1
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Wijayaratna D, Sacchetta F, Pedraza-González L, Fanelli F, Sugihara T, Koyanagi M, Piyawardana S, Ghotra K, Thotamune W, Terakita A, Olivucci M, Karunarathne A. In-silico predicted mouse melanopsins with blue spectral shifts deliver efficient subcellular signaling. Cell Commun Signal 2024; 22:394. [PMID: 39118111 PMCID: PMC11312219 DOI: 10.1186/s12964-024-01753-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Melanopsin is a photopigment belonging to the G Protein-Coupled Receptor (GPCR) family expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) and responsible for a variety of processes. The bistability and, thus, the possibility to function under low retinal availability would make melanopsin a powerful optogenetic tool. Here, we aim to utilize mouse melanopsin to trigger macrophage migration by its subcellular optical activation with localized blue light, while simultaneously imaging the migration with red light. To reduce melanopsin's red light sensitivity, we employ a combination of in silico structure prediction and automated quantum mechanics/molecular mechanics modeling to predict minimally invasive mutations to shift its absorption spectrum towards the shorter wavelength region of the visible spectrum without compromising the signaling efficiency. The results demonstrate that it is possible to achieve melanopsin mutants that resist red light-induced activation but are activated by blue light and display properties indicating preserved bistability. Using the A333T mutant, we show that the blue light-induced subcellular melanopsin activation triggers localized PIP3 generation and macrophage migration, which we imaged using red light, demonstrating the optogenetic utility of minimally engineered melanopsins.
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Affiliation(s)
| | - Filippo Sacchetta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Francesca Fanelli
- Department of Life Sciences, Dulbecco Telethon Institute, University of Modena and Reggio Emilia, Modena, I-41125, Italy
| | - Tomohiro Sugihara
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Mitsumasa Koyanagi
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Senuri Piyawardana
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Kiran Ghotra
- Department of Biology, Siena Heights University, Adrian, MI, 49221, USA
| | - Waruna Thotamune
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Akihisa Terakita
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Ajith Karunarathne
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA.
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2
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Wijesiri K, Gascón JA. Structural Models of the First Molecular Events in the Heliorhodopsin Photocycle. J Phys Chem B 2024; 128:5966-5972. [PMID: 38877606 DOI: 10.1021/acs.jpcb.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Retinylidene conformations and rearrangements of the hydrogen-bond network in the vicinity of the protonated Schiff base (PSB) play a key role in the proton transfer process in the Heliorhodopsin photocycle. Photoisomerization of the retinylidene chromophore and the formation of photoproducts corresponding to the early intermediates were modeled using a combination of molecular dynamics simulations and quantum mechanical/molecular mechanics calculations. The resulting structures were refined, and the respective excitation energies were calculated. Aided by metadynamics simulations, we constructed a photoisomerized intermediate where the 13-cis retinylidene chromophore is rotated about a parallel pair of double bonds at C13=C14 and C15=NZ double bonds. We demonstrate how the deprotonation of the Schiff base and the concomitant protonation of the Glu107 counterion are only favored because of these rearrangements.
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Affiliation(s)
- Kithmini Wijesiri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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3
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Losantos R, Prampolini G, Monari A. A Portrait of the Chromophore as a Young System-Quantum-Derived Force Field Unraveling Solvent Reorganization upon Optical Excitation of Cyclocurcumin Derivatives. Molecules 2024; 29:1752. [PMID: 38675572 PMCID: PMC11052401 DOI: 10.3390/molecules29081752] [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: 02/01/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The study of fast non-equilibrium solvent relaxation in organic chromophores is still challenging for molecular modeling and simulation approaches, and is often overlooked, even in the case of non-adiabatic dynamics simulations. Yet, especially in the case of photoswitches, the interaction with the environment can strongly modulate the photophysical outcomes. To unravel such a delicate interplay, in the present contribution we resorted to a mixed quantum-classical approach, based on quantum mechanically derived force fields. The main task is to rationalize the solvent reorganization pathways in chromophores derived from cyclocurcumin, which are suitable for light-activated chemotherapy to destabilize cellular lipid membranes. The accurate and reliable decryption delivered by the quantum-derived force fields points to important differences in the solvent's reorganization, in terms of both structure and time scale evolution.
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Affiliation(s)
- Raúl Losantos
- Departamento de Química, Instituto de Investigación en Química (IQUR), Universidad de La Rioja, Madre de Dios 53, 26006 Logroño, Spain
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy;
| | - Antonio Monari
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
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4
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Kojima K, Yanagawa M, Imamoto Y, Yamano Y, Wada A, Shichida Y, Yamashita T. Convergent mechanism underlying the acquisition of vertebrate scotopic vision. J Biol Chem 2024; 300:107175. [PMID: 38499150 PMCID: PMC11007431 DOI: 10.1016/j.jbc.2024.107175] [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: 01/10/2024] [Revised: 03/10/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
High sensitivity of scotopic vision (vision in dim light conditions) is achieved by the rods' low background noise, which is attributed to a much lower thermal activation rate (kth) of rhodopsin compared with cone pigments. Frogs and nocturnal geckos uniquely possess atypical rods containing noncanonical cone pigments that exhibit low kth, mimicking rhodopsin. Here, we investigated the convergent mechanism underlying the low kth of rhodopsins and noncanonical cone pigments. Our biochemical analysis revealed that the kth of canonical cone pigments depends on their absorption maximum (λmax). However, rhodopsin and noncanonical cone pigments showed a substantially lower kth than predicted from the λmax dependency. Given that the λmax is inversely proportional to the activation energy of the pigments in the Hinshelwood distribution-based model, our findings suggest that rhodopsin and noncanonical cone pigments have convergently acquired low frequency of spontaneous-activation attempts, including thermal fluctuations of the protein moiety, in the molecular evolutionary processes from canonical cone pigments, which contributes to highly sensitive scotopic vision.
