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Tejero O, Pamula F, Koyanagi M, Nagata T, Afanasyev P, Das I, Deupi X, Sheves M, Terakita A, Schertler GFX, Rodrigues MJ, Tsai CJ. Active state structures of a bistable visual opsin bound to G proteins. Nat Commun 2024; 15:8928. [PMID: 39414813 PMCID: PMC11484933 DOI: 10.1038/s41467-024-53208-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 10/04/2024] [Indexed: 10/18/2024] Open
Abstract
Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption, causing conformational changes that result in receptor activation. Monostable opsins, responsible for vision in vertebrates, release the chromophore after activation and must bind another retinal molecule to remain functional. In contrast, bistable opsins, responsible for non-visual light perception in vertebrates and for vision in invertebrates, absorb a second photon in the active state to return the chromophore and protein to the inactive state. Structures of bistable opsins in the activated state have proven elusive, limiting our understanding of how they function as bidirectional photoswitches. Here we present active state structures of a bistable opsin, jumping spider rhodopsin isoform-1 (JSR1), in complex with its downstream signaling partners, the Gi and Gq heterotrimers. These structures elucidate key differences in the activation mechanisms between monostable and bistable opsins, offering essential insights for the rational engineering of bistable opsins into diverse optogenetic tools to control G protein signaling pathways.
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Affiliation(s)
- Oliver Tejero
- Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Filip Pamula
- Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
- The OMU Advanced Research Institute of Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Takashi Nagata
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Xavier Deupi
- Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland
- Condensed Matter Theory Group, Laboratory of Theoretical and Computational Physics, PSI Center for Scientific Computing, Theory and Data, Villigen-PSI, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
- The OMU Advanced Research Institute of Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland.
| | - Matthew J Rodrigues
- Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland.
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland.
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2
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Abstract
Rhodopsin is the photoreceptor in human rod cells responsible for dim-light vision. The visual receptors are part of the large superfamily of G protein-coupled receptors (GPCRs) that mediate signal transduction in response to diverse diffusible ligands. The high level of sequence conservation within the transmembrane helices of the visual receptors and the family A GPCRs has long been considered evidence for a common pathway for signal transduction. I review recent studies that reveal a comprehensive mechanism for how light absorption by the retinylidene chromophore drives rhodopsin activation and highlight those features of the mechanism that are conserved across the ligand-activated GPCRs.
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Affiliation(s)
- Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA;
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3
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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4
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Structure-guided optimization of light-activated chimeric G-protein-coupled receptors. Structure 2022; 30:1075-1087.e4. [PMID: 35588733 DOI: 10.1016/j.str.2022.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/22/2022] [Accepted: 04/22/2022] [Indexed: 01/11/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest human receptor family and involved in virtually every physiological process. One hallmark of their function is specific coupling to selected signaling pathways. The ability to tune this coupling would make development of receptors with new capabilities possible. Complexes of GPCRs and G-proteins have recently been resolved at high resolution, but this information was in only few cases harnessed for rational receptor engineering. Here, we demonstrate structure-guided optimization of light-activated OptoXRs. Our hypothesis was that incorporation of GPCR-Gα contacts would lead to improved coupling. We first evaluated structure-based alignments for chimeric receptor fusion. We then show in a light-activated β2AR that including Gα contacts increased signaling 7- to 20-fold compared with other designs. In turn, contact elimination diminished function. Finally, this platform allowed optimization of a further OptoXR and spectral tuning. Our work exemplifies structure-based OptoXR development for targeted cell and network manipulation.
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5
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New insights into the molecular mechanism of rhodopsin retinitis pigmentosa from the biochemical and functional characterization of G90V, Y102H and I307N mutations. Cell Mol Life Sci 2022; 79:58. [PMID: 34997336 PMCID: PMC8741697 DOI: 10.1007/s00018-021-04086-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022]
Abstract
Mutations in the photoreceptor protein rhodopsin are known as one of the leading causes of retinal degeneration in humans. Two rhodopsin mutations, Y102H and I307N, obtained in chemically mutagenized mice, are currently the subject of increased interest as relevant models for studying the process of retinal degeneration in humans. Here, we report on the biochemical and functional characterization of the structural and functional alterations of these two rhodopsin mutants and we compare them with the G90V mutant previously analyzed, as a basis for a better understanding of in vivo studies. This mechanistic knowledge is fundamental to use it for developing novel therapeutic approaches for the treatment of inherited retinal degeneration in retinitis pigmentosa. We find that Y102H and I307N mutations affect the inactive–active equilibrium of the receptor. In this regard, the mutations reduce the stability of the inactive conformation but increase the stability of the active conformation. Furthermore, the initial rate of the functional activation of transducin, by the I307N mutant is reduced, but its kinetic profile shows an unusual increase with time suggesting a profound effect on the signal transduction process. This latter effect can be associated with a change in the flexibility of helix 7 and an indirect effect of the mutation on helix 8 and the C-terminal tail of rhodopsin, whose potential role in the functional activation of the receptor has been usually underestimated. In the case of the Y102H mutant, the observed changes can be associated with conformational alterations affecting the folding of the rhodopsin intradiscal domain, and its presumed involvement in the retinal binding process by the receptor.
