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Singh M, Hashimoto M, Katayama K, Furutani Y, Kandori H. Internal Proton Transfer in the Activation of Heliorhodopsin. J Mol Biol 2024; 436:168273. [PMID: 37709010 DOI: 10.1016/j.jmb.2023.168273] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Heliorhodopsin (HeR), a recently discovered new rhodopsin family, contains a single counterion of the protonated Schiff base, E108 in HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR). Upon light absorption, the M and O intermediates form in HeRs, as well as type-1 microbial rhodopsins, indicating that the proton transfer from the Schiff base leads to the activation of HeRs. The present flash photolysis study of TaHeR in the presence of a pH-sensitive dye showed that TaHeR contains a proton-accepting group (PAG) inside protein. Comprehensive mutation study of TaHeR found the E108D mutant abolishing the M formation, which is not only at pH 8, but also at pH 9 and 10. The lack of M observation does not originate from the short lifetime of the M intermediate in E108D, as FTIR spectroscopy revealed that a red-shifted K-like intermediate is long lived in E108D. It is likely that the K-like intermediate returns to the unphotolyzed state without internal proton transfer in E108D. E108 and D108 are the Schiff base counterions of the wild-type and E108D mutant TaHeR, respectively, whereas small difference in length of side chains determine internal proton transfer reaction from the Schiff base. Based on the present finding, we propose that the internal water cluster (four water molecules) constitutes PAG in the M intermediate of TaHeR. In the wild type TaHeR, a protonated water cluster is stabilized by forming a salt bridge with E108. In contrast, slightly shortened counterion (D108) cannot stabilize the protonated water cluster in E108D, and thus impairs internal proton transfer from the Schiff base.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Masanori Hashimoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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2
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Hong JD, Palczewski K. A short story on how chromophore is hydrolyzed from rhodopsin for recycling. Bioessays 2023; 45:e2300068. [PMID: 37454357 PMCID: PMC10614701 DOI: 10.1002/bies.202300068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
Abstract
The photocycle of visual opsins is essential to maintain the light sensitivity of the retina. The early physical observations of the rhodopsin photocycle by Böll and Kühne in the 1870s inspired over a century's worth of investigations on rhodopsin biochemistry. A single photon isomerizes the Schiff-base linked 11-cis-retinylidene chromophore of rhodopsin, converting it to the all-trans agonist to elicit phototransduction through photoactivated rhodopsin (Rho*). Schiff base hydrolysis of the agonist is a key step in the photocycle, not only diminishing ongoing phototransduction but also allowing for entry and binding of fresh 11-cis chromophore to regenerate the rhodopsin pigment and maintain light sensitivity. Many challenges have been encountered in measuring the rate of this hydrolysis, but recent advancements have facilitated studies of the hydrolysis within the native membrane environment of rhodopsin. These techniques can now be applied to study hydrolysis of agonist in other opsin proteins that mediate phototransduction or chromophore turnover. In this review, we discuss the progress that has been made in characterizing the rhodopsin photocycle and the journey to characterize the hydrolysis of its all-trans-retinylidene agonist.
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Affiliation(s)
- John D. Hong
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
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3
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Wu A, Salom D, Hong JD, Tworak A, Watanabe K, Pardon E, Steyaert J, Kandori H, Katayama K, Kiser PD, Palczewski K. Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain. Nat Commun 2023; 14:5209. [PMID: 37626045 PMCID: PMC10457330 DOI: 10.1038/s41467-023-40911-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six - a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.
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Affiliation(s)
- Arum Wu
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - Kohei Watanabe
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan.
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Clinical Pharmacy Practice, University of California, Irvine, CA, USA.
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA.
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.
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4
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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Kojima K, Sudo Y. Convergent evolution of animal and microbial rhodopsins. RSC Adv 2023; 13:5367-5381. [PMID: 36793294 PMCID: PMC9923458 DOI: 10.1039/d2ra07073a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
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Interdisciplinary biophysical studies of membrane proteins bacteriorhodopsin and rhodopsin. Biophys Rev 2023; 15:111-125. [PMID: 36909961 PMCID: PMC9995646 DOI: 10.1007/s12551-022-01003-y] [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: 05/12/2022] [Accepted: 09/28/2022] [Indexed: 10/10/2022] Open
Abstract
The centenary of the birth of H. Gobind Khorana provides an auspicious opportunity to review the origins and evolution of parallel advances in biophysical methodology and molecular genetics technology used to study membrane proteins. Interdisciplinary work in the Khorana laboratory in the late 1970s and for the next three decades led to productive collaborations and fostered three subsequent scientific generations whose biophysical work on membrane proteins has led to detailed elucidation of the molecular mechanisms of energy transduction by the light-driven proton pump bacteriorhodopsin (bR) and signal transduction by the G protein-coupled receptor (GPCR) rhodopsin. This review will highlight the origins and advances of biophysical studies of membrane proteins made possible by the application of molecular genetics approaches to engineer site-specific alterations of membrane protein structures.
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7
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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8
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Salih PAŞA. Synthesis and characterization of di-Schiff based boronic structures: Therapeutic investigation against cancer and implementation for antioxidant. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.05.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Paşa S, Erdoğan Ö, Yenisey Ç. Synthesis and structural identification of boron based Schiff compounds with Ishikawa endometrial cancer and antioxidant activity. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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van Keulen SC, Solano A, Rothlisberger U. How Rhodopsin Tunes the Equilibrium between Protonated and Deprotonated Forms of the Retinal Chromophore. J Chem Theory Comput 2017; 13:4524-4534. [PMID: 28731695 DOI: 10.1021/acs.jctc.7b00229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerization of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state. PSB deprotonation is crucial for achieving full activation of rhodopsin; however, the specific structural rearrangements that have to take place to induce this pKa shift are not well understood. Classical molecular dynamics (MD) simulations were employed to identify intermediate states after the cis-trans isomerization of rhodopsin's retinal moiety. In order to select the intermediate state in which PSB deprotonation is experimentally known to occur, the validity of the intermediate configurations was checked through an evaluation of the optical properties in comparison with experiment. Subsequently, the selected state was used to investigate the molecular factors that enable PSB deprotonation at body temperature to obtain a better understanding of the difference between the protonated and the deprotonated state of the chromophore. To this end, the deprotonation reaction has been investigated by applying QM/MM MD simulations in combination with thermodynamic integration. The study shows that, compared to the inactive 11-cis-retinal case, trans-retinal rhodopsin is able to undergo PSB deprotonation due to a change in the conformation of the retinal and a consequent alteration in the hydrogen-bond (HB) network in which PSB and the counterion Glu113 are embedded. Besides the retinal moiety and Glu113, also two water molecules as well as Thr94 and Gly90 that are related to congenital night blindness are part of this essential HB network.