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Affiliation(s)
- Keiichi Kojima
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan; Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan; Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yumiko Yamano
- Comprehensive Education and Research Center, Kobe Pharmaceutical University, Kobe, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan; Research Organization for Science and Technology, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
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5
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O'Connor MS, Bragg ZT, Dearworth JR, Hendrickson HP. Quantum Mechanics/Molecular mechanics calculations predict A1, not A2, is present in melanopsin (Opn4m) of red-eared slider turtles (Trachemys scripta elegans). Vision Res 2023; 209:108245. [PMID: 37290221 DOI: 10.1016/j.visres.2023.108245] [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: 01/12/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 06/10/2023]
Abstract
Melanopsin is a photopigment that plays a role in non-visual, light-driven, cellular processes such as modulation of circadian rhythms, retinal vascular development, and the pupillary light reflex (PLR). In this study, computational methods were used to understand which chromophore is harbored by melanopsin in red-eared slider turtles (Trachemys scripta elegans). In mammals, the vitamin A derivative 11-cis-retinal (A1) is the chromophore, which provides functionality for melanopsin. However, in red-eared slider turtles, a member of the reptilian class, the identity of the chromophore remains unclear. Red-eared slider turtles, similar to other freshwater vertebrates, possess visual pigments that harbor a different vitamin A derivative, 11-cis-3,4-didehydroretinal (A2), making their pigments more sensitive to red-light than blue-light, therefore, suggesting the chromophore to be the A2 derivative instead of the A1. To help resolve the chromophore identity, in this work, computational homology models of melanopsin in red-eared slider turtles were first constructed. Next, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to compare how A1 and A2 derivatives bind to melanopsin. Time dependent density functional theory (TDDFT) calculations were then used to determine the excitation energy of the pigments. Lastly, calculated excitation energies were compared to experimental spectral sensitivity data from responses by the irises of red-eared sliders. Contrary to what was expected, our results suggest that melanopsin in red-eared slider turtles is more likely to harbor the A1 chromophore than the A2. Furthermore, a glutamine (Q622.56) and tyrosine (Y853.28) residue in the chromophore binding pocket are shown to play a role in the spectral tuning of the chromophore.
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Affiliation(s)
- Michael S O'Connor
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - Zoey T Bragg
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States
| | - James R Dearworth
- Department of Biology, Lafayette College, Easton, PA 18042, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, PA 18042, United States.
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6
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Zhang X, Liu L, Li W, Wang C, Wang J, Fang WH, Chen X. Extended Single-Electron Transfer Model and Dynamically Associated Energy Transfer Event in a Dual-Functional Catalyst System. JACS AU 2023; 3:1452-1463. [PMID: 37234115 PMCID: PMC10206599 DOI: 10.1021/jacsau.3c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Organic photocatalysis has been developed flourishingly to rely on bimolecular energy transfer (EnT) or oxidative/reductive electron transfer (ET), promoting a variety of synthetic transformations. However, there are rare examples to merge EnT and ET processes rationally within one chemical system, of which the mechanistic investigation still remains in its infancy. Herein, the first mechanistic illustration and kinetic assessments of the dynamically associated EnT and ET paths were conducted for realizing the C-H functionalization in a cascade photochemical transformation of isomerization and cyclization by using the dual-functional organic photocatalyst of riboflavin. An extended single-electron transfer model of transition-state-coupled dual-nonadiabatic crossings was explored to analyze the dynamic behaviors in the proton transfer-coupled cyclization. This can also be used to clarify the dynamic correlation with the EnT-driven E → Z photoisomerization that has been kinetically evaluated by using Fermi's golden rule with the Dexter model. The present computational results of electron structures and kinetic data contribute to a fundamental basis for understanding the photocatalytic mechanism of the combined operation of EnT and ET strategies, which will guide the design and manipulation for the implementation of multiple activation modes based on a single photosensitizer.
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Affiliation(s)
- Xiaorui Zhang
- Department
of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing 100875, China
| | - Lin Liu
- Department
of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing 100875, China
| | - Weijia Li
- Department
of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing 100875, China
| | - Chu Wang
- Department
of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing 100875, China
| | - Juanjuan Wang
- College
of Nuclear Science and Technology, Beijing
Normal University, Xin-wai-da-jie
No. 19, Beijing 100875, China
- Laboratory
of Beam Technology and Energy Materials, Advanced Institute of Natural
Science, Beijing Normal University, Zhuhai 519087, China
| | - Wei-Hai Fang
- Department
of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing 100875, China
| | - Xuebo Chen
- Department
of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing 100875, China
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7
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Barneschi L, Marsili E, Pedraza-González L, Padula D, De Vico L, Kaliakin D, Blanco-González A, Ferré N, Huix-Rotllant M, Filatov M, Olivucci M. On the fluorescence enhancement of arch neuronal optogenetic reporters. Nat Commun 2022; 13:6432. [PMID: 36307417 PMCID: PMC9616920 DOI: 10.1038/s41467-022-33993-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.