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6
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McKee AG, Kuntz CP, Ortega JT, Woods H, Most V, Roushar FJ, Meiler J, Jastrzebska B, Schlebach JP. Systematic Profiling of Temperature- and Retinal-Sensitive Rhodopsin Variants by Deep Mutational Scanning. J Biol Chem 2021; 297:101359. [PMID: 34756884 PMCID: PMC8649220 DOI: 10.1016/j.jbc.2021.101359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 01/29/2023] Open
Abstract
Membrane protein variants with diminished conformational stability often exhibit enhanced cellular expression at reduced growth temperatures. The expression of “temperature-sensitive” variants is also typically sensitive to corrector molecules that bind and stabilize the native conformation. There are many examples of temperature-sensitive rhodopsin variants, the misfolding of which is associated with the molecular basis of retinitis pigmentosa. In this work, we employ deep mutational scanning to compare the effects of reduced growth temperature and 9-cis-retinal, an investigational corrector, on the plasma membrane expression of 700 rhodopsin variants in HEK293T cells. We find that the change in expression at reduced growth temperatures correlates with the response to 9-cis-retinal among variants bearing mutations within a hydrophobic transmembrane domain (TM2). The most sensitive variants appear to disrupt a native helical kink within this transmembrane domain. By comparison, mutants that alter the structure of a polar transmembrane domain (TM7) exhibit weaker responses to temperature and retinal that are poorly correlated. Statistical analyses suggest that this observed insensitivity cannot be attributed to a single variable, but likely arises from the composite effects of mutations on the energetics of membrane integration, the stability of the native conformation, and the integrity of the retinal-binding pocket. Finally, we show that the characteristics of purified temperature- and retinal-sensitive variants suggest that the proteostatic effects of retinal may be manifested during translation and cotranslational folding. Together, our findings highlight several biophysical constraints that appear to influence the sensitivity of genetic variants to temperature and small-molecule correctors.
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Affiliation(s)
- Andrew G McKee
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Charles P Kuntz
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Joseph T Ortega
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Hope Woods
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Victoria Most
- Institute for Drug Development, Leipzig University, Leipzig, SAC, Germany
| | - Francis J Roushar
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Institute for Drug Development, Leipzig University, Leipzig, SAC, Germany
| | - Beata Jastrzebska
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
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7
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Fernandez-Gonzalez P, Mas-Sanchez A, Garriga P. Polyphenols and Visual Health: Potential Effects on Degenerative Retinal Diseases. Molecules 2021; 26:3407. [PMID: 34199888 PMCID: PMC8200069 DOI: 10.3390/molecules26113407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/26/2022] Open
Abstract
Dietary polyphenols are a group of natural compounds that have been proposed to have beneficial effects on human health. They were first known for their antioxidant properties, but several studies over the years have shown that these compounds can exert protective effects against chronic diseases. Nonetheless, the mechanisms underlying these potential benefits are still uncertain and contradictory effects have been reported. In this review, we analyze the potential effects of polyphenol compounds on some visual diseases, with a special focus on retinal degenerative diseases. Current effective therapies for the treatment of such retinal diseases are lacking and new strategies need to be developed. For this reason, there is currently a renewed interest in finding novel ligands (or known ligands with previously unexpected features) that could bind to retinal photoreceptors and modulate their molecular properties. Some polyphenols, especially flavonoids (e.g., quercetin and tannic acid), could attenuate light-induced receptor damage and promote visual health benefits. Recent evidence suggests that certain flavonoids could help stabilize the correctly folded conformation of the visual photoreceptor protein rhodopsin and offset the deleterious effect of retinitis pigmentosa mutations. In this regard, certain polyphenols, like the flavonoids mentioned before, have been shown to improve the stability, expression, regeneration and folding of rhodopsin mutants in experimental in vitro studies. Moreover, these compounds appear to improve the integration of the receptor into the cell membrane while acting against oxidative stress at the same time. We anticipate that polyphenol compounds can be used to target visual photoreceptor proteins, such as rhodopsin, in a way that has only been recently proposed and that these can be used in novel approaches for the treatment of retinal degenerative diseases like retinitis pigmentosa; however, studies in this field are limited and further research is needed in order to properly characterize the effects of these compounds on retinal degenerative diseases through the proposed mechanisms.
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Affiliation(s)
| | | | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d’Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, 08222 Terrassa, Spain; (P.F.-G.); (A.M.-S.)
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8
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Fanelli F, Felline A, Marigo V. Structural aspects of rod opsin and their implication in genetic diseases. Pflugers Arch 2021; 473:1339-1359. [PMID: 33728518 DOI: 10.1007/s00424-021-02546-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 01/04/2023]
Abstract
Vision in dim-light conditions is triggered by photoactivation of rhodopsin, the visual pigment of rod photoreceptor cells. Rhodopsin is made of a protein, the G protein coupled receptor (GPCR) opsin, and the chromophore 11-cis-retinal. Vertebrate rod opsin is the GPCR best characterized at the atomic level of detail. Since the release of the first crystal structure 20 years ago, a huge number of structures have been released that, in combination with valuable spectroscopic determinations, unveiled most aspects of the photobleaching process. A number of spontaneous mutations of rod opsin have been found linked to vision-impairing diseases like autosomal dominant or autosomal recessive retinitis pigmentosa (adRP or arRP, respectively) and autosomal congenital stationary night blindness (adCSNB). While adCSNB is mainly caused by constitutive activation of rod opsin, RP shows more variegate determinants affecting different aspects of rod opsin function. The vast majority of missense rod opsin mutations affects folding and trafficking and is linked to adRP, an incurable disease that awaits light on its molecular structure determinants. This review article summarizes all major structural information available on vertebrate rod opsin conformational states and the insights gained so far into the structural determinants of adCSNB and adRP linked to rod opsin mutations. Strategies to design small chaperones with therapeutic potential for selected adRP rod opsin mutants will be discussed as well.
