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Modak A, Kilic Z, Chattrakun K, Terry DS, Kalathur RC, Blanchard SC. Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function. Annu Rev Biophys 2024; 53:427-453. [PMID: 39013028 DOI: 10.1146/annurev-biophys-070323-024308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Integral membrane proteins (IMPs) play central roles in cellular physiology and represent the majority of known drug targets. Single-molecule fluorescence and fluorescence resonance energy transfer (FRET) methods have recently emerged as valuable tools for investigating structure-function relationships in IMPs. This review focuses on the practical foundations required for examining polytopic IMP function using single-molecule FRET (smFRET) and provides an overview of the technical and conceptual frameworks emerging from this area of investigation. In this context, we highlight the utility of smFRET methods to reveal transient conformational states critical to IMP function and the use of smFRET data to guide structural and drug mechanism-of-action investigations. We also identify frontiers where progress is likely to be paramount to advancing the field.
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Affiliation(s)
- Arnab Modak
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Kanokporn Chattrakun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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2
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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: 21] [Impact Index Per Article: 21.0] [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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3
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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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4
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Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
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5
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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6
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Zhang Q, Cherezov V. Chemical tools for membrane protein structural biology. Curr Opin Struct Biol 2019; 58:278-285. [PMID: 31285102 DOI: 10.1016/j.sbi.2019.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/24/2023]
Abstract
Solving high-resolution structures of membrane proteins has been an important challenge for decades, still lagging far behind that of soluble proteins even with the recent remarkable technological advances in X-ray crystallography and electron microscopy. Central to this challenge is the necessity to isolate and solubilize membrane proteins in a stable, natively folded and functional state, a process influenced by not only the proteins but also their surrounding chemical environment. This review highlights recent community efforts in the development and characterization of novel membrane agents and ligand tools to stabilize individual proteins and protein complexes, which together have accelerated progress in membrane protein structural biology.
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Affiliation(s)
- Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
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7
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Abstract
G protein-coupled receptors (GPCRs), which mediate processes as diverse as olfaction and maintenance of metabolic homeostasis, have become the single most effective class of therapeutic drug targets. As a result, understanding the molecular basis for their activity is of paramount importance. Recent technological advances have made GPCR structural biology increasingly tractable, offering views of these receptors in unprecedented atomic detail. Structural and biophysical data have shown that GPCRs function as complex allosteric machines, communicating ligand-binding events through conformational change. Changes in receptor conformation lead to activation of effector proteins, such as G proteins and arrestins, which are themselves conformational switches. Here, we review how structural biology has illuminated the agonist-induced cascade of conformational changes that culminate in a cellular response to GPCR activation.
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Affiliation(s)
- Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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8
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Vass M, Kooistra AJ, Verhoeven S, Gloriam D, de Esch IJP, de Graaf C. A Structural Framework for GPCR Chemogenomics: What's In a Residue Number? Methods Mol Biol 2018; 1705:73-113. [PMID: 29188559 DOI: 10.1007/978-1-4939-7465-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The recent surge of crystal structures of G protein-coupled receptors (GPCRs), as well as comprehensive collections of sequence, structural, ligand bioactivity, and mutation data, has enabled the development of integrated chemogenomics workflows for this important target family. This chapter will focus on cross-family and cross-class studies of GPCRs that have pinpointed the need for, and the implementation of, a generic numbering scheme for referring to specific structural elements of GPCRs. Sequence- and structure-based numbering schemes for different receptor classes will be introduced and the remaining caveats will be discussed. The use of these numbering schemes has facilitated many chemogenomics studies such as consensus binding site definition, binding site comparison, ligand repurposing (e.g. for orphan receptors), sequence-based pharmacophore generation for homology modeling or virtual screening, and class-wide chemogenomics studies of GPCRs.
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Affiliation(s)
- Márton Vass
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
| | - Albert J Kooistra
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Stefan Verhoeven
- Netherlands eScience Center, 1098 XG, Amsterdam, The Netherlands
| | - David Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Iwan J P de Esch
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
| | - Chris de Graaf
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands.
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9
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Abstract
Rhodopsin is the classical light sensor. Although rhodopsin has long been known to be important for image formation in the eye, the requirements for opsins in non-image formation and in extraocular light sensation were revealed much later. Most recent is the demonstration that an opsin in the fruit fly, Drosophila melanogaster, is expressed in pacemaker neurons in the brain and functions in light entrainment of circadian rhythms. However, the biggest surprise is that opsins have light-independent roles, countering more than a century of dogma that they function exclusively as light sensors. Through studies in Drosophila, light-independent roles of opsins have emerged in temperature sensation and hearing. Although these findings have been uncovered in the fruit fly, there are hints that opsins have light-independent roles in a wide array of animals, including mammals. Thus, despite the decades of focus on opsins as light detectors, they represent an important new class of polymodal sensory receptor.