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Affiliation(s)
- Leonardo Barneschi
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Emanuele Marsili
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.8250.f0000 0000 8700 0572University of Durham, Department of Chemistry, South Road, Durham, DH1 3LE United Kingdom ,grid.5337.20000 0004 1936 7603Present Address: Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Laura Pedraza-González
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.5395.a0000 0004 1757 3729Present Address: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Daniele Padula
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Danil Kaliakin
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Alejandro Blanco-González
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Nicolas Ferré
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Miquel Huix-Rotllant
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Michael Filatov
- grid.258803.40000 0001 0661 1556Department of Chemistry, Kyungpook National University, Daegu, 702-701 South Korea
| | - Massimo Olivucci
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA ,grid.11843.3f0000 0001 2157 9291University of Strasbourg Institute for Advanced Studies, 5, alleé duGeń eŕ al Rouvillois, F-67083 Strasbourg, France
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8
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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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9
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Broser M. Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases. Front Mol Biosci 2022; 8:806922. [PMID: 35127823 PMCID: PMC8815786 DOI: 10.3389/fmolb.2021.806922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi show completely unexpected properties for microbial rhodopsins. These photoreceptors function exclusively as heterodimers, with the two subunits that have very different retinal chromophores. Among them is the bimodal photoswitchable Neorhodopsin (NeoR), which exhibits a near-infrared absorbing, highly fluorescent state. These are features that have never been described for any retinal photoreceptor. Here these properties are discussed in the context of color-tuning approaches of retinal chromophores, which have been extensively studied since the discovery of the first microbial rhodopsin, bacteriorhodopsin, in 1971 (Oesterhelt et al., Nature New Biology, 1971, 233 (39), 149-152). Further a brief review about the concept of heterodimerization is given, which is widely present in class III cyclases but is unknown for rhodopsins. NIR-sensitive retinal chromophores have greatly expanded our understanding of the spectral range of natural retinal photoreceptors and provide a novel perspective for the development of optogenetic tools.
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Affiliation(s)
- Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
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10
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Chatterjee G, Jha A, Blanco-Gonzalez A, Tiwari V, Manathunga M, Duan HG, Tellkamp F, Prokhorenko VI, Ferré N, Dasgupta J, Olivucci M, Miller RJD. Torsionally broken symmetry assists infrared excitation of biomimetic charge-coupled nuclear motions in the electronic ground state. Chem Sci 2022; 13:9392-9400. [PMID: 36093002 PMCID: PMC9384489 DOI: 10.1039/d2sc02133a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
The concerted interplay between reactive nuclear and electronic motions in molecules actuates chemistry. Here, we demonstrate that out-of-plane torsional deformation and vibrational excitation of stretching motions in the electronic ground...
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Affiliation(s)
- Gourab Chatterjee
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Ajay Jha
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | | | - Vandana Tiwari
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- Department of Chemistry, University of Hamburg Martin-Luther-King Platz 6 20146 Hamburg Germany
| | | | - Hong-Guang Duan
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Friedjof Tellkamp
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Valentyn I Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR 13013 Marseille France
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research Mumbai 400005 India
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University Bowling Green OH 43403 USA
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena I-53100 Siena Italy
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto 80 St. George Street Toronto M5S 3H6 Canada
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11
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Park JW. Analytical Gradient Theory for Resolvent-Fitted Second-Order Extended Multiconfiguration Perturbation Theory (XMCQDPT2). J Chem Theory Comput 2021; 17:6122-6133. [PMID: 34582217 DOI: 10.1021/acs.jctc.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We present the formulation and implementation of an analytical gradient algorithm for extended multiconfiguration quasidegenerate perturbation theory (XMCQDPT2) with the resolvent-fitting approximation by Granovsky. This algorithm is powerful when optimizing molecular configurations with a moderate-sized active space and many electronic states. First, we present the powerfulness and accuracy of resolvent-fitting approximations compared to canonical XMCQDPT2 theory. Then, we demonstrate the utility of the current algorithm in frequency analyses, optimizing the minimum energy conical intersection geometries of the retinal chromophore model RPSB6 and evaluating nuclear gradients when there are many electronic states. Furthermore, we parallelize the algorithm using the OpenMP/MPI hybrid approach. Additionally, we report the computational cost and parallel efficiency of the program.
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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12
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Matsika S. Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections. Chem Rev 2021; 121:9407-9449. [PMID: 34156838 DOI: 10.1021/acs.chemrev.1c00074] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.