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Affiliation(s)
- Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy. .,Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy
| | - Valeria Marigo
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125, Modena, Italy
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9
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Kobal N, Krašovec T, Šuštar M, Volk M, Peterlin B, Hawlina M, Fakin A. Stationary and Progressive Phenotypes Caused by the p.G90D Mutation in Rhodopsin Gene. Int J Mol Sci 2021; 22:ijms22042133. [PMID: 33669941 PMCID: PMC7924842 DOI: 10.3390/ijms22042133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in rhodopsin gene (RHO) are a frequent cause of retinitis pigmentosa (RP) and less often, congenital stationary night blindness (CSNB). Mutation p.G90D has previously been associated with CSNB based on the examination of one family. This study screened 60 patients. Out of these 60 patients, 32 were affected and a full characterization was conducted in 15 patients. We described the clinical characteristics of these 15 patients (12 male, median age 42 years, range 8-71) from three families including visual field (Campus Goldmann), fundus autofluorescence (FAF), optical coherence tomography (OCT) and electrophysiology. Phenotypes were classified into four categories: CSNB (N = 3, 20%) sector RP (N = 3, 20%), pericentral RP (N = 1, 6.7%) and classic RP (N = 8, 53.3% (8/15)). The phenotypes were not associated with family, sex or age (Kruskal-Wallis, p > 0.05), however, cystoid macular edema (CME) was observed only in one family. Among the subjects reporting nyctalopia, 69% (22/32) were male. The clinical characteristics of the largest p.G90D cohort so far showed a large frequency of progressive retinal degeneration with 53.3% developing RP, contrary to the previous report.
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Affiliation(s)
- Nina Kobal
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Tjaša Krašovec
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Maja Šuštar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Marija Volk
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (B.P.)
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (B.P.)
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva ulica 46, 1000 Ljubljana, Slovenia; (N.K.); (T.K.); (M.Š.); (M.H.)
- Correspondence:
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10
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Mantovani V, Hauzman E, Corredor VH, Goulart PRK, Galvão O, Talebi M, Pessoa DMA, Soares JGM, Fiorani M, Gattass R, Fix Ventura D, Bonci DMO. Genetic variability of the sws1 cone opsin gene among New World monkeys. Am J Primatol 2020; 82:e23199. [PMID: 32990997 DOI: 10.1002/ajp.23199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Vision is a major sense for Primates and the ability to perceive colors has great importance for the species ecology and behavior. Visual processing begins with the activation of the visual opsins in the retina, and the spectral absorption peaks are highly variable among species. In most Primates, LWS/MWS opsins are responsible for sensitivity to long/middle wavelengths within the visible light spectrum, and SWS1 opsins provide sensitivity to short wavelengths, in the violet region of the spectrum. In this study, we aimed to investigate the genetic variation on the sws1 opsin gene of New World monkeys (NWM) and search for amino acid substitutions that might be associated with the different color vision phenotypes described for a few species. We sequenced the exon 1 of the sws1 opsin gene of seven species from the families Callitrichidae, Cebidae, and Atelidae, and searched for variation at the spectral tuning sites 46, 49, 52, 86, 90, 93, 114, 116, and 118. Among the known spectral tuning sites, only residue 114 was variable. To investigate whether other residues have a functional role in the SWS1 absorption peak, we performed computational modeling of wild-type SWS1 and mutants A50I and A50V, found naturally among the species investigated. Although in silico analysis did not show any visible effect caused by these substitutions, it is possible that interactions of residue 50 with other sites might have some effect in the spectral shifts in the order of ~14 nm, found among the NWM. We also performed phylogenetic reconstruction of the sws1 gene, which partially recovered the species phylogeny. Further studies will be important to uncover the mutations responsible for the phenotypic variability of the SWS1 of NWM, and how spectral tuning may be associated with specific ecological features such as preferred food items and habitat use.
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Affiliation(s)
- Viviani Mantovani
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Vitor H Corredor
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo R K Goulart
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Olavo Galvão
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Mauricio Talebi
- Departamento de Ciências Ambientais, Universidade Federal de São Paulo, Campus Diadema, São Paulo, São Paulo, Brazil
| | - Daniel M A Pessoa
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Juliana G M Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mario Fiorani
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Gattass
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Daniela M O Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
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11
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Abstract
Numerous rhodopsin mutations have been implicated in night blindness and retinal degeneration, often with unclear etiology. D190N-rhodopsin (D190N-Rho) is a well-known inherited human mutation causing retinitis pigmentosa. Both higher-than-normal spontaneous-isomerization activity and misfolding/mistargeting of the mutant protein have been proposed as causes of the disease, but neither explanation has been thoroughly examined. We replaced wild-type rhodopsin (WT-Rho) in RhoD190N/WT mouse rods with a largely "functionally silenced" rhodopsin mutant to isolate electrical responses triggered by D190N-Rho activity, and found that D190N-Rho at the single-molecule level indeed isomerizes more frequently than WT-Rho by over an order of magnitude. Importantly, however, this higher molecular dark activity does not translate into an overall higher cellular dark noise, owing to diminished D190N-Rho content in the rod outer segment. Separately, we found that much of the degeneration and shortened outer-segment length of RhoD190N/WT mouse rods was not averted by ablating rod transducin in phototransduction-also consistent with D190N-Rho's higher isomerization activity not being the primary cause of disease. Instead, the low pigment content, shortened outer-segment length, and a moderate unfolded protein response implicate protein misfolding as the major pathogenic problem. Finally, D190N-Rho also provided some insight into the mechanism of spontaneous pigment excitation.