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Affiliation(s)
- Nicole Y Leung
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106;
| | - Craig Montell
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106;
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10
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Abstract
Dopamine receptors are targets for drugs with antipsychotic potency, and they are also the primary target in the treatment of Parkinson’s disease. Molecular cloning has identified five genes that code for dopamine receptors. These receptors belong in two functionally distinct classes of G-protein-coupled receptors, known as the D1 class of receptors (D1 and D5) and the D2 class of receptors (D2, D3, and D4). The diversity of dopamine receptor subtypes that belong to the same functional class, their high degree of structural similarity, and the lack of antagonists with selectivity for each of the individual subtypes have challenged studies on the function of the individual receptor subtypes. This review focuses on the recent progress made with studies on the expression and function of D1, D2, and D3 receptors. It summarizes results of studies that suggest that these receptor proteins are expressed in monomeric and oligomeric forms and reviews results of a growing number of gene-targeting studies that begin to illustrate major differences in the phenotypes of D1-, D2-, and D3-mutant mice.
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Affiliation(s)
- Claudia Schmauss
- Department of Psychiatry/Neuroscience, Columbia University, New York, NY
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11
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Tesmer JJG. Hitchhiking on the heptahelical highway: structure and function of 7TM receptor complexes. Nat Rev Mol Cell Biol 2016; 17:439-50. [PMID: 27093944 DOI: 10.1038/nrm.2016.36] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A revolution in the analysis of seven transmembrane domain (7TM) receptors has provided detailed information about how these physiologically important signalling proteins interact with extracellular cues. However, it has proved much more challenging to understand how 7TM receptors convey information to their principal intracellular targets: heterotrimeric G proteins, G protein-coupled receptor kinases and arrestins. Recent structures now suggest a common mechanism that enables these structurally diverse cytoplasmic proteins to 'hitch a ride' on hundreds of different activated 7TM receptors in order to instigate physiological change.
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Affiliation(s)
- John J G Tesmer
- Life Sciences Institute and Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
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12
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Liu M, Sun Z, Hu W. Three-dimensional pharmacophore screening for fentanyl derivatives. Neural Regen Res 2015; 7:1398-405. [PMID: 25657673 PMCID: PMC4308790 DOI: 10.3969/j.issn.1673-5374.2012.18.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 04/11/2012] [Indexed: 01/08/2023] Open
Abstract
Fentanyl is a highly selective μ-opioid receptor agonist with high analgesic activity. Three-dimensional pharmacophore models were built from a set of 50 fentanyl derivatives. These were employed to elucidate ligand-receptor interactions using information derived only from the ligand structure to identify new potential lead compounds. The present studies demonstrated that three hydrophobic regions, one positive ionizable region and two hydrogen bond acceptor region sites located on the molecule seem to be essential for analgesic activity. The results of the comparative molecular field analysis model suggested that both steric and electrostatic interactions play important roles. The contributions from steric and electrostatic fields for the model were 0.621 and 0.379, respectively. The pharmacophore model provides crucial information about how well the common features of a subject molecule overlap with the hypothesis model, which is very valuable for designing and optimizing new active structures.
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Affiliation(s)
- Ming Liu
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Zhiguo Sun
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Wenxiang Hu
- College of Life Science, Capital Normal University, Beijing 100048, China ; Department of Chemistry, Capital Normal University, Beijing 100048, China
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13
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Prazeres DMF, Martins SAM. G protein-coupled receptors: an overview of signaling mechanisms and screening assays. Methods Mol Biol 2015; 1272:3-19. [PMID: 25563173 DOI: 10.1007/978-1-4939-2336-6_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The existence of cellular receptors, a group of specialized biomolecules to which endogenous and exogenous compounds bind and exert an effect, is one of the most exciting aspects of cell biology. Among the different receptor types recognized today, G-protein-coupled receptors (GPCRs) constitute, undoubtedly, one of the most important classes, in part due to their versatility, but particularly, due to their central role in a multitude of physiological states. The unveiling of GPCR function and mode of action is a challenging task that prevails until our days, as the full potential of these receptors is far from being established. Such an undertaking calls for a joint effort of multidisciplinary teams that must combine state-of-the-art technologies with in-depth knowledge of cell biology to probe such specialized molecules. This review provides a concise coverage of the scientific progress that has been made in GPCR research to provide researchers with an updated overview of the field. A brief outline of the historical breakthroughs is followed by a discussion of GPCR signaling mechanisms and by a description of the role played by assay technologies.
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Affiliation(s)
- Duarte Miguel F Prazeres
- IBB - Institute for Biotechnology and Bioengineering, Av. Rovisco Pais, 1049-001, Lisbon, Portugal,
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14
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Kim SK, Goddard WA, Yi KY, Lee BH, Lim CJ, Trzaskowski B. Predicted ligands for the human urotensin-II G protein-coupled receptor with some experimental validation. ChemMedChem 2014; 9:1732-43. [PMID: 24989481 DOI: 10.1002/cmdc.201402087] [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: 03/26/2014] [Indexed: 11/12/2022]
Abstract
Human Urotensin-II (U-II) is the most potent mammalian vasoconstrictor known.1 Thus, a U-II antagonist would be of therapeutic value in a number of cardiovascular disorders.2 Here, we describe our work on the prediction of the structure of the human U-II receptor (hUT2 R) using GEnSeMBLE (GPCR Ensemble of Structures in Membrane BiLayer Environment) complete sampling Monte Carlo method. With the validation of our predicted structures, we designed a series of new potential antagonists predicted to bind more strongly than known ligands. Next, we carried out R-group screening to suggest a new ligand predicted to bind with 7 kcal mol(-1) better energy than 1-{2-[4-(2-bromobenzyl)-4-hydroxypiperidin-1-yl]ethyl}-3-(thieno[3,2-b]pyridin-7-yl)urea, the designed antagonist predicted to have the highest affinity for the receptor. Some of these predictions were tested experimentally, validating the computational results. Using the pharmacophore generated from the predicted structure for hUT2 R bound to ACT-058362, we carried out virtual screening based on this binding site. The most potent hit compounds identified contained 2-(phenoxymethyl)-1,3,4-thiadiazole core, with the best derivative exhibiting an IC50 value of 0.581 μM against hUT2 R when tested in vitro. Our efforts identified a new scaffold as a potential new lead structure for the development of novel hUT2 R antagonists, and the computational methods used could find more general applicability to other GPCRs.
