Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

Church, Jonathan R.; Amoyal, Gil S.; Borin, Veniamin; Adam, Suliman; Olsen, Jógvan Magnus Haugaard; Schapiro, Igor

doi:10.1002/chem.202200139

Cited by 8 publications

(35 citation statements)

References 87 publications

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“…3A) via through-space 15 N-13 C dipolar interactions in [ 13 C′-Ile, 15 Nε-Trp]-PR samples (text S11E). In 2D 15 N- 13 C TEDOR (transferred echo double resonance) spectra of these samples, two Trp Nε1-Ile C′ cross peaks have been detected (Fig. 3D, left).…”

Section: Exploring the Retinal Binding Pocket By Dnp-enhanced Ssnmr S...mentioning

confidence: 97%

“…the observed 13 c and 1 h chemical shift changes highlight structural chromophore differences between GPR and BPR. (E) Summary of isotropic 1 h, 13 c, and 15 n chemical shift differences (bar charts) and 13 c-cSA and 15 n-cSA changes (dots) between BPR and GPR. For the cSA, principal value differences are provided.…”

Section: The Pr Color Switch and The Psb Counterionsmentioning

confidence: 99%

“…Our previous ssNMR work has been restricted on retinal carbons C14 and C15 (15). To obtain a more comprehensive picture, we have explored other retinal atoms via multiple 13 C isotope labeling schemes (Fig. 2A and table S1).…”

Section: Localized Perturbations Of the Retinal Chromophorementioning

confidence: 99%

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Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

Mao,

Jin,

Shi

et al. 2024

Sci. Adv.

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Proteorhodopsins are widely distributed photoreceptors from marine bacteria. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. On the basis of an integrated approach combining sensitivity-enhanced solid-state nuclear magnetic resonance (ssNMR) spectroscopy and linear-scaling quantum mechanics/molecular mechanics (QM/MM) methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shift between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation.

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Section: Exploring the Retinal Binding Pocket By Dnp-enhanced Ssnmr S...mentioning

confidence: 97%

Section: The Pr Color Switch and The Psb Counterionsmentioning

confidence: 99%

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Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

Mao,

Jin,

Shi

et al. 2024

Sci. Adv.

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“…Thus, the excitation energy in this retinylidene moiety is strongly reduced, compared to free retinal, which results in a red-shift of the absorbance profile. The magnitude of the red-shift strongly depends on the structure of the H-bonded network and counterion complex involving variable electrostatic interactions with the protonated Schiff base and to a lesser extent on the properties of protein residues in the opsin binding pocket ( Lesca et al, 2018 ; Nikolaev et al, 2020 ; Shen et al, 2021 ; Shtyrov et al, 2021 ; Church et al, 2022a ). By modifying these elements Nature created the spectacular broad variance in the spectral profile of rhodopsins, allowing them to cover the entire visible region.…”

Section: Spectral and Structural Properties And Solubilizationmentioning

confidence: 99%

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

Grip

Ganapathy

2022

Front. Chem.

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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.

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“…The extent of this spectral tuning is controlled by the protein environment, which includes the protonation states of titratable residues and the interactions with nearby residues within the binding pocket of the protein. JSR1 has been experimentally measured to absorb at 505 nm while a hybrid QM/MM simulation on JSR1 using the EE scheme with TD-CAM-B3LYP/cc-pVDZ resulted in excitation energy of 484 nm [22,[32][33][34].…”

Section: Introductionmentioning

confidence: 99%

Induction effects on the absorption maxima of photoreceptor proteins

2023

Self Cite

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Multiscale simulations have been established as a powerful tool to calculate and predict excitation energies in complex systems such as photoreceptor proteins. In these simulations the chromophore is typically treated using quantum mechanical (QM) methods while the protein and surrounding environment are described by a classical molecular mechanics (MM) force field. The electrostatic interactions between these regions are often treated using electrostatic embedding where the point charges in the MM region polarize the QM region. A more sophisticated treatment accounts also for the polarization of the MM region. In this work, the effect of such a polarizable embedding on excitation energies was benchmarked and compared to electrostatic embedding. This was done for two different proteins, the lipid membrane-embedded jumping spider rhodopsin and the soluble cyanobacteriochrome Slr1393g3. It was found that the polarizable embedding scheme produces absorption maxima closer to experimental values. The polarizable embedding scheme was also benchmarked against expanded QM regions and found to be in qualitative agreement. Treating individual residues as polarizable recovered between 50% and 71% of the QM improvement in the excitation energies, depending on the system. A detailed analysis of each amino acid residue in the chromophore binding pocket revealed that aromatic residues result in the largest change in excitation energy compared to the electrostatic embedding. Furthermore, the computational efficiency of polarizable embedding allowed it to go beyond the binding pocket and describe a larger portion of the environment, further improving the results.

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Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

Cited by 8 publications

References 87 publications

Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

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

Induction effects on the absorption maxima of photoreceptor proteins

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