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12
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Kubatova N, Mao J, Eckert CE, Saxena K, Gande SL, Wachtveitl J, Glaubitz C, Schwalbe H. Light Dynamics of the Retinal-Disease-Relevant G90D Bovine Rhodopsin Mutant. Angew Chem Int Ed Engl 2020; 59:15656-15664. [PMID: 32602600 PMCID: PMC7496284 DOI: 10.1002/anie.202003671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/25/2020] [Indexed: 12/11/2022]
Abstract
The RHO gene encodes the G-protein-coupled receptor (GPCR) rhodopsin. Numerous mutations associated with impaired visual cycle have been reported; the G90D mutation leads to a constitutively active mutant form of rhodopsin that causes CSNB disease. We report on the structural investigation of the retinal configuration and conformation in the binding pocket in the dark and light-activated state by solution and MAS-NMR spectroscopy. We found two long-lived dark states for the G90D mutant with the 11-cis retinal bound as Schiff base in both populations. The second minor population in the dark state is attributed to a slight shift in conformation of the covalently bound 11-cis retinal caused by the mutation-induced distortion on the salt bridge formation in the binding pocket. Time-resolved UV/Vis spectroscopy was used to monitor the functional dynamics of the G90D mutant rhodopsin for all relevant time scales of the photocycle. The G90D mutant retains its conformational heterogeneity during the photocycle.
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Affiliation(s)
- Nina Kubatova
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Jiafei Mao
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 960438FrankfurtGermany
| | - Carl Elias Eckert
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Krishna Saxena
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Santosh L. Gande
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Clemens Glaubitz
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 960438FrankfurtGermany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
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13
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Kubatova N, Mao J, Eckert CE, Saxena K, Gande SL, Wachtveitl J, Glaubitz C, Schwalbe H. Light Dynamics of the Retinal‐Disease‐Relevant G90D Bovine Rhodopsin Mutant. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Nina Kubatova
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Jiafei Mao
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute of Biophysical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Carl Elias Eckert
- Institute of Physical and Theoretical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Santosh L. Gande
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Clemens Glaubitz
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute of Biophysical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
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14
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Katayama K, Takeyama Y, Enomoto A, Imai H, Kandori H. Disruption of Hydrogen-Bond Network in Rhodopsin Mutations Cause Night Blindness. J Mol Biol 2020; 432:5378-5389. [PMID: 32795534 DOI: 10.1016/j.jmb.2020.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/14/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]
Abstract
Rhodopsin is the photosensitive protein, which binds to 11-cis-retinal as its chromophore. In the dark, rhodopsin exists as a stable complex between the opsin moiety and 11-cis-retinal. The absorption of a light photon converts 11-cis-retinal to all-trans-retinal and initiates our vision. As a result, the increase in the rate of dark activation of rhodopsin reduces its photosensitivity resulting in night blindness. The mutations, G90D and T94I are night blindness-causing mutations that exhibit completely different physicochemical characteristics associated with the dark activation of rhodopsin, such as a high rate of thermal isomerization of 11-cis-retinal and a slow pigment regeneration. To elucidate the molecular mechanism by which G90D and T94I mutations affect rhodopsin dark activation and regeneration, we performed light-induced difference FTIR spectroscopy on dark and primary photo-intermediate states of G90D and T94I mutants. The FTIR spectra clearly show that both charged G90D and hydrophobic T94I mutants alter the H-bond network at the Schiff base region of the chromophore, which weakens the electrostatic interaction with Glu113 counterion. Our results further show an altered water-mediated H-bond network around the central transmembrane region of mutant rhodopsin, which is reminiscent of the active Meta-II state. This altered water-mediated H-bond network may cause thermal isomerization of the chromophore and facilitate rhodopsin dark activation.
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Affiliation(s)
- 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.
| | - Yuri Takeyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Akiko Enomoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama 484-8506, 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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15
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Pope AL, Sanchez-Reyes OB, South K, Zaitseva E, Ziliox M, Vogel R, Reeves PJ, Smith SO. A Conserved Proline Hinge Mediates Helix Dynamics and Activation of Rhodopsin. Structure 2020; 28:1004-1013.e4. [PMID: 32470317 DOI: 10.1016/j.str.2020.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 01/05/2023]
Abstract
Despite high-resolution crystal structures of both inactive and active G protein-coupled receptors (GPCRs), it is still not known how ligands trigger the large structural change on the intracellular side of the receptor since the conformational changes that occur within the extracellular ligand-binding region upon activation are subtle. Here, we use solid-state NMR and Fourier transform infrared spectroscopy on rhodopsin to show that Trp2656.48 within the CWxP motif on transmembrane helix H6 constrains a proline hinge in the inactive state, suggesting that activation results in unraveling of the H6 backbone within this motif, a local change in dynamics that allows helix H6 to swing outward. Notably, Tyr3017.48 within activation switch 2 appears to mimic the negative allosteric sodium ion found in other family A GPCRs, a finding that is broadly relevant to the mechanism of receptor activation.
