1
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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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2
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Alachkar A. Aromatic patterns: Tryptophan aromaticity as a catalyst for the emergence of life and rise of consciousness. Phys Life Rev 2022; 42:93-114. [PMID: 35905538 DOI: 10.1016/j.plrev.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022]
Abstract
Sunlight held the key to the origin of life on Earth. The earliest life forms, cyanobacteria, captured the sunlight to generate energy through photosynthesis. Life on Earth evolved in accordance with the circadian rhythms tied to sensitivity to sunlight patterns. A unique feature of cyanobacterial photosynthetic proteins and circadian rhythms' molecules, and later of nearly all photon-sensing molecules throughout evolution, is that the aromatic amino acid tryptophan (Trp) resides at the center of light-harvesting active sites. In this perspective, I review the literature and integrate evidence from different scientific fields to explore the role Trp plays in photon-sensing capabilities of living organisms through its resonance delocalization of π-electrons. The observations presented here are the product of apparently unrelated phenomena throughout evolution, but nevertheless share consistent patterns of photon-sensing by Trp-containing and Trp-derived molecules. I posit the unique capacity to transfer electrons during photosynthesis in the earliest life forms is conferred to Trp due to its aromaticity. I propose this ability evolved to assume more complex functions, serving as a host for mechanisms underlying mental aptitudes - a concept which provides a theoretical basis for defining the neural correlates of consciousness. The argument made here is that Trp aromaticity may have allowed for the inception of the mechanistic building blocks used to fabricate complexity in higher forms of life. More specifically, Trp aromatic non-locality may have acted as a catalyst for the emergence of consciousness by instigating long-range synchronization and stabilizing the large-scale coherence of neural networks, which mediate functional brain activity. The concepts proposed in this perspective provide a conceptual foundation that invites further interdisciplinary dialogue aimed at examining and defining the role of aromaticity (beyond Trp) in the emergence of life and consciousness.
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Affiliation(s)
- Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA; UC Irvine Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA.
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3
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Srinivasan S, Fernández-Sampedro MA, Morillo M, Ramon E, Jiménez-Rosés M, Cordomí A, Garriga P. Human Blue Cone Opsin Regeneration Involves Secondary Retinal Binding with Analog Specificity. Biophys J 2018; 114:1285-1294. [PMID: 29590586 PMCID: PMC5883618 DOI: 10.1016/j.bpj.2018.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigments.
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Affiliation(s)
| | | | | | - Eva Ramon
- Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Mireia Jiménez-Rosés
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Garriga
- Universitat Politècnica de Catalunya, Terrassa, Spain.
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4
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Elgeti M, Kazmin R, Rose AS, Szczepek M, Hildebrand PW, Bartl FJ, Scheerer P, Hofmann KP. The arrestin-1 finger loop interacts with two distinct conformations of active rhodopsin. J Biol Chem 2018; 293:4403-4410. [PMID: 29363577 DOI: 10.1074/jbc.m117.817890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/17/2018] [Indexed: 11/06/2022] Open
Abstract
Signaling of the prototypical G protein-coupled receptor (GPCR) rhodopsin through its cognate G protein transducin (Gt) is quenched when arrestin binds to the activated receptor. Although the overall architecture of the rhodopsin/arrestin complex is known, many questions regarding its specificity remain unresolved. Here, using FTIR difference spectroscopy and a dual pH/peptide titration assay, we show that rhodopsin maintains certain flexibility upon binding the "finger loop" of visual arrestin (prepared as synthetic peptide ArrFL-1). We found that two distinct complexes can be stabilized depending on the protonation state of E3.49 in the conserved (D)ERY motif. Both complexes exhibit different interaction modes and affinities of ArrFL-1 binding. The plasticity of the receptor within the rhodopsin/ArrFL-1 complex stands in contrast to the complex with the C terminus of the Gt α-subunit (GαCT), which stabilizes only one specific substate out of the conformational ensemble. However, Gt α-subunit binding and both ArrFL-1-binding modes involve a direct interaction to conserved R3.50, as determined by site-directed mutagenesis. Our findings highlight the importance of receptor conformational flexibility and cytoplasmic proton uptake for modulation of rhodopsin signaling and thereby extend the picture provided by crystal structures of the rhodopsin/arrestin and rhodopsin/ArrFL-1 complexes. Furthermore, the two binding modes of ArrFL-1 identified here involve motifs of conserved amino acids, which indicates that our results may have elucidated a common modulation mechanism of class A GPCR-G protein/-arrestin signaling.
