1
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Ghysbrecht S, Keller BG. Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. J Comput Chem 2024; 45:1390-1403. [PMID: 38414274 DOI: 10.1002/jcc.27332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.
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Affiliation(s)
- Simon Ghysbrecht
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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2
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Goti G, Manal K, Sivaguru J, Dell'Amico L. The impact of UV light on synthetic photochemistry and photocatalysis. Nat Chem 2024; 16:684-692. [PMID: 38429343 DOI: 10.1038/s41557-024-01472-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
During the past 15 years, an increasing number of research groups have embraced visible-light-mediated synthetic transformations as a powerful strategy for the construction and functionalization of organic molecules. This trend has followed the advent and development of photocatalysis, which often operates under mild visible-light irradiation. Nowadays, the general perception of UV-light photochemistry is often as an out-of-fashion approach that is difficult to perform and leads to unselective reaction pathways. Here we wish to propose an alternative and more realistic point of view to the scientific community. First, we will provide an overview of the use of UV light in modern photochemistry, highlighting the pivotal role it still plays in the development of new, efficient synthetic methods. We will then show how the high levels of mechanistic understanding reached for UV-light-driven processes have been key in the implementation of the related visible-light-driven transformations.
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Affiliation(s)
- Giulio Goti
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Kavyasree Manal
- Center for Photochemical Sciences and Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA
| | - Jayaraman Sivaguru
- Center for Photochemical Sciences and Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA.
| | - Luca Dell'Amico
- Department of Chemical Sciences, University of Padova, Padova, Italy.
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3
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Beck WF. Intramolecular charge transfer and the function of vibronic excitons in photosynthetic light harvesting. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01095-5. [PMID: 38656684 DOI: 10.1007/s11120-024-01095-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
A widely discussed explanation for the prevalence of pairs or clusters of closely spaced electronic chromophores in photosynthetic light-harvesting proteins is the presence of ultrafast and highly directional excitation energy transfer pathways mediated by vibronic excitons, the delocalized optical excitations derived from mixing of the electronic and vibrational states of the chromophores. We discuss herein the hypothesis that internal conversion processes between exciton states on the <100 fs timescale are possible when the excitonic potential energy surfaces are controlled by the vibrational modes that induce charge transfer character in a strongly coupled system of chromophores. We discuss two examples, the peridinin-chlorophyll protein from marine dinoflagellates and the intact phycobilisome from cyanobacteria, in which the intramolecular charge-transfer (ICT) character arising from out-of-plane distortion of the conjugation of carotenoid or bilin chromophores also results in localization of the initially delocalized optical excitation on the vibrational timescale. Tuning of the ground state conformations of the chromophores to manipulate their ICT character provides a natural photoregulatory mechanism, which would control the overall quantum yield of excitation energy transfer by turning on and off the delocalized character of the optical excitations.
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Affiliation(s)
- Warren F Beck
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
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4
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Palombo R, Barneschi L, Pedraza-González L, Yang X, Olivucci M. Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin. Phys Chem Chem Phys 2024; 26:10343-10356. [PMID: 38501246 DOI: 10.1039/d4cp00193a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.
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Affiliation(s)
- Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
| | - Laura Pedraza-González
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
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5
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Kaziannis S, Broser M, van Stokkum IHM, Dostal J, Busse W, Munhoven A, Bernardo C, Kloz M, Hegemann P, Kennis JTM. Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction. Proc Natl Acad Sci U S A 2024; 121:e2318996121. [PMID: 38478688 PMCID: PMC10962995 DOI: 10.1073/pnas.2318996121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.
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Affiliation(s)
- Spyridon Kaziannis
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
- Department of Physics, University of Ioannina, IoanninaGr-45110, Greece
| | - Matthias Broser
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Ivo H. M. van Stokkum
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Jakub Dostal
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Wayne Busse
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Arno Munhoven
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Cesar Bernardo
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Miroslav Kloz
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Peter Hegemann
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - John T. M. Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
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6
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Di Prima D, Reinholdt P, Kongsted J. Color Tuning in Bovine Rhodopsin through Polarizable Embedding. J Phys Chem B 2024. [PMID: 38489248 DOI: 10.1021/acs.jpcb.3c07891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Bovine rhodopsin is among the most studied proteins in the rhodopsin family. Its primary activation mechanism is the photoisomerization of 11-cis retinal, triggered by the absorption of a UV-visible photon. Different mutants of the same rhodopsin show different absorption wavelengths due to the influence of the specific amino acid residues forming the cavity in which the retinal chromophore is embedded, and rhodopsins activated at different wavelengths are, for example, exploited in the field of optogenetics. In this letter, we present a procedure for systematically investigating color tuning in models of bovine rhodopsin and a set of its mutants embedded in a membrane bilayer. Vertical excitation energy calculations were carried out with the polarizable embedding potential for describing the environment surrounding the chromophore. We show that polarizable embedding outperformed regular electrostatic embedding in determining both the vertical excitation energies and associated oscillator strengths of the systems studied.
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Affiliation(s)
- Duccio Di Prima
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
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7
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Kim SS, Rhee YM. Potential energy interpolation with target-customized weighting coordinates: application to excited-state dynamics of photoactive yellow protein chromophore in water. Phys Chem Chem Phys 2024; 26:9021-9036. [PMID: 38440829 DOI: 10.1039/d3cp05643k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Interpolation of potential energy surfaces (PESs) can provide a practical route to performing molecular dynamics simulations with a reliability matching a high-level quantum chemical calculation. An obstacle to its widespread use is perhaps the lack of general and optimal interpolation settings that can be applied in a black-box manner for any given molecular system. How to set up the weights for interpolation is one such task, and we still need to diversify the approaches in order to treat various systems. Here, we develop a new interpolation weighting scheme, which allows us to choose the weighting coordinates in a system-specific manner, by amplifying the contribution from specific internal coordinates. The new weighting scheme with an appropriate selection of coordinates is proved to be effective in reducing the interpolation error along the reaction pathway. As a demonstration, we consider the photoactive yellow protein chromophore system, as it constitutes itself as an interesting target that bears long-standing questions related to excited-state dynamics inside protein environments. We build its two-state diabatic interpolated PES with the new weighting scheme. We indeed see the utility of our scheme by conducting nonadiabatic molecular dynamics simulations with the required semi-global PES based on a limited number of data points.