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Affiliation(s)
- Siri C van Keulen
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Alicia Solano
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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12
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Sandoval A, Eichler S, Madathil S, Reeves PJ, Fahmy K, Böckmann RA. The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs. Biophys J 2017; 111:79-89. [PMID: 27410736 DOI: 10.1016/j.bpj.2016.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
Abstract
The disruption of ionic and H-bond interactions between the cytosolic ends of transmembrane helices TM3 and TM6 of class-A (rhodopsin-like) G protein-coupled receptors (GPCRs) is a hallmark for their activation by chemical or physical stimuli. In the bovine photoreceptor rhodopsin, this is accompanied by proton uptake at Glu(134) in the class-conserved D(E)RY motif. Studies on TM3 model peptides proposed a crucial role of the lipid bilayer in linking protonation to stabilization of an active state-like conformation. However, the molecular details of this linkage could not be resolved and have been addressed in this study by molecular dynamics (MD) simulations on TM3 model peptides in a bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We show that protonation of the conserved glutamic acid alters the peptide insertion depth in the membrane, its side-chain rotamer preferences, and stabilizes the C-terminal helical structure. These factors contribute to the rise of the side-chain pKa (> 6) and to reduced polarity around the TM3 C terminus as confirmed by fluorescence spectroscopy. Helix stabilization requires the protonated carboxyl group; unexpectedly, this stabilization could not be evoked with an amide in MD simulations. Additionally, time-resolved Fourier transform infrared (FTIR) spectroscopy of TM3 model peptides revealed a different kinetics for lipid ester carbonyl hydration, suggesting that the carboxyl is linked to more extended H-bond clusters than an amide. Remarkably, this was seen as well in DOPC-reconstituted Glu(134)- and Gln(134)-containing bovine opsin mutants and demonstrates that the D(E)RY motif is a hydrated microdomain. The function of the D(E)RY motif as a proton switch is suggested to be based on the reorganization of the H-bond network at the membrane interface.
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Affiliation(s)
- Angelica Sandoval
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stefanie Eichler
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, and Technische Universität Dresden, Dresden, Germany
| | - Sineej Madathil
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, and Technische Universität Dresden, Dresden, Germany.
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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13
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Lans I, Dalton JAR, Giraldo J. Selective Protonation of Acidic Residues Triggers Opsin Activation. J Phys Chem B 2015; 119:9510-9. [DOI: 10.1021/acs.jpcb.5b01908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Isaias Lans
- Laboratory of Molecular Neuropharmacology
and Bioinformatics, Institut de Neurociències and Unitat de
Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - James A. R. Dalton
- Laboratory of Molecular Neuropharmacology
and Bioinformatics, Institut de Neurociències and Unitat de
Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology
and Bioinformatics, Institut de Neurociències and Unitat de
Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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14
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Structure-Based Biophysical Analysis of the Interaction of Rhodopsin with G Protein and Arrestin. Methods Enzymol 2015; 556:563-608. [DOI: 10.1016/bs.mie.2014.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Maeda S, Sun D, Singhal A, Foggetta M, Schmid G, Standfuss J, Hennig M, Dawson RJP, Veprintsev DB, Schertler GFX. Crystallization scale preparation of a stable GPCR signaling complex between constitutively active rhodopsin and G-protein. PLoS One 2014; 9:e98714. [PMID: 24979345 PMCID: PMC4076187 DOI: 10.1371/journal.pone.0098714] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Abstract
The activation of the G-protein transducin (Gt) by rhodopsin (Rho) has been intensively studied for several decades. It is the best understood example of GPCR activation mechanism and serves as a template for other GPCRs. The structure of the Rho/G protein complex, which is transiently formed during the signaling reaction, is of particular interest. It can help understanding the molecular details of how retinal isomerization leads to the G protein activation, as well as shed some light on how GPCR recognizes its cognate G protein. The native Rho/Gt complex isolated from bovine retina suffers from low stability and loss of the retinal ligand. Recently, we reported that constitutively active mutant of rhodopsin E113Q forms a Rho/Gt complex that is stable in detergent solution. Here, we introduce methods for a large scale preparation of the complex formed by the thermo-stabilized and constitutively active rhodopsin mutant N2C/M257Y/D282C(RhoM257Y) and the native Gt purified from bovine retinas. We demonstrate that the light-activated rhodopsin in this complex contains a covalently bound unprotonated retinal and therefore corresponds to the active metarhodopin II state; that the isolated complex is active and dissociates upon addition of GTPγS; and that the stoichiometry corresponds to a 1∶1 molar ratio of rhodopsin to the heterotrimeric G-protein. And finally, we show that the rhodopsin also forms stable complex with Gi. This complex has significantly higher thermostability than RhoM257Y/Gt complex and is resistant to a variety of detergents. Overall, our data suggest that the RhoM257Y/Gi complex is an ideal target for future structural and mechanistic studies of signaling in the visual system.
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Affiliation(s)
- Shoji Maeda
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dawei Sun
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ankita Singhal
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marcello Foggetta
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Georg Schmid
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Michael Hennig
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Roger J. P. Dawson
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Dmitry B. Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
- * E-mail: (DBV); (GFXS)
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
- * E-mail: (DBV); (GFXS)
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16
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Yamazaki Y, Nagata T, Terakita A, Kandori H, Shichida Y, Imamoto Y. Intramolecular interactions that induce helical rearrangement upon rhodopsin activation: light-induced structural changes in metarhodopsin IIa probed by cysteine S-H stretching vibrations. J Biol Chem 2014; 289:13792-800. [PMID: 24692562 DOI: 10.1074/jbc.m113.527606] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin undergoes rearrangements of its transmembrane helices after photon absorption to transfer a light signal to the G-protein transducin. To investigate the mechanism by which rhodopsin adopts the transducin-activating conformation, the local environmental changes in the transmembrane region were probed using the cysteine S-H group, whose stretching frequency is well isolated from the other protein vibrational modes. The S-H stretching modes of cysteine residues introduced into Helix III, which contains several key residues for the helical movements, and of native cysteine residues were measured by Fourier transform infrared spectroscopy. This method was applied to metarhodopsin IIa, a precursor of the transducin-activating state in which the intramolecular interactions are likely to produce a state ready for helical movements. No environmental change was observed near the ionic lock between Arg-135 in Helix III and Glu-247 in Helix VI that maintains the inactive conformation. Rather, the cysteine residues that showed environmental changes were located around the chromophore, Ala-164, His-211, and Phe-261. These findings imply that the hydrogen bond between Helix III and Helix V involving Glu-122 and His-211 and the hydrophobic packing between Helix III and Helix VI involving Gly-121, Leu-125, Phe-261, and Trp-265 are altered before the helical rearrangement leading toward the active conformation.