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Affiliation(s)
- Matthias Elgeti
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,
| | - Roman Kazmin
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Alexander S Rose
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Group ProteInformatics
| | - Michal Szczepek
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction
| | - Peter W Hildebrand
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Franz J Bartl
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Patrick Scheerer
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction
| | - Klaus Peter Hofmann
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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5
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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6
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Kazmin R, Rose A, Szczepek M, Elgeti M, Ritter E, Piechnick R, Hofmann KP, Scheerer P, Hildebrand PW, Bartl FJ. The Activation Pathway of Human Rhodopsin in Comparison to Bovine Rhodopsin. J Biol Chem 2015; 290:20117-27. [PMID: 26105054 DOI: 10.1074/jbc.m115.652172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin, the photoreceptor of rod cells, absorbs light to mediate the first step of vision by activating the G protein transducin (Gt). Several human diseases, such as retinitis pigmentosa or congenital night blindness, are linked to rhodopsin malfunctions. Most of the corresponding in vivo studies and structure-function analyses (e.g. based on protein x-ray crystallography or spectroscopy) have been carried out on murine or bovine rhodopsin. Because these rhodopsins differ at several amino acid positions from human rhodopsin, we conducted a comprehensive spectroscopic characterization of human rhodopsin in combination with molecular dynamics simulations. We show by FTIR and UV-visible difference spectroscopy that the light-induced transformations of the early photointermediates are very similar. Significant differences between the pigments appear with formation of the still inactive Meta I state and the transition to active Meta II. However, the conformation of Meta II and its activity toward the G protein are essentially the same, presumably reflecting the evolutionary pressure under which the active state has developed. Altogether, our results show that although the basic activation pathways of human and bovine rhodopsin are similar, structural deviations exist in the inactive conformation and during receptor activation, even between closely related rhodopsins. These differences between the well studied bovine or murine rhodopsins and human rhodopsin have to be taken into account when the influence of point mutations on the activation pathway of human rhodopsin are investigated using the bovine or murine rhodopsin template sequences.
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Affiliation(s)
- Roman Kazmin
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, 10115 Berlin, Germany, and
| | - Alexander Rose
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG ProteInformatics, Charitéplatz 1, 10117 Berlin, Germany
| | - Michal Szczepek
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG Protein X-ray Crystallography and Signal Transduction, and
| | - Matthias Elgeti
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin
| | - Eglof Ritter
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, 10115 Berlin, Germany, and
| | - Ronny Piechnick
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin
| | - Klaus Peter Hofmann
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Zentrum für Biophysik und Bioinformatik (BPI), Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Patrick Scheerer
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG Protein X-ray Crystallography and Signal Transduction, and
| | - Peter W Hildebrand
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG ProteInformatics, Charitéplatz 1, 10117 Berlin, Germany
| | - Franz J Bartl
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin,
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7
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Struts AV, Barmasov AV, Brown MF. SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. I. VIBRATIONAL AND ELECTRONIC SPECTROSCOPY. OPTICS AND SPECTROSCOPY 2015; 118:711-717. [PMID: 28260815 PMCID: PMC5334778 DOI: 10.1134/s0030400x15050240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we review the application of modern spectral methods for the study of G-protein-coupled receptors (GPCRs) using rhodopsin as a prototype. Because X-ray analysis gives us immobile snapshots of protein conformations, it is imperative to apply spectroscopic methods for elucidating their function: vibrational (Raman, FTIR), electronic (UV-visible absorption, fluorescence) spectroscopies, and magnetic resonance (electron paramagnetic resonance, EPR), and nuclear magnetic resonance, NMR). In the first of the two companion articles, we discuss the application of optical spectroscopy for studying rhodopsin in a membrane environment. Information is obtained regarding the time-ordered sequence of events in rhodopsin activation. Isomerization of the chromophore and deprotonation of the retinal Schiff base leads to a structural change of the protein involving the motion of helices H5 and H6 in a pH-dependent process. Information is obtained that is unavailable from X-ray crystallography, which can be combined with spectroscopic studies to achieve a more complete understanding of GPCR function.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- University of Arizona, Tucson, AZ 85721 USA