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Affiliation(s)
- Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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8
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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9
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Anderson B, Bryant DL, Gozem S, Brambley C, Handy ST, Farone A, Miller JM. Solvent-Dependent Emissions Properties of a Model Aurone Enable Use in Biological Applications. J Fluoresc 2024:10.1007/s10895-024-03607-x. [PMID: 38411859 DOI: 10.1007/s10895-024-03607-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/27/2024] [Indexed: 02/28/2024]
Abstract
Fluorophores are powerful visualization tools and the development of novel small organic fluorophores are in great demand. Small organic fluorophores have been derived from the aurone skeleton, 2-benzylidenebenzofuran-3(2H)-one. In this study, we have utilized a model aurone derivative with a methoxy group at the 3' position and a hydroxyl group at the 4' position, termed vanillin aurone, to develop a foundational understanding of structural factors impacting aurone fluorescence properties. The fluorescent behaviors of the model aurone were characterized in solvent environments differing in relative polarity and dielectric constant. These data suggested that hydrogen bonding or electrostatic interactions between excited state aurone and solvent directly impact emissions properties such as peak emission wavelength, emission intensity, and Stokes shift. Time-dependent Density Functional Theory (TD-DFT) model calculations suggest that quenched aurone emissions observed in water are a consequence of stabilization of a twisted excited state conformation that disrupts conjugation. In contrast, the calculations indicate that low polarity solvents such as toluene or acetone stabilize a brightly fluorescent planar state. Based on this, additional experiments were performed to demonstrate use as a turn-on probe in an aqueous environment in response to conditions leading to planar excited state stabilization. Vanillin aurone was observed to bind to a model ATP binding protein, YME1L, leading to enhanced emissions intensities with a dissociation equilibrium constant equal to ~ 30 µM. Separately, the aurone was observed to be cell permeable with significant toxicity at doses exceeding 6.25 µM. Taken together, these results suggest that aurones may be broadly useful as turn-on probes in aqueous environments that promote either a change in relative solvent polarity or through direct stabilization of a planar excited state through macromolecular binding.
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Affiliation(s)
- Beth Anderson
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Daniel L Bryant
- Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Samer Gozem
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30302, USA
| | - Chad Brambley
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Scott T Handy
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Anthony Farone
- Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Justin M Miller
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA.
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10
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Pieri E, Weingart O, Huix-Rotllant M, Ledentu V, Garavelli M, Ferré N. Modeling pH-Dependent Biomolecular Photochemistry. J Chem Theory Comput 2024; 20:842-855. [PMID: 38198619 DOI: 10.1021/acs.jctc.3c00980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Oliver Weingart
- Faculty of Mathematics and Natural Sciences, Institute for Theoretical and Computational Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Miquel Huix-Rotllant
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Vincent Ledentu
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
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11
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Toldo JM, Mattos RS, Pinheiro M, Mukherjee S, Barbatti M. Recommendations for Velocity Adjustment in Surface Hopping. J Chem Theory Comput 2024; 20:614-624. [PMID: 38207213 DOI: 10.1021/acs.jctc.3c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
This study investigates velocity adjustment directions after hopping in surface hopping dynamics. Using fulvene and a protonated Schiff base (PSB4) as case studies, we investigate the population decay and reaction yields of different sets of dynamics with the velocity adjusted in either the nonadiabatic coupling, gradient difference, or momentum directions. For the latter, in addition to the conventional algorithm, we investigated the performance of a reduced kinetic energy reservoir approach recently proposed. Our evaluation also considered velocity adjustment in the directions of approximate nonadiabatic coupling vectors. While results for fulvene are susceptible to the adjustment approach, PSB4 is not. We correlated this dependence to the topography near the conical intersections. When nonadiabatic coupling vectors are unavailable, the gradient difference direction is the best adjustment option. If the gradient difference is also unavailable, a semiempirical vector direction or the momentum direction with a reduced kinetic energy reservoir becomes an excellent option to prevent an artificial excess of back hoppings. The precise velocity adjustment direction is less crucial for describing the nonadiabatic dynamics than the kinetic energy reservoir's size.
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Affiliation(s)
- Josene M Toldo
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Rafael S Mattos
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Max Pinheiro
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | | | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, Paris 75231, France
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12
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Liu XY, Chen WK, Fang WH, Cui G. Nonadiabatic Dynamics Simulations for Photoinduced Processes in Molecules and Semiconductors: Methodologies and Applications. J Chem Theory Comput 2023. [PMID: 37984502 DOI: 10.1021/acs.jctc.3c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Nonadiabatic dynamics (NAMD) simulations have become powerful tools for elucidating complicated photoinduced processes in various systems from molecules to semiconductor materials. In this review, we present an overview of our recent research on photophysics of molecular systems and periodic semiconductor materials with the aid of ab initio NAMD simulation methods implemented in the generalized trajectory surface-hopping (GTSH) package. Both theoretical backgrounds and applications of the developed NAMD methods are presented in detail. For molecular systems, the linear-response time-dependent density functional theory (LR-TDDFT) method is primarily used to model electronic structures in NAMD simulations owing to its balanced efficiency and accuracy. Moreover, the efficient algorithms for calculating nonadiabatic coupling terms (NACTs) and spin-orbit couplings (SOCs) have been coded into the package to increase the simulation efficiency. In combination with various analysis techniques, we can explore the mechanistic details of the photoinduced dynamics of a range of molecular systems, including charge separation and energy transfer processes in organic donor-acceptor structures, ultrafast intersystem crossing (ISC) processes in transition metal complexes (TMCs), and exciton dynamics in molecular aggregates. For semiconductor materials, we developed the NAMD methods for simulating the photoinduced carrier dynamics within the framework of the Kohn-Sham density functional theory (KS-DFT), in which SOC effects are explicitly accounted for using the two-component, noncollinear DFT method. Using this method, we have investigated the photoinduced carrier dynamics at the interface of a variety of van der Waals (vdW) heterojunctions, such as two-dimensional transition metal dichalcogenides (TMDs), carbon nanotubes (CNTs), and perovskites-related systems. Recently, we extended the LR-TDDFT-based NAMD method for semiconductor materials, allowing us to study the excitonic effects in the photoinduced energy transfer process. These results demonstrate that the NAMD simulations are powerful tools for exploring the photodynamics of molecular systems and semiconductor materials. In future studies, the NAMD simulation methods can be employed to elucidate experimental phenomena and reveal microscopic details as well as rationally design novel photofunctional materials with desired properties.