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Affiliation(s)
- Yoichi Yamazaki
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, the Graduate School of Materials Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Tomoko Nagata
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Akihisa Terakita
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, the Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan, and
| | - Hideki Kandori
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, the Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Yoshinori Shichida
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yasushi Imamoto
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan,
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17
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 759] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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18
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Park PSH. Constitutively active rhodopsin and retinal disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2014; 70:1-36. [PMID: 24931191 DOI: 10.1016/b978-0-12-417197-8.00001-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells of the retina that initiates scotopic vision. In the dark, rhodopsin is bound to the chromophore 11-cis retinal, which locks the receptor in an inactive state. The maintenance of an inactive rhodopsin in the dark is critical for rod photoreceptor cells to remain highly sensitive. Perturbations by mutation or the absence of 11-cis retinal can cause rhodopsin to become constitutively active, which leads to the desensitization of photoreceptor cells and, in some instances, retinal degeneration. Constitutive activity can arise in rhodopsin by various mechanisms and can cause a variety of inherited retinal diseases including Leber congenital amaurosis, congenital night blindness, and retinitis pigmentosa. In this review, the molecular and structural properties of different constitutively active forms of rhodopsin are overviewed, and the possibility that constitutive activity can arise from different active-state conformations is discussed.
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Affiliation(s)
- Paul Shin-Hyun Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio, USA.
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19
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Siebert F. Application of FTIR Spectroscopy to the Investigation of Dark Structures and Photoreactions of Visual Pigments. Isr J Chem 2013. [DOI: 10.1002/ijch.199500033] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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21
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22
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Zang J, Matthews HR. Origin and control of the dominant time constant of salamander cone photoreceptors. ACTA ACUST UNITED AC 2012; 140:219-33. [PMID: 22802362 PMCID: PMC3409105 DOI: 10.1085/jgp.201110762] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recovery of the light response in vertebrate photoreceptors requires the shutoff of both active intermediates in the phototransduction cascade: the visual pigment and the transducin–phosphodiesterase complex. Whichever intermediate quenches more slowly will dominate photoresponse recovery. In suction pipette recordings from isolated salamander ultraviolet- and blue-sensitive cones, response recovery was delayed, and the dominant time constant slowed when internal [Ca2+] was prevented from changing after a bright flash by exposure to 0Ca2+/0Na+ solution. Taken together with a similar prior observation in salamander red-sensitive cones, these observations indicate that the dominance of response recovery by a Ca2+-sensitive process is a general feature of amphibian cone phototransduction. Moreover, changes in the external pH also influenced the dominant time constant of red-sensitive cones even when changes in internal [Ca2+] were prevented. Because the cone photopigment is, uniquely, exposed to the external solution, this may represent a direct effect of protons on the equilibrium between its inactive Meta I and active Meta II forms, consistent with the notion that the process dominating recovery of the bright flash response represents quenching of the active Meta II form of the cone photopigment.
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Affiliation(s)
- Jingjing Zang
- Physiological Laboratory, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3EG, England, UK
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23
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Kaila VRI, Send R, Sundholm D. The effect of protein environment on photoexcitation properties of retinal. J Phys Chem B 2012; 116:2249-58. [PMID: 22166007 DOI: 10.1021/jp205918m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.
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Affiliation(s)
- Ville R I Kaila
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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24
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Kim TY, Schlieter T, Haase S, Alexiev U. Activation and molecular recognition of the GPCR rhodopsin--insights from time-resolved fluorescence depolarisation and single molecule experiments. Eur J Cell Biol 2011; 91:300-10. [PMID: 21803442 DOI: 10.1016/j.ejcb.2011.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022] Open
Abstract
The cytoplasmic surface of the G-protein coupled receptor (GPCR) rhodopsin is a key element in membrane receptor activation, molecular recognition by signalling molecules, and receptor deactivation. Understanding of the coupling between conformational changes in the intramembrane domain and the membrane-exposed surface of the photoreceptor rhodopsin is crucial for the elucidation of the molecular mechanism in GPCR activation. As little is known about protein dynamics, particularly the conformational dynamics of the cytoplasmic surface elements on the nanoseconds timescale, we utilised time-resolved fluorescence anisotropy experiments and site-directed fluorescence labelling to provide information on both, conformational space and motion. We summarise our recent advances in understanding rhodopsin dynamics and function using time-resolved fluorescence depolarisation and single molecule fluorescence experiments, with particular focus on the amphipathic helix 8, lying parallel to the cytoplasmic membrane surface and connecting transmembrane helix 7 with the long C-terminal tail.
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Affiliation(s)
- Tai-Yang Kim
- Physics Department, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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25
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Tarttelin EE, Fransen MP, Edwards PC, Hankins MW, Schertler GFX, Vogel R, Lucas RJ, Bellingham J. Adaptation of pineal expressed teleost exo-rod opsin to non-image forming photoreception through enhanced Meta II decay. Cell Mol Life Sci 2011; 68:3713-23. [PMID: 21416149 PMCID: PMC3203999 DOI: 10.1007/s00018-011-0665-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/01/2011] [Accepted: 03/01/2011] [Indexed: 12/03/2022]
Abstract
Photoreception by vertebrates enables both image-forming vision and non-image-forming responses such as circadian photoentrainment. Over the recent years, distinct non-rod non-cone photopigments have been found to support circadian photoreception in diverse species. By allowing specialization to this sensory task a selective advantage is implied, but the nature of that specialization remains elusive. We have used the presence of distinct rod opsin genes specialized to either image-forming (retinal rod opsin) or non-image-forming (pineal exo-rod opsin) photoreception in ray-finned fish (Actinopterygii) to gain a unique insight into this problem. A comparison of biochemical features for these paralogous opsins in two model teleosts, Fugu pufferfish (Takifugu rubripes) and zebrafish (Danio rerio), reveals striking differences. While spectral sensitivity is largely unaltered by specialization to the pineal environment, in other aspects exo-rod opsins exhibit a behavior that is quite distinct from the cardinal features of the rod opsin family. While they display a similar thermal stability, they show a greater than tenfold reduction in the lifetime of the signaling active Meta II photoproduct. We show that these features reflect structural changes in retinal association domains of helices 3 and 5 but, interestingly, not at either of the two residues known to define these characteristics in cone opsins. Our findings suggest that the requirements of non-image-forming photoreception have lead exo-rod opsin to adopt a characteristic that seemingly favors efficient bleach recovery but not at the expense of absolute sensitivity.
