1
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Hong JD, Salom D, Choi EH, Du SW, Tworak A, Smidak R, Gao F, Solano YJ, Zhang J, Kiser PD, Palczewski K. Retinylidene chromophore hydrolysis from mammalian visual and non-visual opsins. J Biol Chem 2024; 300:105678. [PMID: 38272218 PMCID: PMC10877631 DOI: 10.1016/j.jbc.2024.105678] [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: 11/30/2023] [Revised: 01/06/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
Rhodopsin (Rho) and cone opsins are essential for detection of light. They respond via photoisomerization, converting their Schiff-base-adducted 11-cis-retinylidene chromophores to the all-trans configuration, eliciting conformational changes to activate opsin signaling. Subsequent Schiff-base hydrolysis releases all-trans-retinal, initiating two important cycles that maintain continuous vision-the Rho photocycle and visual cycle pathway. Schiff-base hydrolysis has been thoroughly studied with photoactivated Rho but not with cone opsins. Using established methodology, we directly measured the formation of Schiff-base between retinal chromophores with mammalian visual and nonvisual opsins of the eye. Next, we determined the rate of light-induced chromophore hydrolysis. We found that retinal hydrolysis from photoactivated cone opsins was markedly faster than from photoactivated Rho. Bovine retinal G protein-coupled receptor (bRGR) displayed rapid hydrolysis of its 11-cis-retinylidene photoproduct to quickly supply 11-cis-retinal and re-bind all-trans-retinal. Hydrolysis within bRGR in native retinal pigment epithelium microsomal membranes was >6-times faster than that of bRGR purified in detergent micelles. N-terminal-targeted antibodies significantly slowed bRGR hydrolysis, while C-terminal antibodies had no effect. Our study highlights the much faster photocycle of cone opsins relative to Rho and the crucial role of RGR in chromophore recycling in daylight. By contrast, in our experimental conditions, bovine peropsin did not form pigment in the presence of all-trans-retinal nor with any mono-cis retinal isomers, leaving uncertain the role of this opsin as a light sensor.
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Affiliation(s)
- John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA.
| | - Elliot H Choi
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Samuel W Du
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Roman Smidak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Fangyuan Gao
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Yasmeen J Solano
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Jianye Zhang
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA; Department of Clinical Pharmacy Practice, University of California Irvine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Chemistry, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA; Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA.
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2
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Greife P, Schönborn M, Capone M, Assunção R, Narzi D, Guidoni L, Dau H. The electron-proton bottleneck of photosynthetic oxygen evolution. Nature 2023; 617:623-628. [PMID: 37138082 DOI: 10.1038/s41586-023-06008-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today's oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S4 state-which was postulated half a century ago1 and remains largely uncharacterized. Here we resolve this key stage of photosynthetic O2 formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combining these results with computational chemistry reveals that a crucial proton vacancy is initally created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in a single-electron, multi-proton transfer event. This is the slowest step in photosynthetic O2 formation, with a moderate energetic barrier and marked entropic slowdown. We identify the S4 state as the oxygen-radical state; its formation is followed by fast O-O bonding and O2 release. In conjunction with previous breakthroughs in experimental and computational investigations, a compelling atomistic picture of photosynthetic O2 formation emerges. Our results provide insights into a biological process that is likely to have occurred unchanged for the past three billion years, which we expect to support the knowledge-based design of artificial water-splitting systems.
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Affiliation(s)
- Paul Greife
- Department of Physics, Freie Universität, Berlin, Germany
| | | | - Matteo Capone
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, L'Aquila, Italy
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Daniele Narzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Holger Dau
- Department of Physics, Freie Universität, Berlin, Germany.