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Affiliation(s)
- Andreyah L Pope
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Omar B Sanchez-Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Kieron South
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Ekaterina Zaitseva
- Biophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Hermann Herder Strasse, 79104 Freiburg, Germany
| | - Martine Ziliox
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Reiner Vogel
- Biophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Hermann Herder Strasse, 79104 Freiburg, Germany
| | - Philip J Reeves
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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16
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Pamula F, Mühle J, Blanc A, Nehmé R, Edwards PC, Tate CG, Tsai CJ. Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization. J Vis Exp 2020. [PMID: 32225143 PMCID: PMC7250641 DOI: 10.3791/60747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The key to determining crystal structures of membrane protein complexes is the quality of the sample prior to crystallization. In particular, the choice of detergent is critical, because it affects both the stability and monodispersity of the complex. We recently determined the crystal structure of an active state of bovine rhodopsin coupled to an engineered G protein, mini-Go, at 3.1 Å resolution. Here, we detail the procedure for optimizing the preparation of the rhodopsin–mini-Go complex. Dark-state rhodopsin was prepared in classical and neopentyl glycol (NPG) detergents, followed by complex formation with mini-Go under light exposure. The stability of the rhodopsin was assessed by ultraviolet-visible (UV-VIS) spectroscopy, which monitors the reconstitution into rhodopsin of the light-sensitive ligand, 9-cis retinal. Automated size-exclusion chromatography (SEC) was used to characterize the monodispersity of rhodopsin and the rhodopsin–mini-Go complex. SDS-polyacrylamide electrophoresis (SDS-PAGE) confirmed the formation of the complex by identifying a 1:1 molar ratio between rhodopsin and mini-Go after staining the gel with Coomassie blue. After cross-validating all this analytical data, we eliminated unsuitable detergents and continued with the best candidate detergent for large-scale preparation and crystallization. An additional problem arose from the heterogeneity of N-glycosylation. Heterologously-expressed rhodopsin was observed on SDS-PAGE to have two different N-glycosylated populations, which would probably have hindered crystallogenesis. Therefore, different deglycosylation enzymes were tested, and endoglycosidase F1 (EndoF1) produced rhodopsin with a single species of N-glycosylation. With this strategic pipeline for characterizing protein quality, preparation of the rhodopsin–mini-Go complex was optimized to deliver the crystal structure. This was only the third crystal structure of a GPCR–G protein signaling complex. This approach can also be generalized for other membrane proteins and their complexes to facilitate sample preparation and structure determination.
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Affiliation(s)
- Filip Pamula
- Laboratory of Biomolecular Research, Paul Scherrer Institute; Department of Biology, ETH Zürich;
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Paul Scherrer Institute
| | - Alain Blanc
- Center for Radiopharmaceutical Sciences, Paul Scherrer Institute
| | - Rony Nehmé
- Laboratory of Molecular Biology, Medical Research Council
| | | | | | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute;
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17
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Varma N, Mutt E, Mühle J, Panneels V, Terakita A, Deupi X, Nogly P, Schertler GFX, Lesca E. Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR. Proc Natl Acad Sci U S A 2019; 116:14547-14556. [PMID: 31249143 PMCID: PMC6642406 DOI: 10.1073/pnas.1902192116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Light-sensitive G protein-coupled receptors (GPCRs)-rhodopsins-absorb photons to isomerize their covalently bound retinal, triggering conformational changes that result in downstream signaling cascades. Monostable rhodopsins release retinal upon isomerization as opposed to the retinal in bistable rhodopsins that "reisomerize" upon absorption of a second photon. Understanding the mechanistic differences between these light-sensitive GPCRs has been hindered by the scarcity of recombinant models of the latter. Here, we reveal the high-resolution crystal structure of a recombinant bistable rhodopsin, jumping spider rhodopsin-1, bound to the inverse agonist 9-cis retinal. We observe a water-mediated network around the ligand hinting toward the basis of their bistable nature. In contrast to bovine rhodopsin (monostable), the transmembrane bundle of jumping spider rhodopsin-1 as well that of the bistable squid rhodopsin adopts a more "activation-ready" conformation often observed in other nonphotosensitive class A GPCRs. These similarities suggest the role of jumping spider rhodopsin-1 as a potential model system in the study of the structure-function relationship of both photosensitive and nonphotosensitive class A GPCRs.