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Affiliation(s)
- Soo-Kyung Kim
- Materials & Process Simulation Center, California Institute of Technology, Beckman Institute (BI);Code (139-74), 1200 E. California Blvd., Pasadena, CA 91125 (USA)
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15
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Pasquier J, Kamech N, Lafont AG, Vaudry H, Rousseau K, Dufour S. Molecular evolution of GPCRs: Kisspeptin/kisspeptin receptors. J Mol Endocrinol 2014; 52:T101-17. [PMID: 24577719 DOI: 10.1530/jme-13-0224] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Following the discovery of kisspeptin (Kiss) and its receptor (GPR54 or KissR) in mammals, phylogenetic studies revealed up to three Kiss and four KissR paralogous genes in other vertebrates. The multiplicity of Kiss and KissR types in vertebrates probably originated from the two rounds of whole-genome duplication (1R and 2R) that occurred in early vertebrates. This review examines compelling recent advances on molecular diversity and phylogenetic evolution of vertebrate Kiss and KissR. It also addresses, from an evolutionary point of view, the issues of the structure-activity relationships and interaction of Kiss with KissR and of their signaling pathways. Independent gene losses, during vertebrate evolution, have shaped the repertoire of Kiss and KissR in the extant vertebrate species. In particular, there is no conserved combination of a given Kiss type with a KissR type, across vertebrate evolution. The striking conservation of the biologically active ten-amino-acid C-terminal sequence of all vertebrate kisspeptins, probably allowed this evolutionary flexibility of Kiss/KissR pairs. KissR mutations, responsible for hypogonadotropic hypogonadism in humans, mostly occurred at highly conserved amino acid positions among vertebrate KissR. This further highlights the key role of these amino acids in KissR function. In contrast, less conserved KissR regions, notably in the intracellular C-terminal domain, may account for differential intracellular signaling pathways between vertebrate KissR. Cross talk between evolutionary and biomedical studies should contribute to further understanding of the Kiss/KissR structure-activity relationships and biological functions.
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Affiliation(s)
- Jérémy Pasquier
- Laboratory of Biology of Aquatic Organisms and Ecosystems (BOREA)UMR CNRS 7208, IRD207, Université Pierre and Marie Curie - Paris 6, Muséum National d'Histoire Naturelle, 7 rue Cuvier, CP32, 75231 Paris Cedex 05, FranceLaboratory of Neuronal and Neuroendocrine Differentiation and CommunicationINSERM U982, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen, 76821 Mont-Saint-Aignan, France
| | - Nédia Kamech
- Laboratory of Biology of Aquatic Organisms and Ecosystems (BOREA)UMR CNRS 7208, IRD207, Université Pierre and Marie Curie - Paris 6, Muséum National d'Histoire Naturelle, 7 rue Cuvier, CP32, 75231 Paris Cedex 05, FranceLaboratory of Neuronal and Neuroendocrine Differentiation and CommunicationINSERM U982, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen, 76821 Mont-Saint-Aignan, France
| | - Anne-Gaëlle Lafont
- Laboratory of Biology of Aquatic Organisms and Ecosystems (BOREA)UMR CNRS 7208, IRD207, Université Pierre and Marie Curie - Paris 6, Muséum National d'Histoire Naturelle, 7 rue Cuvier, CP32, 75231 Paris Cedex 05, FranceLaboratory of Neuronal and Neuroendocrine Differentiation and CommunicationINSERM U982, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen, 76821 Mont-Saint-Aignan, France
| | - Hubert Vaudry
- Laboratory of Biology of Aquatic Organisms and Ecosystems (BOREA)UMR CNRS 7208, IRD207, Université Pierre and Marie Curie - Paris 6, Muséum National d'Histoire Naturelle, 7 rue Cuvier, CP32, 75231 Paris Cedex 05, FranceLaboratory of Neuronal and Neuroendocrine Differentiation and CommunicationINSERM U982, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen, 76821 Mont-Saint-Aignan, France
| | - Karine Rousseau
- Laboratory of Biology of Aquatic Organisms and Ecosystems (BOREA)UMR CNRS 7208, IRD207, Université Pierre and Marie Curie - Paris 6, Muséum National d'Histoire Naturelle, 7 rue Cuvier, CP32, 75231 Paris Cedex 05, FranceLaboratory of Neuronal and Neuroendocrine Differentiation and CommunicationINSERM U982, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen, 76821 Mont-Saint-Aignan, France
| | - Sylvie Dufour
- Laboratory of Biology of Aquatic Organisms and Ecosystems (BOREA)UMR CNRS 7208, IRD207, Université Pierre and Marie Curie - Paris 6, Muséum National d'Histoire Naturelle, 7 rue Cuvier, CP32, 75231 Paris Cedex 05, FranceLaboratory of Neuronal and Neuroendocrine Differentiation and CommunicationINSERM U982, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen, 76821 Mont-Saint-Aignan, France
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16
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Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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17