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Affiliation(s)
- Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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13
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Nikolaev DM, Manathunga M, Orozco-Gonzalez Y, Shtyrov AA, Guerrero Martínez YO, Gozem S, Ryazantsev MN, Coutinho K, Canuto S, Olivucci M. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. J Chem Theory Comput 2021; 17:5885-5895. [PMID: 34379429 DOI: 10.1021/acs.jctc.1c00221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | | | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mikhail N Ryazantsev
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia.,Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy.,Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg-CNRS, UMR 7504, F-67034 Strasbourg, France
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14
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Pecourneau J, Losantos R, Monari A, Parant S, Pasc A, Mourer M. Synthesis and Photoswitching Properties of Bioinspired Dissymmetric γ-Pyrone, an Analogue of Cyclocurcumin. J Org Chem 2021; 86:8112-8126. [PMID: 34101450 DOI: 10.1021/acs.joc.1c00598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclocurcumin (CC), a turmeric curcuminoid with potential therapeutic properties, is also a natural photoswitch that may undergo E/Z photoisomerization under UV light. To be further exploited in relevant biological applications, photoactivation under near-infrared (NIR) irradiation is required. Such requirement can be met through opportune chemical modifications, by favoring two-photon absorption (TPA) probability. Herein, a general and efficient synthesis of a biomimetic 2,6-disubstituted-γ-pyrone analogue of CC is described, motivated by the fact that molecular modeling previews an order of magnitude increase of its NIR TPA compared to CC. Three retrosynthetic pathways have been identified (i) via an aryl-oxazole intermediate or via aryl-diynone through (ii) a bottom-up or (iii) a top-down approach. While avoiding the passage through unstable synthons or low-yield intermediate reactions, only the latest approach could conveniently afford the 2,6-disubstituted-γ-pyrone analogue of CC, in ten steps and with an overall yield of 18%. The photophysical properties of our biomimetic analogue have also been characterized showing an improved photoisomerization yield over the parent natural compound. The potentially improved nonlinear optical properties, as well as enhanced stability, may be correlated to the enforcement of the planarity of the pyrone moiety leading to a quadrupolar D-π-A-π-D system.
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Affiliation(s)
- Jérémy Pecourneau
- Université de Lorraine, CNRS, L2CM UMR 7053, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France
| | - Raúl Losantos
- Université de Lorraine, CNRS, L2CM UMR 7053, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France.,Université de Lorraine, CNRS, LPCT UMR 7019, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France
| | - Stéphane Parant
- Université de Lorraine, CNRS, L2CM UMR 7053, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France
| | - Andreea Pasc
- Université de Lorraine, CNRS, L2CM UMR 7053, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France
| | - Maxime Mourer
- Université de Lorraine, CNRS, L2CM UMR 7053, Bvd des Aiguillettes, F-54506 Vandœuvre-lès-Nancy, France
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15
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Hanai S, Katayama K, Imai H, Kandori H. Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K. Biophys Physicobiol 2021; 18:40-49. [PMID: 33954081 PMCID: PMC8049776 DOI: 10.2142/biophysico.bppb-v18.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/01/2022] Open
Abstract
Structural studies of color visual pigments lag far behind those of rhodopsin for scotopic vision. Using difference FTIR spectroscopy at 77 K, we report the first structural data of three primate color visual pigments, monkey red (MR), green (MG), and blue (MB), where the batho-intermediate (Batho) exhibits photoequilibrium with the unphotolyzed state. This photochromic property is highly advantageous for limited samples since the signal-to-noise ratio is improved, but may not be applicable to late intermediates, because of large structural changes to proteins. Here we report the photochromic property of MB at 163 K, where the BL intermediate, formed by the relaxation of Batho, is in photoequilibrium with the initial MB state. A comparison of the difference FTIR spectra at 77 and 163 K provided information on what happens in the process of transition from Batho to BL in MB. The coupled C11=C12 HOOP vibration in the planer structure in MB is decoupled by distortion in Batho after retinal photoisomerization, but returns to the coupled C11=C12 HOOP vibration in the all-trans chromophore in BL. The Batho formation accompanies helical structural perturbation, which is relaxed in BL. Protein-bound water molecules that form an extended water cluster near the retinal chromophore change hydrogen bonds differently for Batho and BL, being stronger in the latter than in the initial state. In addition to structural dynamics, the present FTIR spectra show no signals of protonated carboxylic acids at 77 and 163 K, suggesting that E181 is deprotonated in MB, Batho and BL.
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Affiliation(s)
- Shunpei Hanai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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16
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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17
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Giuliani G, Melaccio F, Gozem S, Cappelli A, Olivucci M. QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase. J Chem Theory Comput 2021; 17:605-613. [PMID: 33449693 PMCID: PMC9220819 DOI: 10.1021/acs.jctc.0c01078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employ replica-exchange molecular dynamics (REMD) and a hybrid ab initio multiconfigurational quantum mechanics/molecular mechanics (QM/MM) approach to model the absorption and fluorescence properties of bacterial luciferin-luciferase. Specifically, we employ complete active space perturbation theory (CASPT2) and study the effect of active space, basis set, and IPEA shift on the computed energies. We discuss the effect of the protein environment on the fluorophore's excited-state potential energy surface and the role that the protein plays in enhancing the fluorescence quantum yield in bacterial bioluminescence.
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Affiliation(s)
- Germano Giuliani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federico Melaccio
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Andrea Cappelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowing Green, Ohio 43403, United States
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18
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Accelerated evolution and positive selection of rhodopsin in Tibetan loaches living in high altitude. Int J Biol Macromol 2020; 165:2598-2606. [PMID: 33470199 DOI: 10.1016/j.ijbiomac.2020.10.151] [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: 07/31/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 11/22/2022]
Abstract
Rhodopsin (RH1), the temperature-sensitive visual pigment, attained cold adaptation by functional trade-offs between protein stability and activity. Recent studies suggested convergent selection pressures drove cold adaptation of rhodopsin in high altitude catfishes through nonparallel molecular mechanisms. Here, we tested whether the similar shift occurred in RH1 of Tibetan loaches on the Qinghai-Tibet Plateau (QTP) by investigating the molecular evolution and potential effect on function of RH1. We sequenced RH1 from 27 Triplophysa species, and four lowland loaches and combined these data with published sequences. Tests using a series of models of molecular evolution resulted in strong evidence for accelerated evolution and positive selection in Triplophysa RH1. Three positively selected sites were near key functional domains modulating nonspectral properties of rhodopsin, substitutions of which were likely to compensate for cold-induced decrease in rhodopsin kinetics in cold environments. Moreover, although accelerated evolutionary rates in Tibetan loaches was convergent with those in high altitude catfishes, the sites under positive selection were nonoverlapping. Our findings provide evidence for convergent shift in selection pressures of RH1 in high altitude fish during the ecological transition to cold environment of the QTP.