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Affiliation(s)
- Niranjan Varma
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Eshita Mutt
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Jonas Mühle
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Valérie Panneels
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Akihisa Terakita
- Department of Biology and Geosciences, Osaka City University, 558-8585 Osaka, Japan
| | - Xavier Deupi
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Gebhard F X Schertler
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland;
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Elena Lesca
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland;
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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18
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Lesca E, Panneels V, Schertler GFX. The role of water molecules in phototransduction of retinal proteins and G protein-coupled receptors. Faraday Discuss 2019; 207:27-37. [PMID: 29410984 DOI: 10.1039/c7fd00207f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G protein coupled receptors (GPCRs) are a key family of membrane proteins in all eukaryotes and also very important drug targets for medical intervention. The extensively studied visual pigment rhodopsin is a prime example of a family A GPCR. Its chromophore ligand retinal is covalently linked to a lysine in helix seven forming a protonated Schiff base. Interestingly, this is the same situation in other-non-GPCR-retinal proteins, like the prototype light-driven microbial proton pump bacteriorhodopsin, albeit there is no (or only a very remote) phylogenetical link. Close to the retinal ligand, several water molecules help to organise a functionally important hydrogen bond network that undergoes significant changes during photo-activation. Such water-mediated networks are also critical for ligand binding of other GPCRs and they are becoming increasingly important in drug discovery. GPCRs also contain a partially conserved water mediated hydrogen bond network that stabilises the ground state of the receptor, and rearrangement of this network leads to the stabilization of the active state. Some water molecules have a specific role in this process to appropriately orient specific residues relative to the Schiff base, and to modulate the fine structure of the transmembrane bundle, particularly near the intracellular G protein binding site. While the atomic details of these mechanisms are still missing, the recent developments in free electron lasers (FELs) are enabling us to begin to observe the changes in waters and relevant side chains shortly after photo activation at an unprecedented level of spatial and temporal resolution.
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Affiliation(s)
- Elena Lesca
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
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19
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Wink LH, Baker DL, Cole JA, Parrill AL. A benchmark study of loop modeling methods applied to G protein-coupled receptors. J Comput Aided Mol Des 2019; 33:573-595. [PMID: 31123958 PMCID: PMC6628340 DOI: 10.1007/s10822-019-00196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.
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Affiliation(s)
- Lee H Wink
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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20
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Haider RS, Wilhelm F, Rizk A, Mutt E, Deupi X, Peterhans C, Mühle J, Berger P, Schertler GFX, Standfuss J, Ostermaier MK. Arrestin-1 engineering facilitates complex stabilization with native rhodopsin. Sci Rep 2019; 9:439. [PMID: 30679635 PMCID: PMC6346018 DOI: 10.1038/s41598-018-36881-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 11/23/2018] [Indexed: 01/14/2023] Open
Abstract
Arrestin-1 desensitizes the activated and phosphorylated photoreceptor rhodopsin by forming transient rhodopsin−arrestin-1 complexes that eventually decay to opsin, retinal and arrestin-1. Via a multi-dimensional screening setup, we identified and combined arrestin-1 mutants that form lasting complexes with light-activated and phosphorylated rhodopsin in harsh conditions, such as high ionic salt concentration. Two quadruple mutants, D303A + T304A + E341A + F375A and R171A + T304A + E341A + F375A share similar heterologous expression and thermo-stability levels with wild type (WT) arrestin-1, but are able to stabilize complexes with rhodopsin with more than seven times higher half-maximal inhibitory concentration (IC50) values for NaCl compared to the WT arrestin-1 protein. These quadruple mutants are also characterized by higher binding affinities to phosphorylated rhodopsin, light-activated rhodopsin and phosphorylated opsin, as compared with WT arrestin-1. Furthermore, the assessed arrestin-1 mutants are still specifically associating with phosphorylated or light-activated receptor states only, while binding to the inactive ground state of the receptor is not significantly altered. Additionally, we propose a novel functionality for R171 in stabilizing the inactive arrestin-1 conformation as well as the rhodopsin–arrestin-1 complex. The achieved stabilization of the active rhodopsin–arrestin-1 complex might be of great interest for future structure determination, antibody development studies as well as drug-screening efforts targeting G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Raphael S Haider
- InterAx Biotech AG, PARK InnovAARE, Villigen, 5234, Switzerland.,Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland.,Institute of Molecular Cell Biology, Jena, 07745, Germany
| | - Florian Wilhelm
- InterAx Biotech AG, PARK InnovAARE, Villigen, 5234, Switzerland
| | - Aurélien Rizk
- InterAx Biotech AG, PARK InnovAARE, Villigen, 5234, Switzerland
| | - Eshita Mutt
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Christian Peterhans
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Philipp Berger
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland.,ETH Zurich, Zurich, 8093, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, 5232, Switzerland
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21
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Tsai CJ, Pamula F, Nehmé R, Mühle J, Weinert T, Flock T, Nogly P, Edwards PC, Carpenter B, Gruhl T, Ma P, Deupi X, Standfuss J, Tate CG, Schertler GFX. Crystal structure of rhodopsin in complex with a mini-G o sheds light on the principles of G protein selectivity. SCIENCE ADVANCES 2018; 4:eaat7052. [PMID: 30255144 PMCID: PMC6154990 DOI: 10.1126/sciadv.aat7052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/10/2018] [Indexed: 05/20/2023]
Abstract
Selective coupling of G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-Go protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a "structural switch," allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR-G protein interface suggests that the precise position of the carboxyl-terminal "hook-like" element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.
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Affiliation(s)
- Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Corresponding author. (C.-J.T.); (G.F.X.S.)
| | - Filip Pamula
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Rony Nehmé
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Tilman Flock
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
- Fitzwilliam College, University of Cambridge, Cambridge, UK
| | - Przemyslaw Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Patricia C. Edwards
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Byron Carpenter
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas Gruhl
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Pikyee Ma
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Condensed Matter Theory Group, PSI, 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher G. Tate
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
- Corresponding author. (C.-J.T.); (G.F.X.S.)