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8
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Malmerberg E, M Bovee-Geurts PH, Katona G, Deupi X, Arnlund D, Wickstrand C, Johansson LC, Westenhoff S, Nazarenko E, Schertler GFX, Menzel A, de Grip WJ, Neutze R. Conformational activation of visual rhodopsin in native disc membranes. Sci Signal 2015; 8:ra26. [PMID: 25759477 DOI: 10.1126/scisignal.2005646] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rhodopsin is the G protein-coupled receptor (GPCR) that serves as a dim-light receptor for vision in vertebrates. We probed light-induced conformational changes in rhodopsin in its native membrane environment at room temperature using time-resolved wide-angle x-ray scattering. We observed a rapid conformational transition that is consistent with an outward tilt of the cytoplasmic portion of transmembrane helix 6 concomitant with an inward movement of the cytoplasmic portion of transmembrane helix 5. These movements were considerably larger than those reported from the basis of crystal structures of activated rhodopsin, implying that light activation of rhodopsin involves a more extended conformational change than was previously suggested.
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Affiliation(s)
- Erik Malmerberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Petra H M Bovee-Geurts
- Department of Biochemistry, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Xavier Deupi
- Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232 Villigen, Switzerland. Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Linda C Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Elena Nazarenko
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland. Department of Biology, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland
| | - Andreas Menzel
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Willem J de Grip
- Department of Biochemistry, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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9
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Srinivasan S, Ramon E, Cordomí A, Garriga P. Binding specificity of retinal analogs to photoactivated visual pigments suggest mechanism for fine-tuning GPCR-ligand interactions. ACTA ACUST UNITED AC 2014; 21:369-78. [PMID: 24560606 DOI: 10.1016/j.chembiol.2014.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/21/2013] [Accepted: 01/13/2014] [Indexed: 11/16/2022]
Abstract
11-cis-retinal acts as an inverse agonist stabilizing the inactive conformation of visual pigments, and upon photoactivation, it isomerizes to all-trans-retinal, initiating signal transduction. We have analyzed opsin regeneration with retinal analogs for rhodopsin and red cone opsin. We find differential binding of the analogs to the receptors after photobleaching and a dependence of the binding kinetics on the oligomerization state of the protein. The results outline the sensitivity of retinal entry to the binding pocket of visual receptors to the specific conformation adopted by the receptor and by the molecular architecture defined by specific amino acids in the binding pocket and the retinal entry site, as well as the topology of the retinal analog. Overall, our findings highlight the specificity of the ligand-opsin interactions, a feature that can be shared by other G-protein-coupled receptors.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Chemical Engineering Department, Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Eva Ramon
- Chemical Engineering Department, Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pere Garriga
- Chemical Engineering Department, Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain.
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10
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Lohse MJ, Maiellaro I, Calebiro D. Kinetics and mechanism of G protein-coupled receptor activation. Curr Opin Cell Biol 2013; 27:87-93. [PMID: 24530699 DOI: 10.1016/j.ceb.2013.11.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 10/25/2022]
Abstract
The activation of a G protein-coupled receptor is generally triggered by binding of an agonist to the receptor's binding pocket, or, in the case of rhodopsin, by light-induced changes of the pre-bound retinal. This is followed by a series of a conformational changes towards an active receptor conformation, which is capable of signalling to G proteins and other downstream proteins. In the past few years, a number of new techniques have been employed to analyze the kinetics of this activation process, including X-ray crystallographic three-dimensional structures of receptors in the inactive and the active states, NMR studies of labelled receptors, molecular simulations, and optical analyses with fluorescence resonance energy transfer (FRET). Here we review our current understanding of the activation process of GPCRs as well as open questions in the sequence of events ranging from (sub-)microsecond activation by light or agonist binding to millisecond activation of receptors by soluble ligands and the subsequent generation of an intracellular signal.