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3
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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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4
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Nasrollahi-Shirazi S, Szöllösi D, Yang Q, Muratspahic E, El-Kasaby A, Sucic S, Stockner T, Nanoff C, Freissmuth M. Functional Impact of the G279S Substitution in the Adenosine A 1-Receptor (A 1R-G279S 7.44), a Mutation Associated with Parkinson's Disease. Mol Pharmacol 2020; 98:250-266. [PMID: 32817461 DOI: 10.1124/molpharm.120.000003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
In medium-size, spiny striatal neurons of the direct pathway, dopamine D1- and adenosine A1-receptors are coexpressed and are mutually antagonistic. Recently, a mutation in the gene encoding the A1-receptor (A1R), A1R-G279S7.44, was identified in an Iranian family: two affected offspring suffered from early-onset l-DOPA-responsive Parkinson's disease. The link between the mutation and the phenotype is unclear. Here, we explored the functional consequence of the G279S substitution on the activity of the A1-receptor after heterologous expression in HEK293 cells. The mutation did not affect surface expression and ligand binding but changed the susceptibility to heat denaturation: the thermodynamic stability of A1R-G279S7.44 was enhanced by about 2 and 8 K when compared with wild-type A1-receptor and A1R-Y288A7.53 (a folding-deficient variant used as a reference), respectively. In contrast, the kinetic stability was reduced, indicating a lower energy barrier for conformational transitions in A1R-G279S7.44 (73 ± 23 kJ/mol) than in wild-type A1R (135 ± 4 kJ/mol) or in A1R-Y288A7.53 (184 ± 24 kJ/mol). Consistent with this lower energy barrier, A1R-G279S7.44 was more effective in promoting guanine nucleotide exchange than wild-type A1R. We detected similar levels of complexes formed between D1-receptors and wild-type A1R or A1R-G279S7.44 by coimmunoprecipitation and bioluminescence resonance energy transfer. However, lower concentrations of agonist were required for half-maximum inhibition of dopamine-induced cAMP accumulation in cells coexpressing D1-receptor and A1R-G279S7.44 than in those coexpressing wild-type A1R. These observations predict enhanced inhibition of dopaminergic signaling by A1R-G279S7.44 in vivo, consistent with a pathogenic role in Parkinson's disease. SIGNIFICANCE STATEMENT: Parkinson's disease is caused by a loss of dopaminergic input from the substantia nigra to the caudate nucleus and the putamen. Activation of the adenosine A1-receptor antagonizes responses elicited by dopamine D1-receptor. We show that this activity is more pronounced in a mutant version of the A1-receptor (A1R-G279S7.44), which was identified in individuals suffering from early-onset Parkinson's disease.
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Affiliation(s)
- Shahrooz Nasrollahi-Shirazi
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Daniel Szöllösi
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Qiong Yang
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Edin Muratspahic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ali El-Kasaby
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Christian Nanoff
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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5
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Li CY, Gupta A, Gáborik Z, Kis E, Prasad B. Organic Anion Transporting Polypeptide–Mediated Hepatic Uptake of Glucuronide Metabolites of Androgens. Mol Pharmacol 2020; 98:234-242. [DOI: 10.1124/mol.120.119891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/11/2020] [Indexed: 12/30/2022] Open
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6
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Sawato T, Yamaguchi M. Sequential self‐catalytic reactions in the formation of hetero‐double‐helix and their self‐assembled gels by pseudoenantiomer mixtures of ethynylhelicene oligomers. Chirality 2020; 32:824-832. [DOI: 10.1002/chir.23224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/14/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Tsukasa Sawato
- Department of Organic Chemistry, Graduate School of Pharmaceutical SciencesTohoku University Sendai Japan
| | - Masahiko Yamaguchi
- Department of Organic Chemistry, Graduate School of Pharmaceutical SciencesTohoku University Sendai Japan
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7
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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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8
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Musbat L, Assis S, Dilger JM, El-Baba TJ, Fuller DR, Knudsen JL, Kiefer HV, Hirshfeld A, Friedman N, Andersen LH, Sheves M, Clemmer DE, Toker Y. Action and Ion Mobility Spectroscopy of a Shortened Retinal Derivative. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2152-2159. [PMID: 30062478 DOI: 10.1007/s13361-018-2033-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
The development of tandem ion mobility spectroscopy (IMS) known as IMS-IMS has led to extensive research into isomerizations of isolated molecules. Many recent works have focused on the retinal chromophore which is the optical switch used in animal vision. Here, we study a shortened derivative of the chromophore, which exhibits a rich IM spectrum allowing for a detailed analysis of its isomerization pathways, and show that the longer the chromophore is, the lower the barrier energies for isomerization are. Graphical Abstract.