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Affiliation(s)
- Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, P. R. China
| | - Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Hefei National Laboratory, Hefei 230088, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Hefei National Laboratory, Hefei 230088, P. R. China
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13
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Broser M, Andruniów T, Kraskov A, Palombo R, Katz S, Kloz M, Dostál J, Bernardo C, Kennis JTM, Hegemann P, Olivucci M, Hildebrandt P. Experimental Assessment of the Electronic and Geometrical Structure of a Near-Infrared Absorbing and Highly Fluorescent Microbial Rhodopsin. J Phys Chem Lett 2023; 14:9291-9295. [PMID: 37815402 DOI: 10.1021/acs.jpclett.3c02167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The recently discovered Neorhodopsin (NeoR) exhibits absorption and emission maxima in the near-infrared spectral region, which together with the high fluorescence quantum yield makes it an attractive retinal protein for optogenetic applications. The unique optical properties can be rationalized by a theoretical model that predicts a high charge transfer character in the electronic ground state (S0) which is otherwise typical of the excited state S1 in canonical retinal proteins. The present study sets out to assess the electronic structure of the NeoR chromophore by resonance Raman (RR) spectroscopy since frequencies and relative intensities of RR bands are controlled by the ground and excited state's properties. The RR spectra of NeoR differ dramatically from those of canonical rhodopsins but can be reliably reproduced by the calculations carried out within two different structural models. The remarkable agreement between the experimental and calculated spectra confirms the consistency and robustness of the theoretical approach.
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Affiliation(s)
- Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Tadeusz Andruniów
- Department of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anastasia Kraskov
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Miroslav Kloz
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - Jakub Dostál
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - César Bernardo
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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14
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Arcidiacono A, Accomasso D, Cupellini L, Mennucci B. How orange carotenoid protein controls the excited state dynamics of canthaxanthin. Chem Sci 2023; 14:11158-11169. [PMID: 37860660 PMCID: PMC10583711 DOI: 10.1039/d3sc02662k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Orange Carotenoid Protein (OCP) is a ketocarotenoid-binding protein essential for photoprotection in cyanobacteria. The main steps of the photoactivated conversion which converts OCP from its resting state to the active one have been extensively investigated. However, the initial photochemical event in the ketocarotenoid which triggers the large structural changes finally leading to the active state is still not understood. Here we employ QM/MM surface hopping nonadiabatic dynamics to investigate the excited-state decay of canthaxanthin in OCP, both in the ultrafast S2 to S1 internal conversion and the slower decay leading back to the ground state. For the former step we show the involvement of an additional excited state, which in the literature has been often named the SX state, and we characterize its nature. For the latter step, we reveal an excited state decay characterized by multiple timescales, which are related to the ground-state conformational heterogeneity of the ketocarotenoid. We assigned the slowly decaying population to the so-called S* state. Finally, we identify a minor decay pathway involving double-bond photoisomerization, which could be the initial trigger to photoactivation of OCP.
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Affiliation(s)
- Amanda Arcidiacono
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Davide Accomasso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
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15
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Ostrovsky MA, Smitienko OA, Bochenkova AV, Feldman TB. Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1528-1543. [PMID: 38105022 DOI: 10.1134/s0006297923100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/20/2023] [Accepted: 08/12/2023] [Indexed: 12/19/2023]
Abstract
The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
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Affiliation(s)
- Mikhail A Ostrovsky
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | - Olga A Smitienko
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | | | - Tatiana B Feldman
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
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16
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Meng X, Ganapathy S, van Roemburg L, Post M, Brinks D. Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway. ACS PHYSICAL CHEMISTRY AU 2023; 3:320-333. [PMID: 37520318 PMCID: PMC10375888 DOI: 10.1021/acsphyschemau.3c00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 08/01/2023]
Abstract
Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.
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Affiliation(s)
- Xin Meng
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Srividya Ganapathy
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, United States
| | - Lars van Roemburg
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Marco Post
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Daan Brinks
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Molecular Genetics, Erasmus University
Medical Center, 3015 GD Rotterdam, The Netherlands
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17
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Fadini A, Hutchison CDM, Morozov D, Chang J, Maghlaoui K, Perrett S, Luo F, Kho JCX, Romei MG, Morgan RML, Orr CM, Cordon-Preciado V, Fujiwara T, Nuemket N, Tosha T, Tanaka R, Owada S, Tono K, Iwata S, Boxer SG, Groenhof G, Nango E, van Thor JJ. Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism. J Am Chem Soc 2023. [PMID: 37418747 PMCID: PMC10375524 DOI: 10.1021/jacs.3c02313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements.
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Affiliation(s)
- Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Christopher D M Hutchison
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Jeffrey Chang
- Department of Physics, Stanford University, Stanford, California 94305, United States
| | - Karim Maghlaoui
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Samuel Perrett
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Fangjia Luo
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
| | - Jeslyn C X Kho
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - R Marc L Morgan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Christian M Orr
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, U.K
| | - Violeta Cordon-Preciado
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Takaaki Fujiwara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
| | - Nipawan Nuemket
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Kyoto 606-8501, Japan
| | - Takehiko Tosha
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Kyoto 606-8501, Japan
| | - Shigeki Owada
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Kyoto 606-8501, Japan
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Eriko Nango
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan
| | - Jasper J van Thor
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
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18
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Chakraborty P, Couto RC, List NH. Deciphering Methylation Effects on S 2( ππ*) Internal Conversion in the Simplest Linear α,β-Unsaturated Carbonyl. J Phys Chem A 2023. [PMID: 37331016 DOI: 10.1021/acs.jpca.3c02582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chemical substituents can influence photodynamics by altering the location of critical points and the topography of the potential energy surfaces (electronic effect) and by selectively modifying the inertia of specific nuclear modes (inertial effects). Using nonadiabatic dynamics simulations, we investigate the impact of methylation on S2(ππ*) internal conversion in acrolein, the simplest linear α,β-unsaturated carbonyl. Consistent with time constants reported in a previous time-resolved photoelectron spectroscopy study, S2 → S1 deactivation occurs on an ultrafast time scale (∼50 fs). However, our simulations do not corroborate the sequential decay model used to fit the experiment. Instead, upon reaching the S1 state, the wavepacket bifurcates: a portion undergoes ballistic S1 → S0 deactivation (∼90 fs) mediated by fast bond-length alternation motion, while the remaining decays on the picosecond time scale. Our analysis reveals that methyl substitution, generally assumed to mainly exert inertial influence, is also manifested in important electronic effects due to its weak electron-donating ability. While methylation at the β C atom gives rise to effects principally of an inertial nature, such as retarding the twisting motion of the terminal -CHCH3 group and increasing its coupling with pyramidalization, methylation at the α or carbonyl C atom modifies the potential energy surfaces in a way that also contributes to altering the late S1-decay behavior. Specifically, our results suggest that the observed slowing of the picosecond component upon α-methylation is a consequence of a tighter surface and reduced amplitude along the central pyramidalization, effectively restricting the access to the S1/S0-intersection seam. Our work offers new insight into the S2(ππ*) internal conversion mechanisms in acrolein and its methylated derivatives and highlights site-selective methylation as a tuning knob to manipulate photochemical reactions.