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G protein-coupled receptor accessory proteins and signaling: pharmacogenomic insights. Methods Mol Biol 2014; 1175:121-52. [PMID: 25150869 DOI: 10.1007/978-1-4939-0956-8_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The identification and characterization of the genes encoding G protein-coupled receptors (GPCRs) and the proteins necessary for the processes of ligand binding, GPCR activation, inactivation, and receptor trafficking to the membrane are discussed in the context of human genetic disease. In addition to functional GPCR variants, the identification of genetic disruptions affecting proteins necessary to GPCR functions have provided insights into the function of these pathways. Gsα and Gβ subunit polymorphisms have been found to result in complex phenotypes. Disruptions in accessory proteins that normally modify or organize heterotrimeric G-protein coupling may also result in disease states. These include the contribution of variants of the regulator of G protein signaling (RGS) protein to hypertension; the role variants of the activator of G protein signaling (AGS) proteins to phenotypes (such as the type III AGS8 variant to hypoxia); the contribution of G protein-coupled receptor kinase (GRK) proteins, such as GRK4, in disorders such as hypertension. The role of accessory proteins in GPCR structure and function is discussed in the context of genetic disorders associated with disruption of the genes that encode them. An understanding of the pharmacogenomics of GPCR and accessory protein signaling provides the basis for examining both GPCR pharmacogenetics and the genetics of monogenic disorders that result from disruption of given receptor systems.
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18
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Pechkova E, Bragazzi NL, Nicolini C. Advances in nanocrystallography as a proteomic tool. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:163-91. [PMID: 24985772 DOI: 10.1016/b978-0-12-800453-1.00005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to overcome the difficulties and hurdles too much often encountered in crystallizing a protein with the conventional techniques, our group has introduced the innovative Langmuir-Blodgett (LB)-based crystallization, as a major advance in the field of both structural and functional proteomics, thus pioneering the emerging field of the so-called nanocrystallography or nanobiocrystallography. This approach uniquely combines protein crystallography and nanotechnologies within an integrated, coherent framework that allows one to obtain highly stable protein crystals and to fully characterize them at a nano- and subnanoscale. A variety of experimental techniques and theoretical/semi-theoretical approaches, ranging from atomic force microscopy, circular dichroism, Raman spectroscopy and other spectroscopic methods, microbeam grazing-incidence small-angle X-ray scattering to in silico simulations, bioinformatics, and molecular dynamics, has been exploited in order to study the LB-films and to investigate the kinetics and the main features of LB-grown crystals. When compared to classical hanging-drop crystallization, LB technique appears strikingly superior and yields results comparable with crystallization in microgravity environments. Therefore, the achievement of LB-based crystallography can have a tremendous impact in the field of industrial and clinical/therapeutic applications, opening new perspectives for personalized medicine. These implications are envisaged and discussed in the present contribution.
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Affiliation(s)
- Eugenia Pechkova
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy
| | - Nicola Luigi Bragazzi
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Claudio Nicolini
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
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Knospe M, Müller CE, Rosa P, Abdelrahman A, von Kügelgen I, Thimm D, Schiedel AC. The rat adenine receptor: pharmacological characterization and mutagenesis studies to investigate its putative ligand binding site. Purinergic Signal 2013; 9:367-81. [PMID: 23413038 PMCID: PMC3757150 DOI: 10.1007/s11302-013-9355-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 01/23/2013] [Indexed: 12/20/2022] Open
Abstract
The rat adenine receptor (rAdeR) was the first member of a family of G protein-coupled receptors (GPCRs) activated by adenine and designated as P0-purine receptors. The present study aimed at gaining insights into structural aspects of ligand binding and function of the rAdeR. We exchanged amino acid residues predicted to be involved in ligand binding (Phe110(3.24), Asn115(3.29), Asn173(4.60), Phe179(45.39), Asn194(5.40), Phe195(5.41), Leu201(5.47), His252(6.54), and Tyr268(7.32)) for alanine and expressed them in Spodoptera frugiperda (Sf9) insect cells. Membrane preparations subjected to [(3)H]adenine binding studies revealed only minor effects indicating that none of the exchanged amino acids is part of the ligand binding pocket, at least in the inactive state of the receptor. Furthermore, we coexpressed the rAdeR and its mutants with mammalian Gi proteins in Sf9 insect cells to probe receptor activation. Two amino acid residues, Asn194(5.40) and Leu201(5.47), were found to be crucial for activation since their alanine mutants did not respond to adenine. Moreover we showed that-in contrast to most other rhodopsin-like GPCRs-the rAdeR does not contain essential disulfide bonds since preincubation with dithiothreitol neither altered adenine binding in Sf9 cell membranes, nor adenine-induced inhibition of adenylate cyclase in 1321N1 astrocytoma cells transfected with the rAdeR. To detect rAdeRs by Western blot analysis, we developed a specific antibody. Finally, we were able to show that the extended N-terminal sequence of the rAdeR constitutes a putative signal peptide of unknown function that is cleaved off in the mature receptor. Our results provide important insights into this new, poorly investigated family of purinergic receptors.