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22
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Convergent evolution of tertiary structure in rhodopsin visual proteins from vertebrates and box jellyfish. Proc Natl Acad Sci U S A 2018; 115:6201-6206. [PMID: 29793939 PMCID: PMC6004467 DOI: 10.1073/pnas.1721333115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Box jellyfish and vertebrates are separated by >500 million years of evolution yet have structurally analogous lens eyes that employ rhodopsin photopigments for vision. All opsins possess a negatively charged residue-the counterion-to maintain visible-light sensitivity and facilitate photoisomerization of their retinaldehyde chromophore. In vertebrate rhodopsins, the molecular evolution of the counterion position-from a highly conserved distal location in the second extracellular loop (E181) to a proximal location in the third transmembrane helix (E113)-is established as a key driver of higher fidelity photoreception. Here, we use computational biology and heterologous action spectroscopy to determine whether the appearance of the advanced visual apparatus in box jellyfish was also accompanied by changes in the opsin tertiary structure. We found that the counterion in an opsin from the lens eye of the box jellyfish Carybdea rastonii (JellyOp) has also moved to a unique proximal location within the transmembrane bundle-E94 in TM2. Furthermore, we reveal that this Schiff base/counterion system includes an additional positive charge-R186-that has coevolved with E94 to functionally separate E94 and E181 in the chromophore-binding pocket of JellyOp. By engineering this pocket-neutralizing R186 and E94, or swapping E94 with the vertebrate counterion E113-we can recreate versions of the invertebrate and vertebrate counterion systems, respectively, supporting a relatively similar overall architecture in this region of animal opsins. In summary, our data establish the third only counterion site in animal opsins and reveal convergent evolution of tertiary structure in opsins from distantly related species with advanced visual systems.
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23
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Mattle D, Kuhn B, Aebi J, Bedoucha M, Kekilli D, Grozinger N, Alker A, Rudolph MG, Schmid G, Schertler GFX, Hennig M, Standfuss J, Dawson RJP. Ligand channel in pharmacologically stabilized rhodopsin. Proc Natl Acad Sci U S A 2018; 115:3640-3645. [PMID: 29555765 PMCID: PMC5889642 DOI: 10.1073/pnas.1718084115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the degenerative eye disease retinitis pigmentosa (RP), protein misfolding leads to fatal consequences for cell metabolism and rod and cone cell survival. To stop disease progression, a therapeutic approach focuses on stabilizing inherited protein mutants of the G protein-coupled receptor (GPCR) rhodopsin using pharmacological chaperones (PC) that improve receptor folding and trafficking. In this study, we discovered stabilizing nonretinal small molecules by virtual and thermofluor screening and determined the crystal structure of pharmacologically stabilized opsin at 2.4 Å resolution using one of the stabilizing hits (S-RS1). Chemical modification of S-RS1 and further structural analysis revealed the core binding motif of this class of rhodopsin stabilizers bound at the orthosteric binding site. Furthermore, previously unobserved conformational changes are visible at the intradiscal side of the seven-transmembrane helix bundle. A hallmark of this conformation is an open channel connecting the ligand binding site with the membrane and the intradiscal lumen of rod outer segments. Sufficient in size, the passage permits the exchange of hydrophobic ligands such as retinal. The results broaden our understanding of rhodopsin's conformational flexibility and enable therapeutic drug intervention against rhodopsin-related retinitis pigmentosa.
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Affiliation(s)
- Daniel Mattle
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Johannes Aebi
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Marc Bedoucha
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Demet Kekilli
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Nathalie Grozinger
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Andre Alker
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Georg Schmid
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Michael Hennig
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland;
| | - Roger J P Dawson
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland;
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24
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Athanasiou D, Aguila M, Bellingham J, Li W, McCulley C, Reeves PJ, Cheetham ME. The molecular and cellular basis of rhodopsin retinitis pigmentosa reveals potential strategies for therapy. Prog Retin Eye Res 2018; 62:1-23. [PMID: 29042326 PMCID: PMC5779616 DOI: 10.1016/j.preteyeres.2017.10.002] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/03/2017] [Accepted: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Inherited mutations in the rod visual pigment, rhodopsin, cause the degenerative blinding condition, retinitis pigmentosa (RP). Over 150 different mutations in rhodopsin have been identified and, collectively, they are the most common cause of autosomal dominant RP (adRP). Mutations in rhodopsin are also associated with dominant congenital stationary night blindness (adCSNB) and, less frequently, recessive RP (arRP). Recessive RP is usually associated with loss of rhodopsin function, whereas the dominant conditions are a consequence of gain of function and/or dominant negative activity. The in-depth characterisation of many rhodopsin mutations has revealed that there are distinct consequences on the protein structure and function associated with different mutations. Here we categorise rhodopsin mutations into seven discrete classes; with defects ranging from misfolding and disruption of proteostasis, through mislocalisation and disrupted intracellular traffic to instability and altered function. Rhodopsin adRP offers a unique paradigm to understand how disturbances in photoreceptor homeostasis can lead to neuronal cell death. Furthermore, a wide range of therapies have been tested in rhodopsin RP, from gene therapy and gene editing to pharmacological interventions. The understanding of the disease mechanisms associated with rhodopsin RP and the development of targeted therapies offer the potential of treatment for this currently untreatable neurodegeneration.