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Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Rafael C Couto
- Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Nanna H List
- Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
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19
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Toldo JM, do Casal MT, Ventura E, do Monte SA, Barbatti M. Surface hopping modeling of charge and energy transfer in active environments. Phys Chem Chem Phys 2023; 25:8293-8316. [PMID: 36916738 PMCID: PMC10034598 DOI: 10.1039/d3cp00247k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes.
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Affiliation(s)
| | | | - Elizete Ventura
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Silmar A do Monte
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille, France.
- Institut Universitaire de France, 75231, Paris, France
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20
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Grigorenko B, Domratcheva T, Nemukhin A. QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase. Molecules 2023; 28:molecules28052405. [PMID: 36903648 PMCID: PMC10005588 DOI: 10.3390/molecules28052405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.
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Affiliation(s)
- Bella Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Tatiana Domratcheva
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Correspondence:
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21
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Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023; 615:939-944. [PMID: 36949205 PMCID: PMC10060157 DOI: 10.1038/s41586-023-05863-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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Affiliation(s)
- Thomas Gruhl
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Matthew J Rodrigues
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Christopher J Milne
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- European XFEL, Schenefeld, Germany
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karol Nass
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Saumik Sen
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Laboratory for Nonlinear Optics, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Petr Skopintsev
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Daniel James
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Physics, Utah Valley University, Orem, UT, USA
| | - Florian Dworkowski
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Demet Kekilli
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hannah Glover
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Camila Bacellar
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Azeglio D Diethelm
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Guillaume Gotthard
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Victoria Kabanova
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gregor Knopp
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Elena Lesca
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pikyee Ma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Filip Pamula
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oliver Tejero
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Niranjan Varma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Anna Wach
- Institute of Nuclear Physics Polish Academy of Sciences, Kraców, Poland
- Operando X-ray Spectroscopy, Energy and Environment Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
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22
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Pinheiro M, Zhang S, Dral PO, Barbatti M. WS22 database, Wigner Sampling and geometry interpolation for configurationally diverse molecular datasets. Sci Data 2023; 10:95. [PMID: 36792601 PMCID: PMC9931705 DOI: 10.1038/s41597-023-01998-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Multidimensional surfaces of quantum chemical properties, such as potential energies and dipole moments, are common targets for machine learning, requiring the development of robust and diverse databases extensively exploring molecular configurational spaces. Here we composed the WS22 database covering several quantum mechanical (QM) properties (including potential energies, forces, dipole moments, polarizabilities, HOMO, and LUMO energies) for ten flexible organic molecules of increasing complexity and with up to 22 atoms. This database consists of 1.18 million equilibrium and non-equilibrium geometries carefully sampled from Wigner distributions centered at different equilibrium conformations (either at the ground or excited electronic states) and further augmented with interpolated structures. The diversity of our datasets is demonstrated by visualizing the geometries distribution with dimensionality reduction as well as via comparison of statistical features of the QM properties with those available in existing datasets. Our sampling targets broader quantum mechanical distribution of the configurational space than provided by commonly used sampling through classical molecular dynamics, upping the challenge for machine learning models.
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Affiliation(s)
- Max Pinheiro
- Aix Marseille University, CNRS, ICR, Marseille, France.
| | - Shuang Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille, France. .,Institut Universitaire de France, 75231, Paris, France.
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23
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Capone M, Sirohiwal A, Aschi M, Pantazis DA, Daidone I. Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II. Angew Chem Int Ed Engl 2023; 62:e202216276. [PMID: 36791234 DOI: 10.1002/anie.202216276] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.
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Affiliation(s)
- Matteo Capone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Present Address: Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
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24
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Pedraza-González L, Barneschi L, Marszałek M, Padula D, De Vico L, Olivucci M. Automated QM/MM Screening of Rhodopsin Variants with Enhanced Fluorescence. J Chem Theory Comput 2023; 19:293-310. [PMID: 36516450 DOI: 10.1021/acs.jctc.2c00928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a computational protocol for the fast and automated screening of excited-state hybrid quantum mechanics/molecular mechanics (QM/MM) models of rhodopsins to be used as fluorescent probes based on the automatic rhodopsin modeling protocol (a-ARM). Such "a-ARM fluorescence screening protocol" is implemented through a general Python-based driver, PyARM, that is also proposed here. The implementation and performance of the protocol are benchmarked using different sets of rhodopsin variants whose absorption and, more relevantly, emission spectra have been experimentally measured. We show that, despite important limitations that make unsafe to use it as a black-box tool, the protocol reproduces the observed trends in fluorescence and it is capable of selecting novel potentially fluorescent rhodopsins. We also show that the protocol can be used in mechanistic investigations to discern fluorescence enhancement effects associated with a near degeneracy of the S1/S2 states or, alternatively, with a barrier generated via coupling of the S0/S1 wave functions.
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Leonardo Barneschi
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Michał Marszałek
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiaǹskiego 27, 50-370 Wrocław, Poland
| | - Daniele Padula
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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25
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Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020505. [PMID: 36677562 PMCID: PMC9863226 DOI: 10.3390/molecules28020505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang, responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the charge-transfer excited-state potential energy surface in the ON-state to locate minimum energy conical intersection points with the ground-state energy surface. Simulations of the further evolution of model systems allow us to characterize the ground-state reaction intermediate tentatively suggested in the femtosecond studies of the light-induced dynamics in Dreiklang and finally to arrive at the reaction product. The obtained results clarify the details of the photoswitching mechanism in Dreiklang, which is governed by the chemical modification of its chromophore.
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26
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Boeije Y, Olivucci M. From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chem Soc Rev 2023; 52:2643-2687. [PMID: 36970950 DOI: 10.1039/d2cs00719c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.
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Affiliation(s)
- Yorrick Boeije
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Massimo Olivucci
- Chemistry Department, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, USA
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27
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Rao AG, Schapiro I. Photoisomerization of phytochrome chromophore models: an XMS-CASPT2 study. Phys Chem Chem Phys 2022; 24:29393-29405. [PMID: 36468544 DOI: 10.1039/d2cp04249e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phytochromes are a superfamily of photoreceptors that harbor linear tetrapyrroles as chromophores. Upon light illumination, the linear tetrapyrrole chromophore undergoes a double bond isomerization which starts a photocycle. In this work, we studied the photoisomerization of chromophore models designed based on the C- and D-rings of the phycocyanobilin (PCB) chromophore. In total, five different models with varying substitutions were investigated. Firstly, the vertical excitation energies were benchmarked using different computational methods to establish the relative order of the excited states. Based on these calculations, we computed the photoisomerization profiles using the extended multi-state (XMS) version of the CASPT2 method. The profiles were obtained for both the clockwise and counterclockwise rotations of the C15C16 bond in the Z and E isomers using a linear interpolation of internal coordinates between the Franck-Condon and MECI geometries. In the minimal chromophore model that lacks the substitutions at the pyrrole rings, the isomerization involves both C14-C15 and C15C16 bonds of the methine bridge between the C- and D-rings, resembling the hula-twist motion. The MECIs are characterized by a partial charge transfer between the two pyrrole rings pointing towards a twisted intramolecular charge transfer. Systematic introduction of substituents leads to an increase in the steric repulsion between the two pyrrole rings causing a pretwist of the dihedral around the C15C16 bond, which creates a preference for the counterclockwise isomerization. An introduction of the carbonyl group at the D-ring increases the extent of charge transfer which changes the isomerization mechanism from hula-twist to one-bond flip.