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Affiliation(s)
- Lihi Musbat
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Shirrel Assis
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Jonathan M Dilger
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, IN, 47522, USA
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | - Daniel R Fuller
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | | | - Hjalte V Kiefer
- Department of Physics and Astronomy, Aarhus University, 8000, Aarhus C, Denmark
| | - Amiram Hirshfeld
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noga Friedman
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, 8000, Aarhus C, Denmark
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - David E Clemmer
- Department of Chemistry, Indiana University Bloomington, Indiana, 47405, USA
| | - Yoni Toker
- Department of Physics and Institute of Nanotechnology, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
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9
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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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10
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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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11
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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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12
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Tian H, Sakmar TP, Huber T. Measurement of Slow Spontaneous Release of 11-cis-Retinal from Rhodopsin. Biophys J 2017; 112:153-161. [PMID: 28076806 DOI: 10.1016/j.bpj.2016.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 12/05/2016] [Indexed: 01/05/2023] Open
Abstract
The vertebrate visual photoreceptor rhodopsin (Rho) is a unique G protein-coupled receptor as it utilizes a covalently tethered inverse agonist (11-cis-retinal) as the native ligand. Previously, electrophysiological studies showed that ligand binding of 11-cis-retinal in dark-adapted Rho was essentially irreversible with a half-life estimated to be 420 years, until after thermal isomerization to all-trans-retinal, which then slowly dissociates. This long lifetime of 11-cis-retinal binding was considered to be physiologically important for minimizing background signal (dark noise) of the visual system. However, in vitro biochemical studies on the thermal stability of Rho showed that Rho decays with a half-life on the order of days. In this study, we resolve the discrepancy by measuring the chromophore exchange rate of the bound 11-cis-retinal chromophore with free 9-cis-retinal from Rho in an in vitro phospholipid/detergent bicelle system. We conclude that the thermal decay of Rho primarily proceeds through spontaneous breaking of the covalent linkage between opsin and 11-cis-retinal, which was overlooked in the electrophysiological recording. We estimate that this slow spontaneous release of 11-cis-retinal from Rho should result in 104 to 105 free opsin molecules in a dark-adapted rod cell-a number that is three orders of magnitude higher than previously expected. We also discuss the physiological implications of these findings on the basal activity of opsins and the associated dark noise in the visual system.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY.
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13
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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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14
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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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15
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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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16
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Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc Natl Acad Sci U S A 2017; 114:E2608-E2615. [PMID: 28289214 DOI: 10.1073/pnas.1617446114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Vertebrate rhodopsin (Rh) contains 11-cis-retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11-cis-retinal is isomerized to all-trans-retinal, constituting a one-way reaction that activates transducin (Gt) followed by chromophore release. Here we report that bovine Rh, regenerated instead with a six-carbon-ring retinal chromophore featuring a C11=C12 double bond locked in its cis conformation (Rh6mr), employs an atypical isomerization mechanism by converting 11-cis to an 11,13-dicis configuration for prolonged Gt activation. Time-dependent UV-vis spectroscopy, HPLC, and molecular mechanics analyses revealed an atypical thermal reisomerization of the 11,13-dicis to the 11-cis configuration on a slow timescale, which enables Rh6mr to function in a photocyclic manner similar to that of microbial Rhs. With this photocyclic behavior, Rh6mr repeatedly recruits and activates Gt in response to light stimuli, making it an excellent candidate for optogenetic tools based on retinal analog-bound vertebrate Rhs. Overall, these comprehensive structure-function studies unveil a unique photocyclic mechanism of Rh activation by an 11-cis-to-11,13-dicis isomerization.
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17
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Iyer ESS, Misra R, Maity A, Liubashevski O, Sudo Y, Sheves M, Ruhman S. Temperature Independence of Ultrafast Photoisomerization in Thermophilic Rhodopsin: Assessment versus Other Microbial Proton Pumps. J Am Chem Soc 2016; 138:12401-7. [DOI: 10.1021/jacs.6b05002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Ramprasad Misra
- Department
of Organic Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arnab Maity
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Oleg Liubashevski
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Yuki Sudo
- Division
of Pharmaceutical sciences, Okayama University, Kita-Ku, Okayama 700-0082, Japan
| | - Mordechai Sheves
- Department
of Organic Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sanford Ruhman
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
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18
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Singhal A, Guo Y, Matkovic M, Schertler G, Deupi X, Yan EC, Standfuss J. Structural role of the T94I rhodopsin mutation in congenital stationary night blindness. EMBO Rep 2016; 17:1431-1440. [PMID: 27458239 DOI: 10.15252/embr.201642671] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/07/2016] [Indexed: 11/09/2022] Open
Abstract
Congenital stationary night blindness (CSNB) is an inherited and non-progressive retinal dysfunction. Here, we present the crystal structure of CSNB-causing T94I2.61 rhodopsin in the active conformation at 2.3 Å resolution. The introduced hydrophobic side chain prolongs the lifetime of the G protein activating metarhodopsin-II state by establishing a direct van der Waals contact with K2967.43, the site of retinal attachment. This is in stark contrast to the light-activated state of the CSNB-causing G90D2.57 mutation, where the charged mutation forms a salt bridge with K2967.43 To find the common denominator between these two functional modifications, we combined our structural data with a kinetic biochemical analysis and molecular dynamics simulations. Our results indicate that both the charged G90D2.57 and the hydrophobic T94I2.61 mutation alter the dark state by weakening the interaction between the Schiff base (SB) and its counterion E1133.28 We propose that this interference with the tight regulation of the dim light photoreceptor rhodopsin increases background noise in the visual system and causes the loss of night vision characteristic for CSNB patients.