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Affiliation(s)
- Martin J Lohse
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany; Rudolf Virchow Center, DFG-Research Center for Experimental Biomedicine, University of Würzburg, 97078 Würzburg, Germany.
| | - Isabella Maiellaro
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany; Rudolf Virchow Center, DFG-Research Center for Experimental Biomedicine, University of Würzburg, 97078 Würzburg, Germany
| | - Davide Calebiro
- Institute of Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany; Rudolf Virchow Center, DFG-Research Center for Experimental Biomedicine, University of Würzburg, 97078 Würzburg, Germany
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11
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Alexiev U, Farrens DL. Fluorescence spectroscopy of rhodopsins: insights and approaches. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:694-709. [PMID: 24183695 DOI: 10.1016/j.bbabio.2013.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Ulrike Alexiev
- Physics Department, Freie Universität Berlin, Berlin, Germany.
| | - David L Farrens
- Departments of Biochemistry and Molecular Biology, Oregon Health Sciences University, USA
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12
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Imamoto Y, Seki I, Yamashita T, Shichida Y. Efficiencies of activation of transducin by cone and rod visual pigments. Biochemistry 2013; 52:3010-8. [PMID: 23570417 DOI: 10.1021/bi3015967] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
How the light-induced transducin (Gt) activation process differs biochemically between cone visual pigments and rod visual pigment (rhodopsin) has remained unclear, because the Gt-activating state (Meta-II) of cone visual pigment decays too fast to precisely measure the activation efficiency by conventional biochemical methods such as the GTPγS binding assay. Here we measured the activation efficiencies of chicken green-sensitive cone visual pigment (cG) and bovine rhodopsin (bRh) in real time by monitoring the intrinsic fluorescence of tryptophan residues in the pigments and Gt. Michaelis-Menten analysis of Gt activation showed that the initial velocity for cG was approximately half that for bRh, while their Michaelis constants were comparable. Gt activation by cG was immediately slowed because of the fast hydrolysis of the retinal Schiff base in Meta-II, but this hydrolysis was suppressed by forming the complex with Gt. Using mutants of cG and bRh for positions 122 and 189, which exhibit altered rates of chromophore hydrolysis in Meta-II, we found that the initial velocity of Gt activation is negatively correlated with the rate of chromophore hydrolysis. These results suggest that the amino acid residues at positions 122 and 189 account for not only the resistance to the chromophore hydrolysis in Meta-II but also the conformation of Meta-II for efficient Gt activation. The substantially longer lifetime of the Gt activating state of Rh would be necessary to suppress the spontaneous quenching by the stochastic decay of the Gt-activating state when a rod responds to a single photon.
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Affiliation(s)
- Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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13
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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Kaye RG, Saldanha JW, Lu ZL, Hulme EC. Helix 8 of the M1 muscarinic acetylcholine receptor: scanning mutagenesis delineates a G protein recognition site. Mol Pharmacol 2011; 79:701-9. [PMID: 21247934 DOI: 10.1124/mol.110.070177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have used alanine-scanning mutagenesis followed by functional expression and molecular modeling to analyze the roles of the 14 residues, Asn422 to Cys435, C-terminal to transmembrane (TM) helix 7 of the M(1) muscarinic acetylcholine receptor. The results suggest that they form an eighth (H8) helix, associated with the cytoplasmic surface of the cell membrane in the active state of the receptor. We suggest that the amide side chain of Asn422 may act as a cap to the C terminus of TM7, stabilizing its junction with H8, whereas the side chain of Phe429 may restrict the relative movements of H8 and the C terminus of TM7 in the inactive ground state of the receptor. We have identified four residues, Phe425, Arg426, Thr428, and Leu432, which are important for G protein binding and signaling. These may form a docking site for the C-terminal helix of the G protein α subunit, and collaborate with G protein recognition residues elsewhere in the cytoplasmic domain of the receptor to form a coherent surface for G protein binding in the activated state of the receptor.