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Affiliation(s)
- Aditya G Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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28
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Dutta Choudhury S. Multiple Effects of an Anionic Cyclodextrin Macrocycle on the Reversible Isomerization of a Photoactive Guest Dye. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14819-14826. [PMID: 36398364 DOI: 10.1021/acs.langmuir.2c02470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding and controlling the reversible isomerization of photoactive molecules in order to obtain a tunable optical response is desirable for many photofunctional applications. This study describes the interesting effects of an anionic cyclodextrin host (sulfated-βCD, SCD) on the photoisomerization and protonation equilibrium of an important hemicyanine dye (trans-4-[4-(dimethylamino)styryl]-1-methylpyridinium iodide, DSP). The SCD host assists in unlocking the photoisomerization potential of DSP by promoting protonation of the dye. It also assists in stabilizing the cis isomer of the protonated dye, thereby significantly delaying the reverse cis to trans isomerization of DSPH+. Furthermore, the interplay of both hydrophobic and electrostatic interactions in the complex formation of SCD with DSPH+ makes the reverse cis to trans isomerization of DSPH+ amenable to influence by the added salt. The stimuli-responsive reversible isomerization of SCD-DSPH+ is an interesting case from the perspective of chemical sensing or light operated functional materials with host-guest systems.
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Affiliation(s)
- Sharmistha Dutta Choudhury
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai400 085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai400094, India
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29
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Weik M, Domratcheva T. Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations. Curr Opin Struct Biol 2022; 77:102496. [PMID: 36462226 DOI: 10.1016/j.sbi.2022.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 12/03/2022]
Abstract
The structural dynamics underlying molecular mechanisms of light-sensitive proteins can be studied by a variety of experimental and computational biophysical techniques. Here we review recent progress in combining time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations to study structural changes in photoenzymes, photosynthetic proteins, photoreceptors, and photoswitchable fluorescent proteins following photoexcitation.
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Affiliation(s)
- Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia; Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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30
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Marchetti L, Nifosì R, Martelli PL, Da Pozzo E, Cappello V, Banterle F, Trincavelli ML, Martini C, D’Elia M. Quantum computing algorithms: getting closer to critical problems in computational biology. Brief Bioinform 2022; 23:6758194. [PMID: 36220772 PMCID: PMC9677474 DOI: 10.1093/bib/bbac437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
The recent biotechnological progress has allowed life scientists and physicians to access an unprecedented, massive amount of data at all levels (molecular, supramolecular, cellular and so on) of biological complexity. So far, mostly classical computational efforts have been dedicated to the simulation, prediction or de novo design of biomolecules, in order to improve the understanding of their function or to develop novel therapeutics. At a higher level of complexity, the progress of omics disciplines (genomics, transcriptomics, proteomics and metabolomics) has prompted researchers to develop informatics means to describe and annotate new biomolecules identified with a resolution down to the single cell, but also with a high-throughput speed. Machine learning approaches have been implemented to both the modelling studies and the handling of biomedical data. Quantum computing (QC) approaches hold the promise to resolve, speed up or refine the analysis of a wide range of these computational problems. Here, we review and comment on recently developed QC algorithms for biocomputing, with a particular focus on multi-scale modelling and genomic analyses. Indeed, differently from other computational approaches such as protein structure prediction, these problems have been shown to be adequately mapped onto quantum architectures, the main limit for their immediate use being the number of qubits and decoherence effects in the available quantum machines. Possible advantages over the classical counterparts are highlighted, along with a description of some hybrid classical/quantum approaches, which could be the closest to be realistically applied in biocomputation.
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Affiliation(s)
| | | | - Pier Luigi Martelli
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Eleonora Da Pozzo
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Valentina Cappello
- Italian Institute of Technology, Center for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | | | | | - Claudia Martini
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Massimo D’Elia
- University of Pisa, Department of Physics, Largo Bruno Pontecorvo 3, 56127, Pisa Italy
- INFN, Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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31
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Protein control of photochemistry and transient intermediates in phytochromes. Nat Commun 2022; 13:6838. [PMID: 36369284 PMCID: PMC9652276 DOI: 10.1038/s41467-022-34640-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.
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32
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Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin. Nat Commun 2022; 13:6652. [PMID: 36333283 PMCID: PMC9636224 DOI: 10.1038/s41467-022-33953-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
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.
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33
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Filiba O, Borin VA, Schapiro I. The involvement of triplet states in the isomerization of retinaloids. Phys Chem Chem Phys 2022; 24:26223-26231. [PMID: 36278932 DOI: 10.1039/d2cp03791b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm-1) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm-1 was found for the aldehyde form, followed by 15 cm-1 for the deprotonated Schiff base.
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Affiliation(s)
- Ofer Filiba
- Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
| | - Veniamin A Borin
- Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
| | - Igor Schapiro
- Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
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34
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Li G, Hu Y, Pei S, Meng J, Wang J, Wang J, Yue S, Wang Z, Wang S, Liu X, Weng Y, Peng X, Zhao Q. Excited-state dynamics of all-trans protonated retinal Schiff base in CRABPII-based rhodopsin mimics. Biophys J 2022; 121:4109-4118. [PMID: 36181266 PMCID: PMC9675042 DOI: 10.1016/j.bpj.2022.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/06/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
The rhodopsin mimic is a chemically synthetized complex with retinyl Schiff base (RSB) formed between protein and the retinal chromophore that can mimic the natural rhodopsin-like protein. The artificial rhodopsin mimic is more stable and designable than the natural protein and hence has wider uses in photon detection devices. The mimic structure RSB, like the case in the actual rhodopsin-like protein, undergoes isomerization and protonation throughout the photoreaction process. As a result, understanding the dynamics of the RSB in the photoreaction process is critical. In this study, the ultrafast transient absorption spectra of three mutants of the cellular retinoic acid-binding protein II-based rhodopsin mimic at acidic environment were recorded, from which the related excited-state dynamics of the all-trans protonated RSB (AT-PRSB) were investigated. The transient fluorescence spectra measurements are used to validate some of the dynamic features. We find that the excited-state dynamics of AT-PRSB in three mutants share a similar pattern that differs significantly from the dynamics of 15-cis PRSB of the rhodopsin mimic in neutral solution. By comparing the dynamics across the three mutants, we discovered that the aromatic residues near the β-ionone ring structure of the retinal may help stabilize the AT-PRSB and hence slow down its isomerization rate. The experimental results provide implications on designing a rhodopsin-like protein with significant infrared fluorescence, which can be particularly useful in the applications in biosensing or bioimaging in deeper tissues.