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Affiliation(s)
- Ankita Singhal
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Ying Guo
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Milos Matkovic
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Deparment of Biology, ETH Zurich, Zürich, Switzerland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland
| | - Elsa Cy Yan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Joerg Standfuss
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
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19
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Hofmann L, Palczewski K. Advances in understanding the molecular basis of the first steps in color vision. Prog Retin Eye Res 2015; 49:46-66. [PMID: 26187035 DOI: 10.1016/j.preteyeres.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
Abstract
Serving as one of our primary environmental inputs, vision is the most sophisticated sensory system in humans. Here, we present recent findings derived from energetics, genetics and physiology that provide a more advanced understanding of color perception in mammals. Energetics of cis-trans isomerization of 11-cis-retinal accounts for color perception in the narrow region of the electromagnetic spectrum and how human eyes can absorb light in the near infrared (IR) range. Structural homology models of visual pigments reveal complex interactions of the protein moieties with the light sensitive chromophore 11-cis-retinal and that certain color blinding mutations impair secondary structural elements of these G protein-coupled receptors (GPCRs). Finally, we identify unsolved critical aspects of color tuning that require future investigation.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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20
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Dilger J, Musbat L, Sheves M, Bochenkova AV, Clemmer DE, Toker Y. Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411894] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Dilger J, Musbat L, Sheves M, Bochenkova AV, Clemmer DE, Toker Y. Direct measurement of the isomerization barrier of the isolated retinal chromophore. Angew Chem Int Ed Engl 2015; 54:4748-52. [PMID: 25756226 DOI: 10.1002/anie.201411894] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/25/2015] [Indexed: 11/07/2022]
Abstract
Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activation voltages for isomerization for each of the reaction pathways, and by measuring the threshold activation voltage for fragmentation, the relative energies of the isomers as well as the energy barriers for isomerization were determined. The energy barrier for a single cis-trans isomerization is (0.64±0.05) eV, which is significantly lower than that observed for the reaction within opsin proteins.
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Affiliation(s)
- Jonathan Dilger
- Spectrum Warfare Systems Department, NSWC Crane Division, Crane, IN 47522 (USA)
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22
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Mooney V, Sekharan S, Liu J, Guo Y, Batista VS, Yan ECY. Kinetics of thermal activation of an ultraviolet cone pigment. J Am Chem Soc 2014; 137:307-13. [PMID: 25514632 DOI: 10.1021/ja510553f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Visual pigments can be thermally activated via isomerization of the retinyl chromophore and hydrolysis of the Schiff base (SB) through which the retinyl chromophore is bound to the opsin protein. Here, we present the first combined experimental and theoretical study of the thermal activation of a Siberian hamster ultraviolet (SHUV) pigment. We measured the rates of thermal isomerization and hydrolysis in the SHUV pigment and bovine rhodopsin. We found that these rates were significantly faster in the UV pigment than in rhodopsin due to the difference in the structural and electrostatic effects surrounding the unprotonated Schiff base (USB) retinyl chromophore in the UV pigment. Theoretical (DFT-QM/MM) calculations of the cis-trans thermal isomerization revealed a barrier of ∼23 kcal/mol for the USB retinyl chromophore in SHUV compared to ∼40 kcal/mol for protonated Schiff base (PSB) chromophore in rhodopsin. The lower barrier for thermal isomerization in the SHUV pigment is attributed to the (i) lessening of the steric restraints near the β-ionone ring and SB ends of the chromophore, (ii) displacement of the transmembrane helix 6 (TM6) away from the binding pocket toward TM5 due to absence of the salt bridge between the USB and the protonated E113 residue, and (iii) change in orientation of the hydrogen-bonding networks (HBNs) in the extracellular loop 2 (EII). The results in comparing thermal stability of UV cone pigment and rhodopsin provide insight into molecular evolution of vertebrate visual pigments in achieving low discrete dark noise and high photosensitivity in rod pigments for dim-light vision.
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Affiliation(s)
- Victoria Mooney
- Department of Chemistry, Yale University , New Haven, Connecticut 06520 United States
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