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19
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Chrayteh A, Blondel A, Loos PF, Jacquemin D. Mountaineering Strategy to Excited States: Highly Accurate Oscillator Strengths and Dipole Moments of Small Molecules. J Chem Theory Comput 2020; 17:416-438. [DOI: 10.1021/acs.jctc.0c01111] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Amara Chrayteh
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Aymeric Blondel
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Denis Jacquemin
- Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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20
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Kandori H. Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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21
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Romei MG, Lin CY, Mathews II, Boxer SG. Electrostatic control of photoisomerization pathways in proteins. Science 2020; 367:76-79. [PMID: 31896714 DOI: 10.1126/science.aax1898] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/04/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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22
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Pedraza-González L, Marín MDC, Jorge AN, Ruck TD, Yang X, Valentini A, Olivucci M, De Vico L. Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins. J Chem Inf Model 2020; 60:1481-1493. [PMID: 31909998 PMCID: PMC7101466 DOI: 10.1021/acs.jcim.9b00615] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article introduces Web-ARM, a specialized tool, online available, designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows the rapidly building of models of rhodopsins with a documented quality and the prediction of trends in UV-vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152] and, as such, necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.
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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
| | - María Del Carmen Marín
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Alejandro N Jorge
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Tyler D Ruck
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Université de Liège, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - 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 of America
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
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23
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Gromov EV, Domratcheva T. Four resonance structures elucidate double-bond isomerisation of a biological chromophore. Phys Chem Chem Phys 2020; 22:8535-8544. [DOI: 10.1039/d0cp00814a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Four resonance structures determining the electronic structure of the chromophore’s ground and first excited states. Changing the relative energies of the structures by hydrogen-bonding interactions tunes all chromophore’s photochemical properties.
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Affiliation(s)
- Evgeniy V. Gromov
- Max-Planck Institute for Medical Research
- Jahnstraße 29
- 69120 Heidelberg
- Germany
| | - Tatiana Domratcheva
- Max-Planck Institute for Medical Research
- Jahnstraße 29
- 69120 Heidelberg
- Germany
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24
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Park JW. Analytical Gradient Theory for Quasidegenerate N-Electron Valence State Perturbation Theory (QD-NEVPT2). J Chem Theory Comput 2019; 16:326-339. [DOI: 10.1021/acs.jctc.9b00919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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25
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Katti C, Stacey-Solis M, Coronel-Rojas NA, Davies WIL. The Diversity and Adaptive Evolution of Visual Photopigments in Reptiles. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00352] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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26
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Misra R, Hirshfeld A, Sheves M. Molecular mechanism for thermal denaturation of thermophilic rhodopsin. Chem Sci 2019; 10:7365-7374. [PMID: 31489158 PMCID: PMC6713869 DOI: 10.1039/c9sc00855a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding the factors affecting the stability and function of proteins at the molecular level is of fundamental importance. In spite of their use in bioelectronics and optogenetics, factors influencing thermal stability of microbial rhodopsins, a class of photoreceptor protein ubiquitous in nature are not yet well-understood. Here we report on the molecular mechanism for thermal denaturation of microbial retinal proteins, including, a highly thermostable protein, thermophilic rhodopsin (TR). External stimuli-dependent thermal denaturation of TR, the proton pumping rhodopsin of Thermus thermophilus bacterium, and other microbial rhodopsins are spectroscopically studied to decipher the common factors guiding their thermal stability. The thermal denaturation process of the studied proteins is light-catalyzed and the apo-protein is thermally less stable than the corresponding retinal-covalently bound opsin. In addition, changes in structure of the retinal chromophore affect the thermal stability of TR. Our results indicate that the hydrolysis of the retinal protonated Schiff base (PSB) is the rate-determining step for denaturation of the TR as well as other retinal proteins. Unusually high thermal stability of TR multilayers, in which PSB hydrolysis is restricted due to lack of bulk water, strongly supports this proposal. Our results also show that the protonation state of the PSB counter-ion does not affect the thermal stability of the studied proteins. Thermal photo-bleaching of an artificial TR pigment derived from non-isomerizable trans-locked retinal suggests, rather counterintuitively, that the photoinduced retinal trans-cis isomerization is not a pre-requisite for light catalyzed thermal denaturation of TR. Protein conformation alteration triggered by light-induced retinal excited state formation is likely to facilitate the PSB hydrolysis.
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Affiliation(s)
- Ramprasad Misra
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
| | - Amiram Hirshfeld
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
| | - Mordechai Sheves
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel .