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Affiliation(s)
- Robert G Kaye
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom
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15
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Hoersch D, Bolourchian F, Otto H, Heyn MP, Bogomolni RA. Dynamics of light-induced activation in the PAS domain proteins LOV2 and PYP probed by time-resolved tryptophan fluorescence. Biochemistry 2010; 49:10811-7. [PMID: 21090690 DOI: 10.1021/bi101413v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Light-induced activation of the LOV2-Jα domain of the photoreceptor phototropin from oat is believed to involve the detachment of the Jα helix from the central β-sheet and its subsequent unfolding. The dynamics of these conformational changes were monitored by time-resolved emission spectroscopy with 100 ns time resolution. Three transitions were detected during the LOV2-Jα photocycle with time constants of 3.4 μs, 500 μs, and 4.3 ms. The fastest transition is due to the decay of the flavin phosphorescence in the transition of the triplet LOV(L)(660) state to the singlet LOV(S)(390) signaling state. The 500 μs and 4.3 ms transitions are due to changes in tryptophan fluorescence and may be associated with the dissociation and unfolding of the Jα helix, respectively. They are absent in the transient absorption signal of the flavin chromophore. The tryptophan fluorescence signal monitors structural changes outside the chromophore binding pocket and indicates that there are at least three LOV(S)(390) intermediates. Since the 500 μs and 4.3 ms components are absent in a construct without the Jα helix and in the mutant W557S, the fluorescence signal is mainly due to tryptophan 557. The kinetics of the main 500 μs component is strongly temperature dependent with activation energy of 18.2 kcal/mol suggesting its association with a major structural change. In the structurally related PAS domain protein PYP the N-terminal cap dissociates from the central β-sheet and unfolds upon signaling state formation with a similar time constant of ∼1 ms. Using transient fluorescence we obtained a nearly identical activation energy of 18.5 kcal/mol for this transition.
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Affiliation(s)
- Daniel Hoersch
- Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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16
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Mansoor SE, Dewitt MA, Farrens DL. Distance mapping in proteins using fluorescence spectroscopy: the tryptophan-induced quenching (TrIQ) method. Biochemistry 2010; 49:9722-31. [PMID: 20886836 DOI: 10.1021/bi100907m] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studying the interplay between protein structure and function remains a daunting task. Especially lacking are methods for measuring structural changes in real time. Here we report our most recent improvements to a method that can be used to address such challenges. This method, which we now call tryptophan-induced quenching (TrIQ), provides a straightforward, sensitive, and inexpensive way to address questions of conformational dynamics and short-range protein interactions. Importantly, TrIQ only occurs over relatively short distances (∼5-15 Å), making it complementary to traditional fluorescence resonance energy transfer (FRET) methods that occur over distances too large for precise studies of protein structure. As implied in the name, TrIQ measures the efficient quenching induced in some fluorophores by tryptophan (Trp). We present here our analysis of the TrIQ effect for five different fluorophores that span a range of sizes and spectral properties. Each probe was attached to four different cysteine residues on T4 lysozyme, and the extent of TrIQ caused by a nearby Trp was measured. Our results show that, at least for smaller probes, the extent of TrIQ is distance dependent. Moreover, we also demonstrate how TrIQ data can be analyzed to determine the fraction of fluorophores involved in a static, nonfluorescent complex with Trp. Based on this analysis, our study shows that each fluorophore has a different TrIQ profile, or "sphere of quenching", which correlates with its size, rotational flexibility, and the length of attachment linker. This TrIQ-based "sphere of quenching" is unique to every Trp-probe pair and reflects the distance within which one can expect to see the TrIQ effect. Thus,TrIQ provides a straightforward, readily accessible approach for mapping distances within proteins and monitoring conformational changes using fluorescence spectroscopy.