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Affiliation(s)
- Melanie Knospe
- />PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Christa E. Müller
- />PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Patrizia Rosa
- />CNR—Institute of Neuroscience and Department of Medical Biotechnologies and Translational Medicine (BIOMETRA), University of Milan, Milan, Italy
| | - Aliaa Abdelrahman
- />PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Ivar von Kügelgen
- />PharmaCenter Bonn, Department of Pharmacology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dominik Thimm
- />PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Anke C. Schiedel
- />PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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Maeda S, Schertler GFX. Production of GPCR and GPCR complexes for structure determination. Curr Opin Struct Biol 2013; 23:381-92. [PMID: 23707225 DOI: 10.1016/j.sbi.2013.04.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/11/2013] [Accepted: 04/11/2013] [Indexed: 01/12/2023]
Abstract
Since the first high-resolution structure of the beta 2 adrenergic receptor (b2AR) in 2007, we have seen a growing number of G-protein-coupled receptor (GPCR) structures coming to the repertory, providing a significant progress in our understanding of the structural basis of their function. This has been achieved by the interdisciplinary collaborative work between scientists with various expertise and the development of new methodologies as well as combining and optimizing existing techniques.
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Affiliation(s)
- Shoji Maeda
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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21
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Kobilka B. The structural basis of G-protein-coupled receptor signaling (Nobel Lecture). Angew Chem Int Ed Engl 2013; 52:6380-8. [PMID: 23650120 DOI: 10.1002/anie.201302116] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Indexed: 01/14/2023]
Affiliation(s)
- Brian Kobilka
- Stanford University School of Medicine, Department of Molecular and Cellular Physiology, 279 Campus Drive, Stanford, CA 94305, USA
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22
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Kobilka B. Die strukturelle Grundlage der Signaltransduktion mit G-Protein-gekoppelten Rezeptoren (Nobel-Aufsatz). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Jastrzebska B, Orban T, Golczak M, Engel A, Palczewski K. Asymmetry of the rhodopsin dimer in complex with transducin. FASEB J 2013; 27:1572-84. [PMID: 23303210 DOI: 10.1096/fj.12-225383] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A large body of evidence for G-protein-coupled receptor (GPCR) oligomerization has accumulated over the past 2 decades. The smallest of these oligomers in vivo most likely is a dimer that buries 1000-Å(2) intramolecular surfaces and on stimulation forms a complex with heterotrimeric G protein in 2:1 stoichiometry. However, it is unclear whether each of the monomers adopts the same or a different conformation and function after activation of this dimer. With bovine rhodopsin (Rho) and its cognate bovine G-protein transducin (Gt) as a model system, we used the retinoid chromophores 11-cis-retinal and 9-cis-retinal to monitor each monomer of the dimeric GPCR within a stable complex with nucleotide-free Gt. We found that only 50% of Rho* in the Rho*-Gt complex is trapped in a Meta II conformation, while 50% evolves toward an opsin conformation and can be regenerated with 9-cis-retinal. We also found that all-trans-retinal can regenerate chromophore-depleted Rho*e complexed with Gt and FAK*TSA peptide containing Lys(296) with the attached all-trans retinoid (m/z of 934.5[MH](+)) was identified by mass spectrometry. Thus, our study shows that each of the monomers contributes unequally to the pentameric (2:1:1:1) complex of Rho dimer and Gt heterotrimer, validating the oligomeric structure of the complex and the asymmetry of the GPCR dimer, and revealing its structural/functional signature. This study provides a clear functional distinction between monomers of family A GPCRs in their oligomeric form.
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Affiliation(s)
- Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA
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Trzaskowski B, Latek D, Yuan S, Ghoshdastider U, Debinski A, Filipek S. Action of molecular switches in GPCRs--theoretical and experimental studies. Curr Med Chem 2012; 19:1090-109. [PMID: 22300046 PMCID: PMC3343417 DOI: 10.2174/092986712799320556] [Citation(s) in RCA: 336] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/30/2011] [Accepted: 01/02/2012] [Indexed: 01/14/2023]
Abstract
G protein coupled receptors (GPCRs), also called 7TM receptors, form a huge superfamily of membrane proteins that, upon activation by extracellular agonists, pass the signal to the cell interior. Ligands can bind either to extracellular N-terminus and loops (e.g. glutamate receptors) or to the binding site within transmembrane helices (Rhodopsin-like family). They are all activated by agonists although a spontaneous auto-activation of an empty receptor can also be observed. Biochemical and crystallographic methods together with molecular dynamics simulations and other theoretical techniques provided models of the receptor activation based on the action of so-called "molecular switches" buried in the receptor structure. They are changed by agonists but also by inverse agonists evoking an ensemble of activation states leading toward different activation pathways. Switches discovered so far include the ionic lock switch, the 3-7 lock switch, the tyrosine toggle switch linked with the nPxxy motif in TM7, and the transmission switch. The latter one was proposed instead of the tryptophan rotamer toggle switch because no change of the rotamer was observed in structures of activated receptors. The global toggle switch suggested earlier consisting of a vertical rigid motion of TM6, seems also to be implausible based on the recent crystal structures of GPCRs with agonists. Theoretical and experimental methods (crystallography, NMR, specific spectroscopic methods like FRET/BRET but also single-molecule-force-spectroscopy) are currently used to study the effect of ligands on the receptor structure, location of stable structural segments/domains of GPCRs, and to answer the still open question on how ligands are binding: either via ensemble of conformational receptor states or rather via induced fit mechanisms. On the other hand the structural investigations of homoand heterodimers and higher oligomers revealed the mechanism of allosteric signal transmission and receptor activation that could lead to design highly effective and selective allosteric or ago-allosteric drugs.