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Affiliation(s)
- Gaoshang Li
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Yongnan Hu
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Sizhu Pei
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Jiajia Meng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ju Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing, China
| | - Shuai Yue
- National Center for Nanoscience and Nanotechnology, Beijing, China
| | - Zhuan Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Shufeng Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing, China
| | - Xinfeng Liu
- National Center for Nanoscience and Nanotechnology, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuxiang Weng
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China; Beijing Academy of Quantum Information Sciences, Beijing, China.
| | - Qing Zhao
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China; Beijing Academy of Quantum Information Sciences, Beijing, China.
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35
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Abiola TT, Toldo JM, do Casal MT, Flourat AL, Rioux B, Woolley JM, Murdock D, Allais F, Barbatti M, Stavros VG. Direct structural observation of ultrafast photoisomerization dynamics in sinapate esters. Commun Chem 2022; 5:141. [PMID: 36697608 PMCID: PMC9814104 DOI: 10.1038/s42004-022-00757-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/13/2022] [Indexed: 01/27/2023] Open
Abstract
Sinapate esters have been extensively studied for their potential application in 'nature-inspired' photoprotection. There is general consensus that the relaxation mechanism of sinapate esters following photoexcitation with ultraviolet radiation is mediated by geometric isomerization. This has been largely inferred through indirect studies involving transient electronic absorption spectroscopy in conjunction with steady-state spectroscopies. However, to-date, there is no direct experimental evidence tracking the formation of the photoisomer in real-time. Using transient vibrational absorption spectroscopy, we report on the direct structural changes that occur upon photoexcitation, resulting in the photoisomer formation. Our mechanistic analysis predicts that, from the photoprepared ππ* state, internal conversion takes place through a conical intersection (CI) near the geometry of the initial isomer. Our calculations suggest that different CI topographies at relevant points on the seam of intersection may influence the isomerization yield. Altogether, we provide compelling evidence suggesting that a sinapate ester's geometric isomerization can be a more complex dynamical process than originally thought.
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Affiliation(s)
- Temitope T. Abiola
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Josene M. Toldo
- grid.462456.70000 0004 4902 8637Aix Marseille Université, CNRS, ICR, Marseille, France
| | - Mariana T. do Casal
- grid.462456.70000 0004 4902 8637Aix Marseille Université, CNRS, ICR, Marseille, France
| | - Amandine L. Flourat
- grid.417885.70000 0001 2185 8223URD Agro-Biotechnologies (ABI), CEBB, AgroParisTech, 51110 Pomacle, France
| | - Benjamin Rioux
- grid.417885.70000 0001 2185 8223URD Agro-Biotechnologies (ABI), CEBB, AgroParisTech, 51110 Pomacle, France
| | - Jack M. Woolley
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Daniel Murdock
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Florent Allais
- grid.417885.70000 0001 2185 8223URD Agro-Biotechnologies (ABI), CEBB, AgroParisTech, 51110 Pomacle, France
| | - Mario Barbatti
- grid.462456.70000 0004 4902 8637Aix Marseille Université, CNRS, ICR, Marseille, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, 75231 Paris, France
| | - Vasilios G. Stavros
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
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36
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Sugiura M, Ishikawa K, Katayama K, Sumii Y, Abe-Yoshizumi R, Tsunoda SP, Furutani Y, Shibata N, Brown LS, Kandori H. Unusual Photoisomerization Pathway in a Near-Infrared Light Absorbing Enzymerhodopsin. J Phys Chem Lett 2022; 13:9539-9543. [PMID: 36201035 DOI: 10.1021/acs.jpclett.2c02334] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbial and animal rhodopsins possess retinal chromophores which capture light and normally photoisomerize from all-trans to 13-cis and from 11-cis to all-trans-retinal, respectively. Here, we show that a near-infrared light-absorbing enzymerhodopsin from Obelidium mucronatum (OmNeoR) contains the all-trans form in the dark but isomerizes into the 7-cis form upon illumination. The photoproduct (λmax = 372 nm; P372) possesses a deprotonated Schiff base, and the system exhibits a bistable nature. The photochemistry of OmNeoR was arrested at <270 K, indicating the presence of a potential barrier in the excited state. Formation of P372 is accompanied by protonation changes of protonated carboxylic acids and peptide backbone changes of an α-helix. Photoisomerization from the all-trans to 7-cis retinal conformation rarely occurs in any solvent and protein environments; thus, the present study reports on a novel photochemistry mediated by a microbial rhodopsin, leading from the all-trans to 7-cis form selectively.
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Affiliation(s)
- Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kazuki Ishikawa
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Sumii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Norio Shibata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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37
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Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages. J Phys Chem A 2022; 126:6021-6031. [PMID: 36069531 DOI: 10.1021/acs.jpca.2c04671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations.
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Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States.,Division of Theoretical Chemistry and Biology, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Samuel McClung
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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38
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Malakar P, Das I, Bhattacharya S, Harris A, Sheves M, Brown LS, Ruhman S. Bidirectional Photochemistry of Antarctic Microbial Rhodopsin: Emerging Trend of Ballistic Photoisomerization from the 13- cis Resting State. J Phys Chem Lett 2022; 13:8134-8140. [PMID: 36000820 PMCID: PMC9442786 DOI: 10.1021/acs.jpclett.2c01974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The decades-long ultrafast examination of nearly a dozen microbial retinal proteins, ion pumps, and sensory photoreceptors has not identified structure-function indicators which predict photoisomerization dynamics, whether it will be sub-picosecond and ballistic or drawn out with complex curve-crossing kinetics. Herein, we report the emergence of such an indicator. Using pH control over retinal isomer ratios, photoinduced transient absorption is recorded in an inward proton pumping Antarctic microbial rhodopsin (AntR) for 13-cis and all-trans retinal resting states. The all-trans fluorescent state decays with 1 ps exponential kinetics. In contrast, in 13-cis it decays within ∼300 fs accompanied by continuous spectral evolution, indicating ballistic internal conversion. The coherent wave packet nature of 13-cis isomerization in AntR matches published results for bacteriorhodopsin (BR) and Anabaena sensory rhodopsin (ASR), which also accommodate both all-trans and 13-cis retinal resting states, marking the emergence of a first structure-photodynamics indicator which holds for all three tested pigments.