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Affiliation(s)
- Emma E Tarttelin
- Faculty of Life Sciences, The University of Manchester, Manchester, UK
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26
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Ou WB, Yi T, Kim JM, Khorana HG. The roles of transmembrane domain helix-III during rhodopsin photoactivation. PLoS One 2011; 6:e17398. [PMID: 21364764 PMCID: PMC3045455 DOI: 10.1371/journal.pone.0017398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 01/31/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Rhodopsin, the prototypic member of G protein-coupled receptors (GPCRs), undergoes isomerization of 11-cis-retinal to all-trans-retinal upon photoactivation. Although the basic mechanism by which rhodopsin is activated is well understood, the roles of whole transmembrane (TM) helix-III during rhodopsin photoactivation in detail are not completely clear. PRINCIPAL FINDINGS We herein use single-cysteine mutagenesis technique to investigate conformational changes in TM helices of rhodopsin upon photoactivation. Specifically, we study changes in accessibility and reactivity of cysteine residues introduced into the TM helix-III of rhodopsin. Twenty-eight single-cysteine mutants of rhodopsin (P107C-R135C) were prepared after substitution of all natural cysteine residues (C140/C167/C185/C222/C264/C316) by alanine. The cysteine mutants were expressed in COS-1 cells and rhodopsin was purified after regeneration with 11-cis-retinal. Cysteine accessibility in these mutants was monitored by reaction with 4, 4'-dithiodipyridine (4-PDS) in the dark and after illumination. Most of the mutants except for T108C, G109C, E113C, I133C, and R135C showed no reaction in the dark. Wide variation in reactivity was observed among cysteines at different positions in the sequence 108-135 after photoactivation. In particular, cysteines at position 115, 119, 121, 129, 131, 132, and 135, facing 11-cis-retinal, reacted with 4-PDS faster than neighboring amino acids. The different reaction rates of mutants with 4-PDS after photoactivation suggest that the amino acids in different positions in helix-III are exposed to aqueous environment to varying degrees. SIGNIFICANCE Accessibility data indicate that an aqueous/hydrophobic boundary in helix-III is near G109 and I133. The lack of reactivity in the dark and the accessibility of cysteine after photoactivation indicate an increase of water/4-PDS accessibility for certain cysteine-mutants at Helix-III during formation of Meta II. We conclude that photoactivation resulted in water-accessible at the chromophore-facing residues of Helix-III.
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Affiliation(s)
- Wen-bin Ou
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Tingfang Yi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jong-Myoung Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - H. Gobind Khorana
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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27
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Katayama K, Furutani Y, Kandori H. FTIR study of the photoreaction of bovine rhodopsin in the presence of hydroxylamine. J Phys Chem B 2010; 114:9039-46. [PMID: 20557105 DOI: 10.1021/jp102288c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In bovine rhodopsin, 11-cis-retinal forms a Schiff base linkage with Lys296. The Schiff base is not reactive to hydroxylamine in the dark, which is consistent with the well-protected retinal binding site. In contrast, under illumination it easily forms all-trans retinal oxime, resulting in the loss of color. This suggests that activation of rhodopsin creates a specific reaction channel for hydroxylamine or loosens the chromophore binding pocket. In the present study, to extract structural information on the Schiff base vicinity and to understand the changes upon activation of rhodopsin, we compared light-induced FTIR difference spectra of bovine rhodopsin in the presence and absence of hydroxylamine under physiological pH (approximately 7). Although the previous FTIR study did not observe the complex formation between rhodopsin and G-protein transducin in hydrated films, the present study clearly shows that hydrated films can be used for studies of the interaction between rhodopsin and hydroxylamine. Hydroxylamine does not react with the Schiff base of Meta-I intermediate trapped at 240 K, possibly because of decreased conformational motions under the frozen environment, while FTIR spectroscopy showed that hydroxylamine affects the hydrogen bonds of the Schiff base and water molecules in Meta-I. In contrast, formation of the retinal oxime was clearly observed at 280 K, the characteristic temperature of Meta-II accumulation in the absence of hydroxylamine, and time-dependent formation of retinal oxime was observed from Meta-II at 265 K as well. The obtained difference FTIR spectra of retinal oxime and opsin are different from that of Meta-II. It is likely that the antiparallel beta-sheet constituting a part of the retinal binding pocket at the extracellular surface is structurally disrupted in the presence of hydroxylamine, which allows the hydrolysis of the Schiff base into retinal oxime.
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Affiliation(s)
- Kota Katayama
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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28
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Tsukamoto H, Terakita A. Diversity and functional properties of bistable pigments. Photochem Photobiol Sci 2010; 9:1435-43. [PMID: 20852774 DOI: 10.1039/c0pp00168f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Rhodopsin and related opsin-based pigments, which are photosensitive membrane proteins, have been extensively studied using a wide variety of techniques, with rhodopsin being the most understood G protein-coupled receptor (GPCR). Animals use various opsin-based pigments for vision and a wide variety of non-visual functions. Many functionally varied pigments are roughly divided into two kinds, based on their photoreaction: bistable and monostable pigments. Bistable pigments are thermally stable before and after photo-activation, but monostable pigments are stable only before activation. Here, we review the diversity of bistable pigments and their molecular characteristics. We also discuss the mechanisms underlying different molecular characteristics of bistable and monostable pigments. In addition, the potential of bistable pigments as a GPCR model is proposed.
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Affiliation(s)
- Hisao Tsukamoto
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Osaka, Osaka 558-8585, Japan
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29
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Tsutsui K, Shichida Y. Multiple functions of Schiff base counterion in rhodopsins. Photochem Photobiol Sci 2010; 9:1426-34. [PMID: 20842311 DOI: 10.1039/c0pp00134a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In rhodopsins, visible-light absorption is achieved by the protonation of the chromophore Schiff base. The Schiff base proton is stabilized by the negative charge of an amino acid residue called the Schiff base counterion. Since E113 was identified as the counterion in bovine rhodopsin, there has been growing evidence that the counterion has multiple functions besides proton stabilization. Here, we first introduce generally accepted findings as well as some controversial theories about the identity of the Schiff base counterion in the dark and in intermediate states and then review multiple functions of the counterion in vertebrate visual pigments. Special focus is placed on the recently demonstrated role in photoisomerization efficiency. Finally, differences in the position of the counterion between vertebrate visual pigments and other opsins and its relevance to the molecular evolution of opsins are discussed.