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Affiliation(s)
- B Trzaskowski
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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25
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Launay G, Sanz G, Pajot-Augy E, Gibrat JF. Modeling of mammalian olfactory receptors and docking of odorants. Biophys Rev 2012; 4:255-269. [PMID: 28510073 DOI: 10.1007/s12551-012-0080-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 05/24/2012] [Indexed: 11/29/2022] Open
Abstract
Olfactory receptors (ORs) belong to the superfamily of G protein-coupled receptors (GPCRs), the second largest class of genes after those related to immunity, and account for about 3 % of mammalian genomes. ORs are present in all multicellular organisms and represent more than half the GPCRs in mammalian species (e.g., the mouse OR repertoire contains >1,000 functional genes). ORs are mainly expressed in the olfactory epithelium where they detect odorant molecules, but they are also expressed in a number of other cells, such as sperm cells, although their functions in these cells remain mostly unknown. It has recently been reported that ORs are present in tumoral tissues where they are expressed at different levels than in healthy tissues. A specific OR is over-expressed in prostate cancer cells, and activation of this OR has been shown to inhibit the proliferation of these cells. Odorant stimulation of some of these receptors results in inhibition of cell proliferation. Even though their biological role has not yet been elucidated, these receptors might constitute new targets for diagnosis and therapeutics. It is important to understand the activation mechanism of these receptors at the molecular level, in particular to be able to predict which ligands are likely to activate a particular receptor ('deorphanization') or to design antagonists for a given receptor. In this review, we describe the in silico methodologies used to model the three-dimensional (3D) structure of ORs (in the more general framework of GPCR modeling) and to dock ligands into these 3D structures.
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Affiliation(s)
- Guillaume Launay
- Equipe interactions hôte-pathogène, Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon1, 7 Passage du Vercors, Lyon cedex 07, France
| | - Guenhaël Sanz
- Neurobiologie de l'Olfaction et Modélisation en Imagerie UR1197, INRA, 78350, Jouy-en-Josas, France
| | - Edith Pajot-Augy
- Neurobiologie de l'Olfaction et Modélisation en Imagerie UR1197, INRA, 78350, Jouy-en-Josas, France
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26
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Salon JA, Lodowski DT, Palczewski K. The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol Rev 2012; 63:901-37. [PMID: 21969326 DOI: 10.1124/pr.110.003350] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination.
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Affiliation(s)
- John A Salon
- Department of Molecular Structure, Amgen Incorporated, Thousand Oaks, California, USA
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27
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Lohse MJ, Nuber S, Hoffmann C. Fluorescence/bioluminescence resonance energy transfer techniques to study G-protein-coupled receptor activation and signaling. Pharmacol Rev 2012; 64:299-336. [PMID: 22407612 DOI: 10.1124/pr.110.004309] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Fluorescence and bioluminescence resonance energy transfer (FRET and BRET) techniques allow the sensitive monitoring of distances between two labels at the nanometer scale. Depending on the placement of the labels, this permits the analysis of conformational changes within a single protein (for example of a receptor) or the monitoring of protein-protein interactions (for example, between receptors and G-protein subunits). Over the past decade, numerous such techniques have been developed to monitor the activation and signaling of G-protein-coupled receptors (GPCRs) in both the purified, reconstituted state and in intact cells. These techniques span the entire spectrum from ligand binding to the receptors down to intracellular second messengers. They allow the determination and the visualization of signaling processes with high temporal and spatial resolution. With these techniques, it has been demonstrated that GPCR signals may show spatial and temporal patterning. In particular, evidence has been provided for spatial compartmentalization of GPCRs and their signals in intact cells and for distinct physiological consequences of such spatial patterning. We review here the FRET and BRET technologies that have been developed for G-protein-coupled receptors and their signaling proteins (G-proteins, effectors) and the concepts that result from such experiments.
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Affiliation(s)
- Martin J Lohse
- Institute of Pharmacology and Toxicology, Versbacher Str. 9, 97078 Würzburg, Germany.
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28
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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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30
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Kaltenböck A, Hibert M, Langer T. Putative Dynamics of Vasopressin in its V1a Receptor Binding Site. ACTA ACUST UNITED AC 2011. [DOI: 10.3109/10606820308251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Hulme EC, Lu ZL, Bee MS. Scanning Mutagenesis Studies of the M 1 Muscarinic Acetylcholine Receptor. ACTA ACUST UNITED AC 2011. [DOI: 10.3109/10606820308261] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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32
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Ostopovici-Halip L, Curpăn R, Mracec M, Bologa CG. Structural determinants of the alpha2 adrenoceptor subtype selectivity. J Mol Graph Model 2011; 29:1030-8. [PMID: 21602069 PMCID: PMC3307019 DOI: 10.1016/j.jmgm.2011.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 11/18/2022]
Abstract
Alpha2-adrenergic receptor (α2-AR) subtypes, acting mainly on the central nervous and cardiovascular systems, represent important targets for drug design, confirmed by the high number of studies published so far. Presently, only a few α2-AR subtype selective compounds are known. Using homology modeling and ligand docking, the present study analyzes the similarities and differences between binding sites, and between extracellular loops of the three subtypes of α2-ARs. Several α2-AR subtype selective ligands were docked into the active sites of the three α2-AR subtypes, key interactions between ligands and receptors were mapped, and the predicted results were compared with the available experimental data. Binding site analysis reveals a strong identity between important amino acid residues in each receptor, the very few differences being the key toward modulating selectivity of α2-AR ligands. The observed differences between binding site residues provide an excellent starting point for virtual screening of chemical databases, in order to identify potentially selective ligands for α2-ARs.
