org/0000-0003-3413-1706 Content not peer-reviewed by ChemRxiv. License: CC BY-NC-ND 4.0 area has been facilitated by application of rhodopsins as tools for optogenetics [71][72][73], which is, along with photopharmacology [74][75][76][77], a widely-used approach to control and monitor biological cell activity using light. Although high fluorescence and, accordingly, inefficient photoisomerization of the chromophore in rhodopsins is an impediment for application of these proteins as actuators, intense fluorescence is a desirable feature for their applications as genetically-encoded voltage indicators.…”

Section: Discussionmentioning

confidence: 99%

Fluorescence of the retinal chromophore in microbial and animal rhodopsins

Nikolaev,

Shtyrov,

Vyazmin

et al. 2023

Preprint

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Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low in accordance with their functions that depend on efficient transduction of absorbed light energy. However, recently proposed several classes of engineered rhodopsins with enhanced fluorescence along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsins property. Here we review available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates as well as different isomers of the protonated retinal Schiff base in different solvents and the gas phase.

show abstract

Perspective Tools for Optogenetics and Photopharmacology: From Design to Implementation

Cited by 9 publications

References 208 publications

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

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

Fluorescence of the Retinal Chromophore in Microbial and Animal Rhodopsins

Fluorescence of the retinal chromophore in microbial and animal rhodopsins

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