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Affiliation(s)
- Kei Tsutsui
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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30
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Sato K, Morizumi T, Yamashita T, Shichida Y. Direct observation of the pH-dependent equilibrium between metarhodopsins I and II and the pH-independent interaction of metarhodopsin II with transducin C-terminal peptide. Biochemistry 2010; 49:736-41. [PMID: 20030396 DOI: 10.1021/bi9018412] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine rhodopsin contains 11-cis-retinal as a light-absorbing chromophore that binds to a lysine residue of the apoprotein opsin via a protonated Schiff base linkage. Light isomerizes 11-cis-retinal into the all-trans form, which eventually leads to the formation of an enzymatically active state, metarhodopsin II (MII). It is widely believed that MII forms a pH-dependent equilibrium with metarhodopsin I (MI), but direct evidence for this equilibrium has not been reported. Here, we confirmed this equilibrium by direct observation of the mutual conversions of MI and MII upon changing the pH of the MI/MII mixture. We also observed a reversible binding of the synthetic peptide constituting the C-terminal 11 amino acids of the transducin alpha-subunit to MII, which resulted in change of the amounts of MI and MII in the equilibrium. Interestingly, addition of the peptide did not induce a simple pK(a) shift but rather induced an increase of the MII fraction at high pH. These results indicate that in addition to the MII that is formed from MI in a pH-dependent manner there also exists another MII, which is in equilibrium with MI in a pH-independent manner and can bind to the peptide. Therefore, there is no need for proton uptake by the protein moiety of opsin for the binding to the peptide.
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Affiliation(s)
- Keita Sato
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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31
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Ahuja S, Eilers M, Hirshfeld A, Yan ECY, Ziliox M, Sakmar TP, Sheves M, Smith SO. 6-s-cis Conformation and polar binding pocket of the retinal chromophore in the photoactivated state of rhodopsin. J Am Chem Soc 2010; 131:15160-9. [PMID: 19795853 DOI: 10.1021/ja9034768] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The visual pigment rhodopsin is unique among the G protein-coupled receptors in having an 11-cis retinal chromophore covalently bound to the protein through a protonated Schiff base linkage. The chromophore locks the visual receptor in an inactive conformation through specific steric and electrostatic interactions. This efficient inverse agonist is rapidly converted to an agonist, the unprotonated Schiff base of all-trans retinal, upon light activation. Here, we use magic angle spinning NMR spectroscopy to obtain the (13)C chemical shifts (C5-C20) of the all-trans retinylidene chromophore and the (15)N chemical shift of the Schiff base nitrogen in the active metarhodopsin II intermediate. The retinal chemical shifts are sensitive to the conformation of the chromophore and its molecular interactions within the protein-binding site. Comparison of the retinal chemical shifts in metarhodopsin II with those of retinal model compounds reveals that the Schiff base environment is polar. In particular, the (13)C15 and (15)Nepsilon chemical shifts indicate that the C horizontal lineN bond is highly polarized in a manner that would facilitate Schiff base hydrolysis. We show that a strong perturbation of the retinal (13)C12 chemical shift observed in rhodopsin is reduced in wild-type metarhodopsin II and in the E181Q mutant of rhodopsin. On the basis of the T(1) relaxation time of the retinal (13)C18 methyl group and the conjugated retinal (13)C5 and (13)C8 chemical shifts, we have determined that the conformation of the retinal C6-C7 single bond connecting the beta-ionone ring and the retinylidene chain is 6-s-cis in both the inactive and the active states of rhodopsin. These results are discussed within the general framework of ligand-activated G protein-coupled receptors.
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Affiliation(s)
- Shivani Ahuja
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-5215, USA
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Kirchberg K, Kim TY, Haase S, Alexiev U. Functional interaction structures of the photochromic retinal protein rhodopsin. Photochem Photobiol Sci 2010; 9:226-33. [PMID: 20126799 DOI: 10.1039/b9pp00134d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied functional interaction structures of the vertebrate membrane photoreceptor rhodopsin containing retinal as a chromophore. Using time-resolved fluorescence depolarization we analyzed real-time dynamics and conformational changes of the cytoplasmic helix 8 (H8) preceding the long C-terminal tail of rhodopsin. H8 runs parallel to the membrane surface and extends from transmembrane helix 7 whose highly conserved NPxxY(x)F motif connects that region of rhodopsin with the retinal binding pocket. Our measurements indicate that photo-induced retinal isomerization from 11-cis to all-trans provokes conformational changes of H8, including slower motion and reduced flexibility, that are specific for the active metarhodopsin-II photo-intermediate. These conformational changes are absent in the retinal-devoid state opsin and in the phosphorylated metarhodopsin-II state upon receptor deactivation. Furthermore we show that membrane rim effects can influence interfacial reactions at the cytoplasmic rhodopsin surface such as proton transfer reactions between surface and aqueous bulk phase or binding of the signaling protein transducin visualized with single-molecule widefield microscopy. These findings are important for an understanding of the effects of membrane structure on the photo-transduction mechanism.
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Affiliation(s)
- Kristina Kirchberg
- Freie Universität Berlin, Inst. für. Experimentalphysik, Arnimallee 14, D-14195 Berlin, Germany
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Matsuyama T, Yamashita T, Imai H, Shichida Y. Covalent bond between ligand and receptor required for efficient activation in rhodopsin. J Biol Chem 2009; 285:8114-21. [PMID: 20042594 DOI: 10.1074/jbc.m109.063875] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin is an extensively studied member of the G protein-coupled receptors (GPCRs). Although rhodopsin shares many features with the other GPCRs, it exhibits unique features as a photoreceptor molecule. A hallmark in the molecular structure of rhodopsin is the covalently bound chromophore that regulates the activity of the receptor acting as an agonist or inverse agonist. Here we show the pivotal role of the covalent bond between the retinal chromophore and the lysine residue at position 296 in the activation pathway of bovine rhodopsin, by use of a rhodopsin mutant K296G reconstituted with retinylidene Schiff bases. Our results show that photoreceptive functions of rhodopsin, such as regiospecific photoisomerization of the ligand, and its quantum yield were not affected by the absence of the covalent bond, whereas the activation mechanism triggered by photoisomerization of the retinal was severely affected. Furthermore, our results show that an active state similar to the Meta-II intermediate of wild-type rhodopsin did not form in the bleaching process of this mutant, although it exhibited relatively weak G protein activity after light irradiation because of an increased basal activity of the receptor. We propose that the covalent bond is required for transmitting structural changes from the photoisomerized agonist to the receptor and that the covalent bond forcibly keeps the low affinity agonist in the receptor, resulting in a more efficient G protein activation.
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Affiliation(s)
- Take Matsuyama
- Department of Biophysics, Graduate School of Science and CREST-JST, Kyoto University, Kyoto 606-8502, Japan
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Shichida Y, Matsuyama T. Evolution of opsins and phototransduction. Philos Trans R Soc Lond B Biol Sci 2009; 364:2881-95. [PMID: 19720651 DOI: 10.1098/rstb.2009.0051] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Opsins are the universal photoreceptor molecules of all visual systems in the animal kingdom. They can change their conformation from a resting state to a signalling state upon light absorption, which activates the G protein, thereby resulting in a signalling cascade that produces physiological responses. This process of capturing a photon and transforming it into a physiological response is known as phototransduction. Recent cloning techniques have revealed the rich and diverse nature of these molecules, found in organisms ranging from jellyfish to humans, functioning in visual and non-visual phototransduction systems and photoisomerases. Here we describe the diversity of these proteins and their role in phototransduction. Then we explore the molecular properties of opsins, by analysing site-directed mutants, strategically designed by phylogenetic comparison. This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules. In particular, we will discuss the evolution of the counterion, the reduction of agonist binding to the receptor, and the molecular properties that characterize rod opsins apart from cone opsins. We will show how the advances in molecular biology and biophysics have given us insights into how evolution works at the molecular level.