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Affiliation(s)
- Partha Malakar
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ishita Das
- Department
of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sudeshna Bhattacharya
- Department
of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Andrew Harris
- Department
of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Mordechai Sheves
- Department
of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Leonid S. Brown
- Department
of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Sanford Ruhman
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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39
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Bochenkova AV, Andersen LH. Action-Absorption Spectroscopy at the Band Origin of the Deprotonated Green Fluorescent Protein Chromophore In Vacuo. J Phys Chem Lett 2022; 13:6683-6685. [PMID: 35848550 DOI: 10.1021/acs.jpclett.2c01791] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The application of action spectroscopy in connection with determination of the S0 to S1 band origin in the GFP anion model chromophore (deprotonated HBDI) is discussed. We specifically address the consequences of the lowest vibrational levels in S1 being located behind a potential-energy barrier that inhibits internal conversion to the S0 electronic ground state. Action spectroscopy based on consecutive absorption of two photons together with internal conversion will as a consequence reveal an apparent band origin that is significantly blue-shifted.
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Affiliation(s)
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
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40
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Ren Z. Photoinduced isomerization sampling of retinal in bacteriorhodopsin. PNAS NEXUS 2022; 1:pgac103. [PMID: 35967979 PMCID: PMC9364214 DOI: 10.1093/pnasnexus/pgac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/28/2022] [Indexed: 02/06/2023]
Abstract
Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, nonvisual light effects, to bacterial light sensing and harvesting. Light-driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here, I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps, hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond together with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
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41
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
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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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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42
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Chuang C, Brumer P. Steady State Photoisomerization Quantum Yield of Model Rhodopsin: Insights from Wavepacket Dynamics? J Phys Chem Lett 2022; 13:4963-4970. [PMID: 35639452 DOI: 10.1021/acs.jpclett.2c01200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We simulate the nonequilibrium steady state cis-trans photoisomerization of retinal chromophore in rhodopsin on the basis of a two-state, two-mode model coupled to a thermal environment. By analyzing the systematic trends within an inhomogeneously broadened ensemble of systems, we find that the steady state reaction quantum yield (QY) correlates strongly with the excess energy above the crossing point of the system, in agreement with the prediction of the short-time dynamical wavepacket picture. However, the nontrivial dependence of the QY on the system-environment interaction indicates that a pure dynamical picture is insufficient and that environment-induced partial internal energy redistribution takes place before the reaction concludes. These results imply that a proper treatment of the photoisomerization reaction, particularly its high QY, must account for the redistribution and dissipation of energy beyond the dynamical wavepacket motion that is typically employed in the literature and that is appropriate only in the transient regime.
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Affiliation(s)
- Chern Chuang
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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43
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Tang L, Fang C. Photoswitchable Fluorescent Proteins: Mechanisms on Ultrafast Timescales. Int J Mol Sci 2022; 23:ijms23126459. [PMID: 35742900 PMCID: PMC9223536 DOI: 10.3390/ijms23126459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
The advancement of super-resolution imaging (SRI) relies on fluorescent proteins with novel photochromic properties. Using light, the reversibly switchable fluorescent proteins (RSFPs) can be converted between bright and dark states for many photocycles and their emergence has inspired the invention of advanced SRI techniques. The general photoswitching mechanism involves the chromophore cis-trans isomerization and proton transfer for negative and positive RSFPs and hydration-dehydration for decoupled RSFPs. However, a detailed understanding of these processes on ultrafast timescales (femtosecond to millisecond) is lacking, which fundamentally hinders the further development of RSFPs. In this review, we summarize the current progress of utilizing various ultrafast electronic and vibrational spectroscopies, and time-resolved crystallography in investigating the on/off photoswitching pathways of RSFPs. We show that significant insights have been gained for some well-studied proteins, but the real-time "action" details regarding the bidirectional cis-trans isomerization, proton transfer, and intermediate states remain unclear for most systems, and many other relevant proteins have not been studied yet. We expect this review to lay the foundation and inspire more ultrafast studies on existing and future engineered RSFPs. The gained mechanistic insights will accelerate the rational development of RSFPs with enhanced two-way switching rate and efficiency, better photostability, higher brightness, and redder emission colors.
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44
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Mališ M, Vandaele E, Luber S. Spin-Orbit Couplings for Nonadiabatic Molecular Dynamics at the ΔSCF Level. J Chem Theory Comput 2022; 18:4082-4094. [PMID: 35666703 DOI: 10.1021/acs.jctc.1c01046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A procedure for the calculation of spin-orbit coupling (SOC) at the delta self-consistent field (ΔSCF) level of theory is presented. Singlet and triplet excited electronic states obtained with the ΔSCF method are expanded into a linear combination of singly excited Slater determinants composed of ground electronic state Kohn-Sham orbitals. This alleviates the nonorthogonality between excited and ground electronic states and introduces a framework, similar to the auxiliary wave function at the time-dependent density functional theory (TD-DFT) level, for the calculation of observables. The ΔSCF observables of the formaldehyde system were compared to reference TD-DFT values. Our procedure gives all components (energies, gradients, nonadiabatic couplings, and SOC terms) at the ΔSCF level of theory for conducting efficient, full-atomistic nonadiabatic molecular dynamics with intersystem crossing, particularly in condensed phase systems.
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Affiliation(s)
- Momir Mališ
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Eva Vandaele
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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45
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Barbatti M. Defining the temperature of an isolated molecule. J Chem Phys 2022; 156:204304. [DOI: 10.1063/5.0090205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The microcanonical temperature of an isolated molecule is derived in terms of Boltzmann and Gibbs volume entropies within the quantum harmonic vibrational and equivalent degenerated model approximations. The effects of the entropy functional choice and various approximations are examined. The difference between Boltzmann and Gibbs volume temperatures is negligible for molecules bigger than ten atoms. However, it is significant for smaller systems, opening a way to probe them experimentally. A simple, analytical expression of the temperature as a function of the vibrational energy is provided, allowing predictions with a ±3% margin of error compared to the exact harmonic estimate. The microcanonical temperature is discussed and exemplified with polycyclic aromatic hydrocarbon molecules and other molecules of astrophysical interest.