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27
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Park JW. Single-State Single-Reference and Multistate Multireference Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections. J Chem Theory Comput 2019; 15:3960-3973. [DOI: 10.1021/acs.jctc.9b00067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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28
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Valentini A, Nucci M, Frutos LM, Marazzi M. Photosensitized Retinal Isomerization in Rhodopsin Mediated by a Triplet State. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alessio Valentini
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena via A. Moro 2 53100 Siena Italy
- Theoretical Physical Chemistry, Research Unit MolSysUniversité de Liège Allée du 6 Aôut, 11 4000 Liège Belgium
| | - Martina Nucci
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
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29
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Red-shifting mutation of light-driven sodium-pump rhodopsin. Nat Commun 2019; 10:1993. [PMID: 31040285 PMCID: PMC6491443 DOI: 10.1038/s41467-019-10000-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/12/2019] [Indexed: 11/08/2022] Open
Abstract
Microbial rhodopsins are photoreceptive membrane proteins that transport various ions using light energy. While they are widely used in optogenetics to optically control neuronal activity, rhodopsins that function with longer-wavelength light are highly demanded because of their low phototoxicity and high tissue penetration. Here, we achieve a 40-nm red-shift in the absorption wavelength of a sodium-pump rhodopsin (KR2) by altering dipole moment of residues around the retinal chromophore (KR2 P219T/S254A) without impairing its ion-transport activity. Structural differences in the chromophore of the red-shifted protein from that of the wildtype are observed by Fourier transform infrared spectroscopy. QM/MM models generated with an automated protocol show that the changes in the electrostatic interaction between protein and chromophore induced by the amino-acid replacements, lowered the energy gap between the ground and the first electronically excited state. Based on these insights, a natural sodium pump with red-shifted absorption is identified from Jannaschia seosinensis. Microbial rhodopsins are photoreceptive and widely used in optogenetics for which they should preferable function with longer-wavelength light. Here, authors achieve a 40-nm red-shift in the absorption wavelength of a sodium-pump rhodopsin (KR2) by altering the distribution of the retinal chromophore.
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30
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Govardovskii VI, Astakhova LA, Rotov AY, Firsov ML. Rejection of the biophoton hypothesis on the origin of photoreceptor dark noise. J Gen Physiol 2019; 151:887-897. [PMID: 30992369 PMCID: PMC6605685 DOI: 10.1085/jgp.201812317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/29/2019] [Indexed: 12/13/2022] Open
Abstract
It has been suggested that retinal “dark light” is caused by photons emitted by the retina itself. The authors show that the “biophoton” radiation from the retina can be detected, but its intensity is ≥100 times lower than necessary to produce the measured physiological noise understood to arise from the spontaneous activation of rhodopsin. Rod photoreceptors of the vertebrate retina produce, in darkness, spontaneous discrete current waves virtually identical to responses to single photons. The waves comprise an irreducible source of noise (discrete dark noise) that may limit the threshold sensitivity of vision. The waves obviously originate from acts of random activation of single rhodopsin molecules. Until recently, it was generally accepted that the activation occurs due to the rhodopsin thermal motion. Yet, a few years ago it was proposed that rhodopsin molecules are activated not by heat but rather by real photons generated within the retina by chemiluminescence. Using a high-sensitive photomultiplier, we measured intensities of biophoton emission from isolated retinas and eyecups of frogs (Rana ridibunda) and fish (sterlet, Acipenser ruthenus). Retinal samples were placed in a perfusion chamber and emitted photons collected by a high-aperture quartz lens. The collected light was sent to the photomultiplier cathode through a rotating chopper so that a long-lasting synchronous accumulation of the light signal was possible. The absolute intensity of bio-emission was estimated by the response of the measuring system to a calibrated light source. The intensity of the source, in turn, was quantified by measuring rhodopsin bleaching with single-rod microspectrophotometry. We also measured the frequency of discrete dark waves in rods of the two species with suction pipette recordings. Expressed as the rate constant of rhodopsin activation, it was 1.2 × 10−11/s in frogs and 7.6 × 10−11/s in sterlets. Approximately two thirds of retinal samples of each species produced reliably measurable biophoton emissions. However, its intensity was ≥100 times lower than necessary to produce the discrete dark noise. We argue that this is just a lower estimate of the discrepancy between the hypothesis and experiment. We conclude that the biophoton hypothesis on the origin of discrete dark noise in photoreceptors must be rejected.
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Affiliation(s)
- Victor I Govardovskii
- Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Science, St. Petersburg, Russia
| | - Luba A Astakhova
- Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Science, St. Petersburg, Russia
| | - Alexander Yu Rotov
- Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Science, St. Petersburg, Russia
| | - Michael L Firsov
- Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Science, St. Petersburg, Russia
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31
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Schott RK, Van Nynatten A, Card DC, Castoe TA, S W Chang B. Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry. Mol Biol Evol 2019; 35:1376-1389. [PMID: 29800394 DOI: 10.1093/molbev/msy025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole-genome and targeted capture sequencing data. We used these data to analyze gene loss and shifts in selection pressures in phototransduction genes that may be associated with snake evolutionary origins and photoreceptor transmutation. We identified the surprising loss of rhodopsin kinase (GRK1), despite a low degree of gene loss overall and a lack of relaxed selection early during snake evolution. These results provide some of the first evolutionary genomic corroboration for a dim-light ancestor that lacks strong fossorial adaptations. Our results also indicate that snakes with photoreceptor transmutation experienced significantly different selection pressures from other reptiles. Significant positive selection was found primarily in cone-specific genes, but not rod-specific genes, contrary to our expectations. These results reveal potential molecular adaptations associated with photoreceptor transmutation and also highlight unappreciated functional differences between rod- and cone-specific phototransduction proteins. This intriguing example of snake visual system evolution illustrates how the underlying molecular components of a complex system can be reshaped in response to changing selection pressures.