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Affiliation(s)
- Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Madathil S, Fahmy K. Lipid protein interactions couple protonation to conformation in a conserved cytosolic domain of G protein-coupled receptors. J Biol Chem 2009; 284:28801-9. [PMID: 19706606 DOI: 10.1074/jbc.m109.002030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The visual photoreceptor rhodopsin is a prototypical class I (rhodopsin-like) G protein-coupled receptor. Photoisomerization of the covalently bound ligand 11-cis-retinal leads to restructuring of the cytosolic face of rhodopsin. The ensuing protonation of Glu-134 in the class-conserved D(E)RY motif at the C-terminal end of transmembrane helix-3 promotes the formation of the G protein-activating state. Using transmembrane segments derived from helix-3 of bovine rhodopsin, we show that lipid protein interactions play a key role in this cytosolic "proton switch." Infrared and fluorescence spectroscopic pK(a) determinations reveal that the D(E)RY motif is an autonomous functional module coupling side chain neutralization to conformation and helix positioning as evidenced by side chain to lipid headgroup Foerster resonance energy transfer. The free enthalpies of helix stabilization and hydrophobic burial of the neutral carboxyl shift the side chain pK(a) into the range typical of Glu-134 in photoactivated rhodopsin. The lipid-mediated coupling mechanism is independent of interhelical contacts allowing its conservation without interference with the diversity of ligand-specific interactions in class I G protein-coupled receptors.
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Affiliation(s)
- Sineej Madathil
- Division of Biophysics, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, PF 510119, D-01314 Dresden, Germany
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Lüdeke S, Mahalingam M, Vogel R. Rhodopsin activation switches in a native membrane environment. Photochem Photobiol 2009; 85:437-41. [PMID: 19267869 DOI: 10.1111/j.1751-1097.2008.00490.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The elucidation of structure-function relationships of membrane proteins still poses a considerable challenge due to the sometimes profound influence of the lipid bilayer on the functional properties of the protein. The visual pigment rhodopsin is a prototype of the family of G protein-coupled transmembrane receptors and a considerable part of our knowledge on its activation mechanisms has been derived from studies on detergent-solubilized proteins. This includes in particular the events associated with the conformational transitions of the receptor from the still inactive Meta I to the Meta II photoproduct states, which are involved in signaling. These events involve disruption of an internal salt bridge of the retinal protonated Schiff base, movement of helices and proton uptake from the solvent by the conserved cytoplasmic E(D)RY network around Glu134. As the equilibria associated with these events are considerably altered by the detergent environment, we set out to investigate these equilibria in the native membrane environment and to develop a coherent thermodynamic model of these activating steps using UV-visible and Fourier-transform infrared spectroscopy as complementary techniques. Particular emphasis is put on the role of protonation of Glu134 from the solvent, which is a thermodynamic prerequisite for full receptor activation in membranes, but not in detergent. In view of the conservation of this carboxylate group in family A G protein-coupled receptors, it may also play a similar role in the activation of other family members.
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Affiliation(s)
- Steffen Lüdeke
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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Möller M, Alexiev U. Surface Charge Changes upon Formation of the Signaling State in Visual Rhodopsin. Photochem Photobiol 2009; 85:501-8. [DOI: 10.1111/j.1751-1097.2008.00528.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Two protonation switches control rhodopsin activation in membranes. Proc Natl Acad Sci U S A 2008; 105:17795-800. [PMID: 18997017 DOI: 10.1073/pnas.0804541105] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation of the G protein-coupled receptor (GPCR) rhodopsin is initiated by light-induced isomerization of the retinal ligand, which triggers 2 protonation switches in the conformational transition to the active receptor state Meta II. The first switch involves disruption of an interhelical salt bridge by internal proton transfer from the retinal protonated Schiff base (PSB) to its counterion, Glu-113, in the transmembrane domain. The second switch consists of uptake of a proton from the solvent by Glu-134 of the conserved E(D)RY motif at the cytoplasmic terminus of helix 3, leading to pH-dependent receptor activation. By using a combination of UV-visible and FTIR spectroscopy, we study the activation mechanism of rhodopsin in different membrane environments and show that these 2 protonation switches become partially uncoupled at physiological temperature. This partial uncoupling leads to approximately 50% population of an entropy-stabilized Meta II state in which the interhelical PSB salt bridge is broken and activating helix movements have taken place but in which Glu-134 remains unprotonated. This partial activation is converted to full activation only by coupling to the pH-dependent protonation of Glu-134 from the solvent, which stabilizes the active receptor conformation by lowering its enthalpy. In a membrane environment, protonation of Glu-134 is therefore a thermodynamic rather than a structural prerequisite for activating helix movements. In light of the conservation of the E(D)RY motif in rhodopsin-like GPCRs, protonation of this carboxylate also may serve a similar function in signal transduction of other members of this receptor family.
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Tikhonova IG, Best RB, Engel S, Gershengorn MC, Hummer G, Costanzi S. Atomistic insights into rhodopsin activation from a dynamic model. J Am Chem Soc 2008; 130:10141-9. [PMID: 18620390 DOI: 10.1021/ja0765520] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.
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Affiliation(s)
- Irina G Tikhonova
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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40
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Functional role of the "ionic lock"--an interhelical hydrogen-bond network in family A heptahelical receptors. J Mol Biol 2008; 380:648-55. [PMID: 18554610 DOI: 10.1016/j.jmb.2008.05.022] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 05/06/2008] [Accepted: 05/09/2008] [Indexed: 11/23/2022]
Abstract
Activation of family A G-protein-coupled receptors involves a rearrangement of a conserved interhelical cytoplasmic hydrogen bond network between the E(D)RY motif on transmembrane helix 3 (H3) and residues on H6, which is commonly termed the cytoplasmic "ionic lock." Glu134(3.49) of the E(D)RY motif also forms an intrahelical salt bridge with neighboring Arg135(3.50) in the dark-state crystal structure of rhodopsin. We examined the roles of Glu134(3.49) and Arg135(3.50) on H3 and Glu247(6.30) and Glu249(6.32) on H6 on the activation of rhodopsin using Fourier transform infrared spectroscopy of wild-type and mutant pigments reconstituted into lipid membranes. Activation of rhodopsin is pH-dependent with proton uptake during the transition from the inactive Meta I to the active Meta II state. Glu134(3.49) of the ERY motif is identified as the proton-accepting group, using the Fourier transform infrared protonation signature and the absence of a pH dependence of activation in the E134Q mutant. Neutralization of Arg135(3.50) similarly leads to pH-independent receptor activation, but with structural alterations in the Meta II state. Neutralization of Glu247(6.30) and Glu249(6.32) on H6, which are involved in interhelical interactions with H3 and H7, respectively, led to a shift toward Meta II in the E247Q and E249Q mutants while retaining the pH sensitivity of the equilibrium. Disruption of the interhelical interaction of Glu247(6.30) and Glu249(6.32) on H6 with H3 and H7 plays its role during receptor activation, but neutralization of the intrahelical salt bridge between Glu134(3.49) and Arg135(3.50) is considerably more critical for shifting the photoproduct equilibrium to the active conformation. These conclusions are discussed in the context of recent structural data of the beta(2)-adrenergic receptor.