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Affiliation(s)
- Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille, France and Institut Universitaire de France, 75231 Paris, France
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46
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Lee IS, Min SK. Generalized Formulation of the Density Functional Tight Binding-Based Restricted Ensemble Kohn-Sham Method with Onsite Correction to Long-Range Correction. J Chem Theory Comput 2022; 18:3391-3409. [PMID: 35549266 DOI: 10.1021/acs.jctc.2c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a generalized formulation for the combination of the density functional tight binding (DFTB) approach and the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method by considering onsite correction (OC) as well as the long-range corrected (LC) functional. The OC contribution provides more accurate energies and analytic gradients for individual microstates, while the multireference character of the SSR provides the correct description for conical intersections. We benchmark the LC-OC-DFTB/SSR method against various DFTB calculation methods for excitation energies and conical intersection structures with π/π* or n/π* characters. Furthermore, we perform excited-state molecular dynamics simulations with a molecular rotary motor with variations of LC-OC-DFTB/SSR approaches. We show that the OC contribution to the LC functional is crucial to obtain the correct geometry of conical intersections.
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Affiliation(s)
- In Seong Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, South Korea
| | - Seung Kyu Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, South Korea
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47
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Ha JK, Min SK. Independent Trajectory Mixed Quantum-Classical Approaches Based on the Exact Factorization. J Chem Phys 2022; 156:174109. [DOI: 10.1063/5.0084493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mixed quantum-classical dynamics based on the exact factorization exploits the "derived" electron-nuclear correlation (ENC) term aiming for the description of quantum coherences. The ENC contains interactions between the phase of electronic states and nuclear quantum momenta which depend on the spatial shape of the nuclear density.The original surface hopping based on the exact factorization (SHXF) [\textit{J. Phys. Chem. Lett.} \textbf{2018}, \textit{9}, 1097] exploits frozen Gaussian functions to construct the nuclear density in the ENC term while the phase of electronic states is approximated as a fictitious nuclear momentum change.However, in reality, the width of nuclear wave packets varies in time depending on the shape of potential energy surfaces.In this work, we present a modified SHXF approach and a newly-developed Ehrenfest dynamics based on the exact factorization (EhXF) with time-dependent Gaussian functions and phases by enforcing total energy conservation.We perform numerical tests for various one-dimensional two-state model Hamiltonians.Overall, the time-dependent width of Gaussian functions and the energy conserving phase show a reliable decoherence compared to the original frozen Gaussian-based SHXF and the exact quantum mechanical calculation.Especially, the energy conserving phase is crucial for EhXF to reproduce the correct quantum dynamics.
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Affiliation(s)
- Jong-Kwon Ha
- Chemistry, Ulsan National Institute of Science and Technology, Korea, Republic of (South Korea)
| | - Seung Kyu Min
- Ulsan National Institute of Science and Technology, Korea, Republic of (South Korea)
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48
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Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B 2022; 126:2647-2657. [PMID: 35357137 PMCID: PMC9014414 DOI: 10.1021/acs.jpcb.2c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of phytochromes
to act as photoswitches in plants and
microorganisms depends on interactions between a bilin-like chromophore
and a host protein. The interconversion occurs between the spectrally
distinct red (Pr) and far-red (Pfr) conformers. This conformational
change is triggered by the photoisomerization of the chromophore D-ring
pyrrole. In this study, as a representative example of a phytochrome-bilin
system, we consider biliverdin IXα (BV) bound to bacteriophytochrome
(BphP) from Deinococcus radiodurans. In the absence
of light, we use an enhanced sampling molecular dynamics (MD) method
to overcome the photoisomerization energy barrier. We find that the
calculated free energy (FE) barriers between essential metastable
states agree with spectroscopic results. We show that the enhanced
dynamics of the BV chromophore in BphP contributes to triggering nanometer-scale
conformational movements that propagate by two experimentally determined
signal transduction pathways. Most importantly, we describe how the
metastable states enable a thermal transition known as the dark reversion
between Pfr and Pr, through a previously unknown intermediate state
of Pfr. We present the heterogeneity of temperature-dependent Pfr
states at the atomistic level. This work paves a way toward understanding
the complete mechanism of the photoisomerization of a bilin-like chromophore
in phytochromes.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Katarzyna Walczewska-Szewc
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Sylwia Czach
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Krzysztof Kuczera
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States.,Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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Liang R, Bakhtiiari A. Effects of Enzyme-Ligand Interactions on the Photoisomerization of a Light-Regulated Chemotherapeutic Drug. J Phys Chem B 2022; 126:2382-2393. [PMID: 35297246 DOI: 10.1021/acs.jpcb.1c10819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular photoswitches permit using light to control protein activity with high spatiotemporal resolutions, thereby alleviating the side effects of conventional chemotherapy. However, due to the challenges in probing ultrafast photoisomerization reactions in biological environments, it remains elusive how the protein influences the photochemistry of the photoswitches, which hampers the rational design of light-regulated therapeutics. To overcome this challenge, we employed first-principles nonadiabatic dynamics simulations to characterize the photodynamics of the phototrexate (PTX), a recently developed photoswitchable anticancer chemotherapeutic that reversibly inhibits its target enzyme dihydrofolate reductase (DHFR). Our simulations show that the protein environment impedes the trans to cis photoisomerization of the PTX. The confinement in the ligand-binding cavity slows down the isomerization kinetics and quantum yield of the photoswitch by reshaping its conical intersection, increasing its excited-state free-energy barrier and quenching its local density fluctuations. Also, the protein environment results in a suboptimal binding mode of the photoproduct that needs to undergo large structural rearrangement to effectively inhibit the enzyme. Therefore, we predict that the PTX's trans → cis photoisomerization in solution precedes its binding with the protein, despite the favorable binding energy of the trans isomer. Our findings highlight the importance of the protein environment on the photochemical reactions of the molecular photoswitches. As such, our work represents an important step toward the rational design of light-regulated drugs in photopharmacology.
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Affiliation(s)
- Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Amirhossein Bakhtiiari
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency. Nat Chem 2022; 14:441-449. [PMID: 35241801 PMCID: PMC8983576 DOI: 10.1038/s41557-022-00892-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/12/2022] [Indexed: 01/12/2023]
Abstract
The activation of rhodopsin, the light-sensitive G-protein coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. Here, we use hundreds of quantum-classical trajectories to show that, 15 femtoseconds after light absorption, a degeneracy between the reactive excited state and a neighboring state causes the splitting of the rhodopsin population into subpopulations. These subpopulations propagate with different velocities and lead to distinct contributions to the quantum efficiency. We also show that such splitting is modulated by protein electrostatics, thus linking amino-acid sequence variations to quantum efficiency modulation. Finally, we discuss how such a linkage that in principle could be exploited to achieve higher quantum efficiencies, would simultaneously increase the receptor thermal noise leading to a trade-off that may have played a role in rhodopsin evolution.
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