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Affiliation(s)
| | - Monica Aguila
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - James Bellingham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Wenwen Li
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Caroline McCulley
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK.
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25
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Lemos A, Melo R, Preto AJ, Almeida JG, Moreira IS, Cordeiro MNDS. In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson's Disease. Curr Neuropharmacol 2018; 16:786-848. [PMID: 29521236 PMCID: PMC6080095 DOI: 10.2174/1570159x16666180308161642] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 02/16/2018] [Accepted: 02/02/2018] [Indexed: 11/22/2022] Open
Abstract
Parkinson's Disease (PD) is a long-term neurodegenerative brain disorder that mainly affects the motor system. The causes are still unknown, and even though currently there is no cure, several therapeutic options are available to manage its symptoms. The development of novel antiparkinsonian agents and an understanding of their proper and optimal use are, indeed, highly demanding. For the last decades, L-3,4-DihydrOxyPhenylAlanine or levodopa (L-DOPA) has been the gold-standard therapy for the symptomatic treatment of motor dysfunctions associated to PD. However, the development of dyskinesias and motor fluctuations (wearing-off and on-off phenomena) associated with long-term L-DOPA replacement therapy have limited its antiparkinsonian efficacy. The investigation for non-dopaminergic therapies has been largely explored as an attempt to counteract the motor side effects associated with dopamine replacement therapy. Being one of the largest cell membrane protein families, G-Protein-Coupled Receptors (GPCRs) have become a relevant target for drug discovery focused on a wide range of therapeutic areas, including Central Nervous System (CNS) diseases. The modulation of specific GPCRs potentially implicated in PD, excluding dopamine receptors, may provide promising non-dopaminergic therapeutic alternatives for symptomatic treatment of PD. In this review, we focused on the impact of specific GPCR subclasses, including dopamine receptors, adenosine receptors, muscarinic acetylcholine receptors, metabotropic glutamate receptors, and 5-hydroxytryptamine receptors, on the pathophysiology of PD and the importance of structure- and ligand-based in silico approaches for the development of small molecules to target these receptors.
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Affiliation(s)
- Agostinho Lemos
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007Porto, Portugal
- GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, 4000Liège, Belgium
| | - Rita Melo
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066 Bobadela LRS, Portugal
| | - Antonio Jose Preto
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
| | - Jose Guilherme Almeida
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
| | - Irina Sousa Moreira
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Maria Natalia Dias Soeiro Cordeiro
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007Porto, Portugal
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26
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Gacasan SB, Baker DL, Parrill AL. G protein-coupled receptors: the evolution of structural insight. AIMS BIOPHYSICS 2017; 4:491-527. [PMID: 29951585 DOI: 10.3934/biophy.2017.3.491] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
G protein-coupled receptors (GPCR) comprise a diverse superfamily of over 800 proteins that have gained relevance as biological targets for pharmaceutical drug design. Although these receptors have been investigated for decades, three-dimensional structures of GPCR have only recently become available. In this review, we focus on the technological advancements that have facilitated efforts to gain insights into GPCR structure. Progress in these efforts began with the initial crystal structure determination of rhodopsin (PDB: 1F88) in 2000 and has continued to the most recently published structure of the A1AR (PDB: 5UEN) in 2017. Numerous experimental developments over the past two decades have opened the door for widespread GPCR structural characterization. These efforts have resulted in the determination of three-dimensional structures for over 40 individual GPCR family members. Herein we present a comprehensive list and comparative analysis of over 180 individual GPCR structures. This includes a summary of different GPCR functional states crystallized with agonists, dual agonists, partial agonists, inverse agonists, antagonists, and allosteric modulators.
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Affiliation(s)
- Samantha B Gacasan
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| | - Daniel L Baker
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| | - Abby L Parrill
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
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27
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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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28
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Singhal A, Guo Y, Matkovic M, Schertler G, Deupi X, Yan EC, Standfuss J. Structural role of the T94I rhodopsin mutation in congenital stationary night blindness. EMBO Rep 2016; 17:1431-1440. [PMID: 27458239 DOI: 10.15252/embr.201642671] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/07/2016] [Indexed: 11/09/2022] Open
Abstract
Congenital stationary night blindness (CSNB) is an inherited and non-progressive retinal dysfunction. Here, we present the crystal structure of CSNB-causing T94I2.61 rhodopsin in the active conformation at 2.3 Å resolution. The introduced hydrophobic side chain prolongs the lifetime of the G protein activating metarhodopsin-II state by establishing a direct van der Waals contact with K2967.43, the site of retinal attachment. This is in stark contrast to the light-activated state of the CSNB-causing G90D2.57 mutation, where the charged mutation forms a salt bridge with K2967.43 To find the common denominator between these two functional modifications, we combined our structural data with a kinetic biochemical analysis and molecular dynamics simulations. Our results indicate that both the charged G90D2.57 and the hydrophobic T94I2.61 mutation alter the dark state by weakening the interaction between the Schiff base (SB) and its counterion E1133.28 We propose that this interference with the tight regulation of the dim light photoreceptor rhodopsin increases background noise in the visual system and causes the loss of night vision characteristic for CSNB patients.
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Affiliation(s)
- Ankita Singhal
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Ying Guo
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Milos Matkovic
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Deparment of Biology, ETH Zurich, Zürich, Switzerland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland
| | - Elsa Cy Yan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Joerg Standfuss
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
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