Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

Pedraza-González, Laura; Barneschi, Leonardo; Padula, Daniele; Vico, Luca De; Olivucci, Massimo

doi:10.1007/s41061-022-00374-w

Cited by 9 publications

(25 citation statements)

References 114 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An initial QM/MM model of NeoR was constructed using the Automatic Rhodopsin Modeling ( a -ARM) technology 20 – 22 starting from the comparative model mentioned above. a- ARM models have been shown to yield congruous (i.e., built by employing exactly the same protocol) animal and microbial rhodopsin models that correctly reproduce trends in λ a max values 9 , 20 , 21 , 23 – 27 .…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin

et al. 2022

Self Cite

View full text Add to dashboard Cite

The understanding of how the rhodopsin sequence can be modified to exactly modulate the spectroscopic properties of its retinal chromophore, is a prerequisite for the rational design of more effective optogenetic tools. One key problem is that of establishing the rules to be satisfied for achieving highly fluorescent rhodopsins with a near infrared absorption. In the present paper we use multi-configurational quantum chemistry to construct a computer model of a recently discovered natural rhodopsin, Neorhodopsin, displaying exactly such properties. We show that the model, that successfully replicates the relevant experimental observables, unveils a geometrical and electronic structure of the chromophore featuring a highly diffuse charge distribution along its conjugated chain. The same model reveals that a charge confinement process occurring along the chromophore excited state isomerization coordinate, is the primary cause of the observed fluorescence enhancement.

show abstract

Section: Resultsmentioning

confidence: 99%

“…The employed hybrid QM/MM modeling of NeoR was performed using the a -ARM protocol 20 – 22 and based on the comparative model structure built and validated by S. Adam et al 7 . Further details about the a -ARM protocol are given as Supplementary Informations (Supplementary Section 1 ).…”

Section: Methodsmentioning

confidence: 99%

Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…This further inspired detailed analysis with modified and/or labeled retinals ( 13 C, 2 H, F) and protein residues ( 13 C, 15 N, F, azido, spin labels) using fluorescence, vibrational, EPR and NMR spectroscopy ( Table 5 ). This profited from as well as steered development of sophisticated theoretical and in-silico procedures, like DFT, QM/MM and molecular dynamics ( Altun et al, 2008 ; Collette et al, 2018 ; Del Carmen Marín et al, 2019b ; Dokukina et al, 2019 ; Pieri et al, 2019 ; Shao et al, 2020 ; Nikolaev et al, 2021 ; Scholz and Neugebauer, 2021 ; Shen et al, 2021 ; Pedraza-González et al, 2022 ). All these elements have already profoundly deepened our insight into the structure and mechanism of bovine rod rhodopsin and bacteriorhodopsin, the frontrunners of type-2 and -1, respectively.…”

Section: Bioengineeringmentioning

confidence: 99%

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

Grip

Ganapathy

2022

Front. Chem.

View full text Add to dashboard Cite

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

show abstract

“…For animal pigments, it would probably be advisable to use cryo-EM in combination with the more easily prepared and more stable nanodisc environment [287], in an ultrarapid mode when possible. Eventually, in silico ab initio structural model building exploiting the newly available algorithms [288][289][290] will allow rapid testing of the chromophoric potential of theoretical promising retinal analogs for (iso)rhodopsins [291]. Atomic insight into the photoisomerization trajectories of isorhodopsins will be of utmost importance, not only from a photochemical point of view, but also for the design of retinal proteins with selected properties-both for bioengineering purposes and in optogenetics [292,293].…”

Section: Overview and Prospectsmentioning

confidence: 99%

Isorhodopsin: An Undervalued Visual Pigment Analog

Grip

Lugtenburg

2022

Colorants

View full text Add to dashboard Cite

Rhodopsin, the first visual pigment identified in the animal retina, was shown to be a photosensitive membrane protein containing covalently bound retinal in the 11-cis configuration, as a chromophore. Upon photoexcitation the chromophore isomerizes in femtoseconds to all-trans, which drives the protein into the active state. Soon thereafter, another geometric isomer—9-cis retinal—was also shown to stably incorporate into the binding pocket, generating a slightly blue-shifted photosensitive protein. This pigment, coined isorhodopsin, was less photosensitive, but could also reach the active state. However, 9-cis retinal was not detected as a chromophore in any of the many animal visual pigments studied, and isorhodopsin was passed over as an exotic and little-relevant rhodopsin analog. Consequently, few in-depth studies of its photochemistry and activation mechanism have been performed. In this review, we aim to illustrate that it is unfortunate that isorhodopsin has received little attention in the visual research and literature. Elementary differences in photoexcitation of rhodopsin and isorhodopsin have already been reported. Further in-depth studies of the photochemical properties and pathways of isorhodopsin would be quite enlightening for the initial steps in vision, as well as being beneficial for biotechnological applications of retinal proteins.

show abstract

Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

Cited by 9 publications

References 114 publications

Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin

Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

Isorhodopsin: An Undervalued Visual Pigment Analog

Contact Info

Product

Resources

About