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Affiliation(s)
- Liliana Ostopovici-Halip
- Computational Chemistry Department, Institute of Chemistry Timisoara, M. Viteazu 24, 300223, Romania.
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33
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Structural insights into agonist-induced activation of G-protein-coupled receptors. Curr Opin Struct Biol 2011; 21:541-51. [PMID: 21723721 DOI: 10.1016/j.sbi.2011.06.002] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/31/2011] [Accepted: 06/10/2011] [Indexed: 11/23/2022]
Abstract
Recent years have seen tremendous breakthroughs in structure determination of G-protein-coupled receptors (GPCRs). In 2011, two agonist-bound active-state structures of rhodopsin have been published. Together with structures of several rhodopsin activation intermediates and a wealth of biochemical and spectroscopic information, they provide a unique structural framework on which to understand GPCR activation. Here we use this framework to compare the recent crystal structures of the agonist-bound active states of the β(2) adrenergic receptor (β(2)AR) and the A(2A) adenosine receptor (A(2A)AR). While activation of these three GPCRs results in rearrangements of TM5 and TM6, the extent of this conformational change varies considerably. Displacements of the cytoplasmic side of TM6 ranges between 3 and 8Å depending on whether selective stabilizers of the active conformation are used (i.e. a G-protein peptide in the case of rhodopsin or a conformationally selective nanobody in the case of the β(2)AR) or not (A(2A)AR). The agonist-induced conformational changes in the ligand-binding pocket are largely receptor specific due to the different chemical nature of the agonists. However, several similarities can be observed, including a relocation of conserved residues W6.48 and F6.44 towards L5.51 and P5.50, and of I/L3.40 away from P5.50. This transmission switch links agonist binding to the movement of TM5 and TM6 through the rearrangement of the TM3-TM5-TM6 interface, and possibly constitutes a common theme of GPCR activation.
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Standfuss J, Edwards PC, D'Antona A, Fransen M, Xie G, Oprian DD, Schertler GFX. The structural basis of agonist-induced activation in constitutively active rhodopsin. Nature 2011; 471:656-60. [PMID: 21389983 DOI: 10.1038/nature09795] [Citation(s) in RCA: 379] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 01/05/2011] [Indexed: 01/19/2023]
Abstract
G-protein-coupled receptors (GPCRs) comprise the largest family of membrane proteins in the human genome and mediate cellular responses to an extensive array of hormones, neurotransmitters and sensory stimuli. Although some crystal structures have been determined for GPCRs, most are for modified forms, showing little basal activity, and are bound to inverse agonists or antagonists. Consequently, these structures correspond to receptors in their inactive states. The visual pigment rhodopsin is the only GPCR for which structures exist that are thought to be in the active state. However, these structures are for the apoprotein, or opsin, form that does not contain the agonist all-trans retinal. Here we present a crystal structure at a resolution of 3 Å for the constitutively active rhodopsin mutant Glu 113 Gln in complex with a peptide derived from the carboxy terminus of the α-subunit of the G protein transducin. The protein is in an active conformation that retains retinal in the binding pocket after photoactivation. Comparison with the structure of ground-state rhodopsin suggests how translocation of the retinal β-ionone ring leads to a rotation of transmembrane helix 6, which is the critical conformational change on activation. A key feature of this conformational change is a reorganization of water-mediated hydrogen-bond networks between the retinal-binding pocket and three of the most conserved GPCR sequence motifs. We thus show how an agonist ligand can activate its GPCR.
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Palfi A, Millington-Ward S, Chadderton N, O'Reilly M, Goldmann T, Humphries MM, Li T, Wolfrum U, Humphries P, Kenna PF, Farrar GJ. Adeno-associated virus-mediated rhodopsin replacement provides therapeutic benefit in mice with a targeted disruption of the rhodopsin gene. Hum Gene Ther 2010; 21:311-23. [PMID: 19824806 DOI: 10.1089/hum.2009.119] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rhodopsin gene (RHO) encodes a highly expressed G protein-coupled receptor that is central to visual transduction in rod photoreceptors. A suite of recombinant 2/5 adeno-associated viral (AAV) RHO replacement vectors has been generated in an attempt to recapitulate endogenous rhodopsin levels from exogenously delivered AAV vectors in the retina of mice with a targeted disruption in the rhodopsin gene (Rho(-/-) mice). Approximately 40% of wild-type mouse rhodopsin mRNA levels (RNA taken from whole retinas) was achieved in vivo in AAV-RHO-injected eyes, representing approximately 50-fold increases in expression compared with the initial vector. The main focus of this study was to test whether expression of AAV-RHO replacement in Rho(-/-) mice provided therapeutic benefit, which to date had not been achieved. Rho(-/-) mice neither elaborate rod outer segments nor have rod-derived electroretinograms (ERGs). Our results indicate for the first time in this model that subretinal AAV-RHO delivery leads not only to RHO immunolabeling but the generation of rod outer segments as evaluated by light and transmission electron microscopy. Improved histology was accompanied by rod photoreceptor activity as assessed by ERG for at least 12 weeks postinjection. The most efficient AAV-RHO constructs presented in this study provide sufficient levels of RHO to be of therapeutic benefit in Rho(-/-) mice and therefore represent important steps toward generating potent AAV-RHO replacement genes for gene therapy in RHO-linked human retinopathies.