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Affiliation(s)
- Steven E Mansoor
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098, United States
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17
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Farrens DL. What site-directed labeling studies tell us about the mechanism of rhodopsin activation and G-protein binding. Photochem Photobiol Sci 2010; 9:1466-74. [PMID: 20967340 DOI: 10.1039/c0pp00283f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rhodopsin is the photoreceptor protein responsible for dim-light vision in mammals. Due to extensive biophysical, structural and computational analysis of this membrane protein, it is presently the best understood G-protein coupled receptor (GPCR). Here I briefly review one approach that has been extensively used to identify dynamic and structural changes in rhodopsin--the use of site-directed labeling methods (SDL) coupled with electron paramagnetic resonance (EPR) and fluorescence spectroscopy. These SDL studies involve introducing individual cysteine residues into the receptor, then labeling them with cysteine-reactive probes for subsequent analysis by the appropriate spectroscopy. I will give a brief overview of how SDL methods are carried out and how the data is analyzed. Then, I will discuss how SDL studies were carried out on rhodopsin, and how they were used to identify a key structural change that occurs in rhodopsin upon activation--movement of transmembrane helix 6 (TM6). I will also briefly discuss how the SDL studies of rhodopsin compare with SDL studies of other GPCRs, and compare the SDL data with early and recent crystal structures of rhodopsin. Finally, I will discuss why the TM6 movement is required for rhodopsin to couple with the G-protein transducin, and speculate how this mechanism might be a universal method used by all GPCRs to bind G-proteins and perhaps other proteins involved in visual signal transduction, such as arrestin and rhodopsin kinase.
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Affiliation(s)
- David L Farrens
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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19
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A G protein-coupled receptor at work: the rhodopsin model. Trends Biochem Sci 2009; 34:540-52. [PMID: 19836958 DOI: 10.1016/j.tibs.2009.07.005] [Citation(s) in RCA: 297] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/17/2009] [Accepted: 07/28/2009] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are ubiquitous signal transducers in cell membranes, as well as important drug targets. Interaction with extracellular agonists turns the seven transmembrane helix (7TM) scaffold of a GPCR into a catalyst for GDP and GTP exchange in heterotrimeric Galphabetagamma proteins. Activation of the model GPCR, rhodopsin, is triggered by photoisomerization of its retinal ligand. From the augmentation of biochemical and biophysical studies by recent high-resolution 3D structures, its activation intermediates can now be interpreted as the stepwise engagement of protein domains. Rearrangement of TM5-TM6 opens a crevice at the cytoplasmic side of the receptor into which the C terminus of the Galpha subunit can bind. The Galpha C-terminal helix is used as a transmission rod to the nucleotide binding site. The mechanism relies on dynamic interactions between conserved residues and could therefore be common to other GPCRs.
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Hoersch D, Otto H, Cusanovich MA, Heyn MP. Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap. Phys Chem Chem Phys 2009; 11:5437-44. [PMID: 19551213 DOI: 10.1039/b821345c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photoreceptor PYP responds to light activation with global conformational changes. These changes are mainly located in the N-terminal cap of the protein, which is approximately 20 A away from the chromophore binding pocket and separated from it by the central beta-sheet. The question of the propagation of the structural change across the central beta-sheet is of general interest for the superfamily of PAS domain proteins, for which PYP is the structural prototype. Here we measured the kinetics of the structural changes in the N-terminal cap by transient absorption spectroscopy on the ns to second timescale. For this purpose the cysteine mutants A5C and N13C were prepared and labeled with thiol reactive 5-iodoacetamidofluorescein (IAF). A5 is located close to the N-terminus, while N13 is part of helix alpha1 near the functionally important salt bridge E12-K110 between the N-terminal cap and the central anti-parallel beta-sheet. The absorption spectrum of the dye is sensitive to its environment, and serves as a sensor for conformational changes near the labeling site. In both labeled mutants light activation results in a transient red-shift of the fluorescein absorption spectrum. To correlate the conformational changes with the photocycle intermediates of the protein, we compared the kinetics of the transient absorption signal of the dye with that of the p-hydroxycinnamoyl chromophore. While the structural change near A5 is synchronized with the rise of the I(2) intermediate, which is formed in approximately 200 mus, the change near N13 is delayed and rises with the next intermediate I(2)', which forms in approximately 2 ms. This indicates that different parts of the N-terminal cap respond to light activation with different kinetics. For the signaling pathway of photoactive yellow protein we propose a model in which the structural signal propagates from the chromophore binding pocket across the central beta-sheet via the N-terminal region to helix alpha1, resulting in a large change in the protein conformation.
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Affiliation(s)
- Daniel Hoersch
- Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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