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Affiliation(s)
- Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | | | - Daren C Card
- Department of Biology, University of Texas, Arlington, TX
| | - Todd A Castoe
- Department of Biology, University of Texas, Arlington, TX
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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32
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Orozco-Gonzalez Y, Kabir MP, Gozem S. Electrostatic Spectral Tuning Maps for Biological Chromophores. J Phys Chem B 2019; 123:4813-4824. [DOI: 10.1021/acs.jpcb.9b00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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33
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Field GD, Uzzell V, Chichilnisky EJ, Rieke F. Temporal resolution of single-photon responses in primate rod photoreceptors and limits imposed by cellular noise. J Neurophysiol 2018; 121:255-268. [PMID: 30485153 DOI: 10.1152/jn.00683.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Sensory receptor noise corrupts sensory signals, contributing to imperfect perception and dictating central processing strategies. For example, noise in rod phototransduction limits our ability to detect light, and minimizing the impact of this noise requires precisely tuned nonlinear processing by the retina. But detection sensitivity is only one aspect of night vision: prompt and accurate behavior also requires that rods reliably encode the timing of photon arrivals. We show here that the temporal resolution of responses of primate rods is much finer than the duration of the light response and identify the key limiting sources of transduction noise. We also find that the thermal activation rate of rhodopsin is lower than previous estimates, implying that other noise sources are more important than previously appreciated. A model of rod single-photon responses reveals that the limiting noise relevant for behavior depends critically on how rod signals are pooled by downstream neurons. NEW & NOTEWORTHY Many studies have focused on the visual system's ability to detect photons, but not on its ability to encode the relative timing of detected photons. Timing is essential for computations such as determining the velocity of moving objects. Here we examine the timing precision of primate rod photoreceptor responses and show that it is more precise than previously appreciated. This motivates an evaluation of whether scotopic vision approaches limits imposed by rod temporal resolution.
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Affiliation(s)
- Greg D Field
- Department of Neurobiology, Duke University School of Medicine , Durham, North Carolina
| | - Valerie Uzzell
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies , La Jolla, California
| | - E J Chichilnisky
- Stanford University, Departments of Neurosurgery and Ophthalmology , Stanford, California
| | - Fred Rieke
- Department of Physiology and Biophysics, University of Washington , Seattle, Washington
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34
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Castiglione GM, Chang BS. Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision. eLife 2018; 7:35957. [PMID: 30362942 PMCID: PMC6203435 DOI: 10.7554/elife.35957] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022] Open
Abstract
Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.
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Affiliation(s)
- Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Belinda Sw Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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35
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Sen S, Schapiro I. A comprehensive benchmark of the XMS-CASPT2 method for the photochemistry of a retinal chromophore model. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1501112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Saumik Sen
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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36
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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37
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Northwestern University , Evanston, IL, USA
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University , Evanston, IL, USA
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38
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Castiglione GM, Schott RK, Hauser FE, Chang BSW. Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms. Evolution 2018; 72:170-186. [DOI: 10.1111/evo.13396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/02/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Gianni M. Castiglione
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Ryan K. Schott
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Belinda S. W. Chang
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
- Centre for the Analysis of Genome Evolution and Function; University of Toronto; Toronto Ontario M5S 3B2 Canada
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39
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Orozco-Gonzalez Y, Manathunga M, Marín MDC, Agathangelou D, Jung KH, Melaccio F, Ferré N, Haacke S, Coutinho K, Canuto S, Olivucci M. An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. J Chem Theory Comput 2017; 13:6391-6404. [DOI: 10.1021/acs.jctc.7b00860] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoelvis Orozco-Gonzalez
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Madushanka Manathunga
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Damianos Agathangelou
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kwang-Hwan Jung
- Department
of Life Science and Institute of Biological Interfaces, Sogang University 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Massimo Olivucci
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
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40
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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41
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Demoulin B, Altavilla SF, Rivalta I, Garavelli M. Fine Tuning of Retinal Photoinduced Decay in Solution. J Phys Chem Lett 2017; 8:4407-4412. [PMID: 28853582 DOI: 10.1021/acs.jpclett.7b01780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single methylation at position C10 of the all-trans retinal protonated Schiff base switches its excited-state decay in methanol from a slower picosecond into an ultrafast, protein-like subpicosecond process. QM/MM modeling in conjunction with on-the-fly excited-state dynamics provides fundamental understanding of the fine-tuning mechanics that "catalyzes" the photoinduced decay of solvated retinals. Methylation alters the interplay between the ionic S1 and covalent S2 states, reducing the excited-state lifetime by favoring the formation of a S1 transient fluorescent state with fully inverted bond lengths that accounts for the recorded transient spectroscopy and from which a space-saving conical intersection seam is quickly (<1 ps) reached. Minimal and apparently innocent chemical modifications thus affect the characteristic intramolecular charge-transfer of the S1 state as well as the interaction with the covalent S2 excited state, eventually providing the high tunability of retinal photophysics and photochemistry and delivering a new concept for the rational design of retinal-based photoactive molecular devices.