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41
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Drees C, Stürmer CA, Möller HM, Fritz G. Expression and purification of neurolin immunoglobulin domain 2 from Carrassius auratus (goldfish) in Escherichia coli. Protein Expr Purif 2008; 59:47-54. [DOI: 10.1016/j.pep.2007.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 12/25/2007] [Accepted: 12/28/2007] [Indexed: 10/22/2022]
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Standfuss J, Zaitseva E, Mahalingam M, Vogel R. Structural impact of the E113Q counterion mutation on the activation and deactivation pathways of the G protein-coupled receptor rhodopsin. J Mol Biol 2008; 380:145-57. [PMID: 18511075 PMCID: PMC2726285 DOI: 10.1016/j.jmb.2008.04.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 03/12/2008] [Accepted: 04/21/2008] [Indexed: 11/16/2022]
Abstract
Disruption of an interhelical salt bridge between the retinal protonated Schiff base linked to H7 and Glu113 on H3 is one of the decisive steps during activation of rhodopsin. Using previously established stabilization strategies, we engineered a stabilized E113Q counterion mutant that converted rhodopsin to a UV-absorbing photoreceptor with deprotonated Schiff base and allowed reconstitution into native-like lipid membranes. Fourier-transform infrared difference spectroscopy reveals a deprotonated Schiff base in the photoproducts of the mutant up to the active state Meta II, the absence of the classical pH-dependent Meta I/Meta II conformational equilibrium in favor of Meta II, and an anticipation of active state features under conditions that stabilize inactive photoproduct states in wildtype rhodopsin. Glu181 on extracellular loop 2, is found to be unable to maintain a counterion function to the Schiff base on the activation pathway of rhodopsin in the absence of the primary counterion, Glu113. The Schiff base becomes protonated in the transition to Meta III. This protonation is, however, not associated with a deactivation of the receptor, in contrast to wildtype rhodopsin. Glu181 is suggested to be the counterion in the Meta III state of the mutant and appears to be capable of stabilizing a protonated Schiff base in Meta III, but not of constraining the receptor in an inactive conformation.
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Affiliation(s)
- Jörg Standfuss
- Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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43
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Knierim B, Hofmann KP, Gärtner W, Hubbell WL, Ernst OP. Rhodopsin and 9-demethyl-retinal analog: effect of a partial agonist on displacement of transmembrane helix 6 in class A G protein-coupled receptors. J Biol Chem 2007; 283:4967-74. [PMID: 18063586 DOI: 10.1074/jbc.m703059200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin is the visual pigment of rod cells and a prototypical G protein-coupled receptor. It is activated by cis-->trans photoisomerization of the covalently bound chromophore 11-cis-retinal, which acts in the cis configuration as an inverse agonist. Light-induced formation of the full agonist all-trans-retinal in situ triggers conformational changes in the protein moiety. Partial agonists of rhodopsin include a retinal analog lacking the methyl group at C-9, termed 9-demethyl-retinal (9-dm-retinal). Rhodopsin reconstituted with this retinal (9-dm-rhodopsin) activates G protein poorly. Here we investigated the molecular nature of the partial agonism in 9-dm-rhodopsin using site-directed spin labeling. Earlier site-directed spin labeling studies of rhodopsin identified a rigid-body tilt of the cytoplasmic segment of [corrected] transmembrane helix 6 (TM6) by approximately 6A as a central event in rhodopsin activation. Data presented here provide additional evidence for this mechanism. Only a small fraction of photoexcited 9-dm pigments reaches the TM6-tilted conformation. This fraction can be increased by increasing proton concentration or [corrected] by anticipation of the activating protonation step by the mutation E134Q in 9-dm-rhodopsin. These results on protein conformation are in complete accord with previous findings regarding the biological activity of the 9-dm pigments. When the proton concentration is further increased, a new state arises in 9-dm pigments that is linked to direct proton uptake at the retinal Schiff base. This state apparently has a conformation distinguishable from the active state.
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Affiliation(s)
- Bernhard Knierim
- Institut für Medizinische Physik und Biophysik (CCM), Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany
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Massaro S, Zlateva T, Torre V, Quaroni L. Detection of molecular processes in the intact retina by ATR-FTIR spectromicroscopy. Anal Bioanal Chem 2007; 390:317-22. [DOI: 10.1007/s00216-007-1710-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 10/10/2007] [Accepted: 10/16/2007] [Indexed: 11/30/2022]
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Vogel R, Sakmar TP, Sheves M, Siebert F. Coupling of Protonation Switches During Rhodopsin Activation†. Photochem Photobiol 2007; 83:286-92. [PMID: 17576345 DOI: 10.1562/2006-06-19-ir-937] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent studies of the activation mechanism of rhodopsin involving Fourier-transform infrared spectroscopy and a combination of chromophore modifications and site-directed mutagenesis reveal an allosteric coupling between two protonation switches. In particular, the ring and the 9-methyl group of the all-trans retinal chromophore serve to couple two proton-dependent activation steps: proton uptake by a cytoplasmic network between transmembrane (TM) helices 3 and 6 around the conserved ERY (Glu-Arg-Tyr) motif and disruption of a salt bridge between the retinal protonated Schiff base (PSB) and a protein counterion in the TM core of the receptor. Retinal analogs lacking the ring or 9-methyl group are only partial agonists--the conformational equilibrium between inactive Meta I and active Meta II photoproduct states is shifted to Meta I. An artificial pigment was engineered, in which the ring of retinal was removed and the PSB salt bridge was weakened by fluorination of C14 of the retinal polyene. These modifications abolished allosteric coupling of the proton switches and resulted in a stabilized Meta I state with a deprotonated Schiff base (Meta I(SB)). This state had a partial Meta II-like conformation due to disruption of the PSB salt bridge, but still lacked the cytoplasmic proton uptake reaction characteristic of the final transition to Meta II. As activation of native rhodopsin is known to involve deprotonation of the retinal Schiff base prior to formation of Meta II, this Meta I(SB) state may serve as a model for the structural characterization of a key transient species in the activation pathway of a prototypical G protein-coupled receptor.
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Affiliation(s)
- Reiner Vogel
- Arbeitsgruppe Biophysik, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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Lehmann N, Alexiev U, Fahmy K. Linkage Between the Intramembrane H-bond Network Around Aspartic Acid 83 and the Cytosolic Environment of Helix 8 in Photoactivated Rhodopsin. J Mol Biol 2007; 366:1129-41. [PMID: 17196983 DOI: 10.1016/j.jmb.2006.11.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Revised: 11/21/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
Understanding the coupling between conformational changes in the intramembrane domain and at the membrane-exposed surface of the bovine photoreceptor rhodopsin, a prototypical G protein-coupled receptor (GPCR), is crucial for the elucidation of molecular mechanisms in GPCR activation. Here, we have combined Fourier transform infrared (FTIR) and fluorescence spectroscopy to address the coupling between conformational changes in the intramembrane region around the retinal and the environment of helix 8, a putative cytosolic surface switch region in class-I GPCRs. Using FTIR/fluorescence cross-correlation we show specifically that surface alterations monitored by emission changes of fluorescein bound to Cys316 in helix 8 of rhodopsin are highly correlated with (i) H-bonding to Asp83 proximal of the retinal Schiff base but not to Glu122 close to the beta-ionone and (ii) with a metarhodopsin II (MII)-specific 1643 cm(-1) IR absorption change, indicative of a partial loss of secondary structure in helix 8 upon MII formation. These correlations are disrupted by limited C-terminal proteolysis but are maintained upon binding of a transducin alpha-subunit (G(talpha))-derived peptide, which stabilizes the MII state. Our results suggest that additional C-terminal cytosolic loop contacts monitored by an amide II absorption at 1557 cm(-1) play a functionally crucial role in keeping helix 8 in the position in which its environment is strongly coupled to the retinal-binding site near the Schiff base. In the intramembrane region, this coupling is mediated by the H-bonding network that connects Asp83 to the NPxxY(x)F motif preceding helix 8.
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Affiliation(s)
- Nicole Lehmann
- Institute of Radiation Physics, Biophysics Division, Forschungszentrum Dresden-Rossendorf, PF 510119, D-01314 Dresden, Germany
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47
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Crozier PS, Stevens MJ, Woolf TB. How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. Proteins 2007; 66:559-74. [PMID: 17109408 PMCID: PMC2848121 DOI: 10.1002/prot.21175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.
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Affiliation(s)
- Paul S Crozier
- Sandia National Laboratories, MS 1322, Albuquerque, New Mexico 87185-1322, USA.
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48
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Ritter E, Elgeti M, Hofmann KP, Bartl FJ. Deactivation and proton transfer in light-induced metarhodopsin II/metarhodopsin III conversion: a time-resolved fourier transform infrared spectroscopic study. J Biol Chem 2007; 282:10720-30. [PMID: 17287211 DOI: 10.1074/jbc.m610658200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vertebrate rhodopsin shares with other retinal proteins the 11-cis-retinal chromophore and the light-induced 11-cis/trans isomerization triggering its activation pathway. However, only in rhodopsin the retinylidene Schiff base bond to the apoprotein is eventually hydrolyzed, making a complex regeneration pathway necessary. Metabolic regeneration cannot be short-cut, and light absorption in the active metarhodopsin (Meta) II intermediate causes anti/syn isomerization around the retinylidene linkage rather than reversed trans/cis isomerization. A new deactivating pathway is thereby triggered, which ends in the Meta III "retinal storage" product. Using time-resolved Fourier transform infrared spectroscopy, we show that the identified steps of receptor activation, including Schiff base deprotonation, protein structural changes, and proton uptake by the apoprotein, are all reversed. However, Schiff base reprotonation is much faster than the activating deprotonation, whereas the protein structural changes are slower. The final proton release occurs with pK approximately 4.5, similar to the pK of a free Glu residue and to the pK at which the isolated opsin apoprotein becomes active. A forced deprotonation, equivalent to the forced protonation in the activating pathway, which occurs against the unfavorable pH of the medium, is not observed. This explains properties of the final Meta III product, which displays much higher residual activity and is less stable than rhodopsin arising from regeneration with 11-cis-retinal. We propose that the anti/syn conversion can only induce a fast reorientation and distance change of the Schiff base but fails to build up the full set of dark ground state constraints, presumably involving the Glu(134)/Arg(135) cluster.
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Affiliation(s)
- Eglof Ritter
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Charitéplatz 1, D-10098 Berlin
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Bartl FJ, Vogel R. Structural and functional properties of metarhodopsin III: recent spectroscopic studies on deactivation pathways of rhodopsin. Phys Chem Chem Phys 2007; 9:1648-58. [PMID: 17396175 DOI: 10.1039/b616365c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The activation of rhodopsin has been the focus of researchers over the past decades, revealing many aspects of the activation pathways of this prototypical G protein-coupled receptor on a molecular level, starting with the light-dependent isomerization of its retinal chromophore from 11-cis to all-trans and leading eventually to the large scale helix movements in the transition to the active receptor state, Meta II. Comparatively little is known, however, on the deactivation pathways of the light receptor, which represent essential steps in maintaining a functional photoreceptor cell. Rhodopsin's active receptor species, Meta II, decays by two fundamentally different pathways, either forming the apoprotein opsin by release of the activating all-trans retinal ligand from its binding pocket, or by a thermal isomerization of this ligand to a less activating species in the transition to metarhodopsin III (Meta III). Both decay products, opsin and Meta III, are largely inactive under physiological conditions, yet they do not restore the complete inactivity of the dark state. Although some properties of Meta III have been described already in the 1960s, its molecular nature and the pathways of its formation have remained rather obscure. In this review, we focus on recent studies from our laboratories, which have provided a major progress in our understanding of the Meta III deactivation pathway and its potential physiological roles. Using Fourier-transform infrared (FTIR) difference spectroscopy in combination with a variety of other spectroscopic and biochemical techniques and quantum chemical calculations, we have developed a general picture of the interplay between the retinal ligand and the receptor protein, which is compared to similar reaction mechanisms in invertebrate photoreceptors and microbial retinal proteins.
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Affiliation(s)
- Franz J Bartl
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Campus Charité Mitte, Schumannstrasse 20-21, 10015, Berlin, Germany.
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Interaction of chromophore, 11-cis-retinal, with amino acid residues of the visual pigment rhodopsin in the region of protonated Schiff base: A molecular dynamics study. Russ Chem Bull 2007. [DOI: 10.1007/s11172-007-0004-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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