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Affiliation(s)
- Baptiste Demoulin
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Salvatore Flavio Altavilla
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , V. F. Selmi 2, 40126 Bologna, Italy
| | - Ivan Rivalta
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Marco Garavelli
- Univ Lyon, ENS de Lyon , CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , V. F. Selmi 2, 40126 Bologna, Italy
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42
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Salari V, Scholkmann F, Vimal RLP, Császár N, Aslani M, Bókkon I. Phosphenes, retinal discrete dark noise, negative afterimages and retinogeniculate projections: A new explanatory framework based on endogenous ocular luminescence. Prog Retin Eye Res 2017; 60:101-119. [DOI: 10.1016/j.preteyeres.2017.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/13/2017] [Accepted: 07/15/2017] [Indexed: 02/07/2023]
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43
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Li J, Joubert-Doriol L, Izmaylov AF. Geometric phase effects in excited state dynamics through a conical intersection in large molecules: N-dimensional linear vibronic coupling model study. J Chem Phys 2017; 147:064106. [DOI: 10.1063/1.4985925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jiaru Li
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Loïc Joubert-Doriol
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Artur F. Izmaylov
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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44
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Abstract
High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.
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45
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Guo Y, Hendrickson HP, Videla PE, Chen YN, Ho J, Sekharan S, Batista VS, Tully JC, Yan ECY. Probing the remarkable thermal kinetics of visual rhodopsin with E181Q and S186A mutants. J Chem Phys 2017; 146:215104. [DOI: 10.1063/1.4984818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ying Guo
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Heidi P. Hendrickson
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Pablo E. Videla
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Ya-Na Chen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Junming Ho
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Sivakumar Sekharan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - John C. Tully
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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46
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Morrow JM, Castiglione GM, Dungan SZ, Tang PL, Bhattacharyya N, Hauser FE, Chang BSW. An experimental comparison of human and bovine rhodopsin provides insight into the molecular basis of retinal disease. FEBS Lett 2017; 591:1720-1731. [PMID: 28369862 DOI: 10.1002/1873-3468.12637] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/22/2017] [Accepted: 03/25/2017] [Indexed: 11/05/2022]
Abstract
Rhodopsin is the visual pigment that mediates dim-light vision in vertebrates and is a model system for the study of retinal disease. The majority of rhodopsin experiments are performed using bovine rhodopsin; however, recent evidence suggests that significant functional differences exist among mammalian rhodopsins. In this study, we identify differences in both thermal decay and light-activated retinal release rates between bovine and human rhodopsin and perform mutagenesis studies to highlight two clusters of substitutions that contribute to these differences. We also demonstrate that the retinitis pigmentosa-associated mutation G51A behaves differently in human rhodopsin compared to bovine rhodopsin and determine that the thermal decay rate of an ancestrally reconstructed mammalian rhodopsin displays an intermediate phenotype compared to the two extant pigments.
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Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | | | - Sarah Z Dungan
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Portia L Tang
- Department of Cell and Systems Biology, University of Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | | | - Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Canada
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47
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Lin CY, Both J, Do K, Boxer SG. Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs). Proc Natl Acad Sci U S A 2017; 114:E2146-E2155. [PMID: 28242710 PMCID: PMC5358378 DOI: 10.1073/pnas.1618087114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Split GFPs have been widely applied for monitoring protein-protein interactions by expressing GFPs as two or more constituent parts linked to separate proteins that only fluoresce on complementing with one another. Although this complementation is typically irreversible, it has been shown previously that light accelerates dissociation of a noncovalently attached β-strand from a circularly permuted split GFP, allowing the interaction to be reversible. Reversible complementation is desirable, but photodissociation has too low of an efficiency (quantum yield <1%) to be useful as an optogenetic tool. Understanding the physical origins of this low efficiency can provide strategies to improve it. We elucidated the mechanism of strand photodissociation by measuring the dependence of its rate on light intensity and point mutations. The results show that strand photodissociation is a two-step process involving light-activated cis-trans isomerization of the chromophore followed by light-independent strand dissociation. The dependence of the rate on temperature was then used to establish a potential energy surface (PES) diagram along the photodissociation reaction coordinate. The resulting energetics-function model reveals the rate-limiting process to be the transition from the electronic excited-state to the ground-state PES accompanying cis-trans isomerization. Comparisons between split GFPs and other photosensory proteins, like photoactive yellow protein and rhodopsin, provide potential strategies for improving the photodissociation quantum yield.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Johan Both
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Keunbong Do
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
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48
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Bauer CA, Hansen A, Grimme S. The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure. Chemistry 2017; 23:6150-6164. [DOI: 10.1002/chem.201604682] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn; Beringstr. 4 53115 Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn; Beringstr. 4 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry; Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn; Beringstr. 4 53115 Bonn Germany
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49
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Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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50
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Musbat L, Nihamkin M, Toker Y, Dilger JM, Fuller DR, El-Baba TJ, Clemmer DE, Sarkar S, Kronik L, Hirshfeld A, Friedman N, Sheves M. Measurements of the stabilities of isolated retinal chromophores. Phys Rev E 2017; 95:012406. [PMID: 28208402 DOI: 10.1103/physreve.95.012406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 06/06/2023]
Abstract
The barrier energies for isomerization and fragmentation were measured for a series of retinal chromophore derivatives using a tandem ion mobility spectrometry approach. These measurements allow us to quantify the effect of charge delocalization on the rigidity of chromophores. We find that the role of the methyl group on the C13 position is pivotal regarding the ground state dynamics of the chromophore. Additionally, a correlation between quasi-equilibrium isomer distribution and fragmentation pathways is observed.
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Affiliation(s)
- L Musbat
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - M Nihamkin
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Y Toker
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - J M Dilger
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, Indiana 47522, USA
| | - D R Fuller
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
| | - T J El-Baba
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
| | - D E Clemmer
- Department of Chemistry, Indiana University Bloomington, Indiana 47405, USA
| | - S Sarkar
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - L Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - A Hirshfeld
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - N Friedman
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - M Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
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