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Affiliation(s)
- Arpad Palfi
- Department of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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37
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Hong WX, Baker KA, Ma X, Stevens RC, Yeager M, Zhang Q. Design, synthesis, and properties of branch-chained maltoside detergents for stabilization and crystallization of integral membrane proteins: human connexin 26. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:8690-6. [PMID: 20232919 PMCID: PMC2877156 DOI: 10.1021/la904893d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A challenging requirement for structural studies of integral membrane proteins (IMPs) is the use of amphiphiles that replicate the hydrophobic environment of membranes. Progress has been impeded by the limited number of useful detergents and the need for a deeper understanding of their structure-activity relationships. To this end, we designed a family of detergents containing short, branched alkyl chains at the interface between the polar head and the apolar tail. This design mimics the second aliphatic chain of lipid molecules and reduces water penetration, thereby increasing the hydrophobicity within the interior of the micelle. To compare with the popular straight-chained maltoside detergents, the branch-chained beta-D-maltosides were synthesized efficiently in pure anomeric form. The branch-chained maltosides form smaller micelles by having shorter main chains, while having comparable hydrophobicity to the detergents with only straight chains. Selected branch-chained and straight-chained maltoside detergents were examined for their ability to solubilize, stabilize, and aid the crystallization of human connexin 26, an alpha-helical IMP that forms hexamers. We showed that the branch-chained maltosides with optimized micellar properties performed as well as or better than the straight-chained analogues and enabled crystallization in different space groups.
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Affiliation(s)
- Wen-Xu Hong
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Kent A. Baker
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Xingquan Ma
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Raymond C. Stevens
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Mark Yeager
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22906
| | - Qinghai Zhang
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Sobhia ME, Singh R, Kare P, Chavan S. Rational design of CCR2 antagonists: a survey of computational studies. Expert Opin Drug Discov 2010; 5:543-57. [DOI: 10.1517/17460441.2010.482559] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Vomaske J, Nelson JA, Streblow DN. Human Cytomegalovirus US28: a functionally selective chemokine binding receptor. Infect Disord Drug Targets 2010; 9:548-56. [PMID: 19594424 DOI: 10.2174/187152609789105696] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 03/06/2009] [Indexed: 11/22/2022]
Abstract
Chemokines are small cytokines that are part of a large family of molecules that bind to G-protein coupled receptors, which, as a family, are the most widely targeted group of molecules in the treatment of disease. Chemokines are critical for recruiting and activating the cells of the immune system during inflammation especially during viral infections. However, a number of viruses including the large herpes virus human cytomegalovirus (HCMV) encode mechanisms to impede the effects of chemokines or has gained the ability to use these molecules to its own advantage. The Human Cytomegalovirus (HCMV)-encoded chemokine receptor US28 is the best characterized of the four unique chemokine receptor-like molecules found in the HCMV genome. US28 has been studied as an important virulence factor for HCMV-mediated vascular disease and, more recently, in models of HCMV-associated malignancy. US28 is a rare multi-chemokine family binding receptor with the ability to bind ligands from two distinct chemokine classes. Ligand binding to US28 activates cell-type and ligand-specific signaling pathways leading to cellular migration, which is an important example of receptor functional selectivity. Additionally, US28 has been demonstrated to constitutively activate phospholipase C (PLC) and NF-kB signaling pathways. Understanding the structure/function relationships between US28, its ligands and intracellular signaling molecules will provide essential clues for effective pharmacological targeting of this multifunctional chemokine receptor.
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Affiliation(s)
- Jennifer Vomaske
- Department of Molecular Microbiology and Immunology and The Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Portland, OR 97201, USA
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40
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Ubarretxena-Belandia I, Stokes DL. Present and future of membrane protein structure determination by electron crystallography. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 81:33-60. [PMID: 21115172 DOI: 10.1016/b978-0-12-381357-2.00002-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins.
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Affiliation(s)
- Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Mt. Sinai School of Medicine, New York, New York, USA
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Ohara K, Kawano M, Inokuma Y, Fujita M. A Porous Coordination Network Catalyzes an Olefin Isomerization Reaction in the Pore. J Am Chem Soc 2009; 132:30-1. [DOI: 10.1021/ja908794n] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuaki Ohara
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, CREST-JST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Pohang 790-784, South Korea
| | - Masaki Kawano
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, CREST-JST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Pohang 790-784, South Korea
| | - Yasuhide Inokuma
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, CREST-JST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Pohang 790-784, South Korea
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, CREST-JST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), San 31, Hyojadong, Pohang 790-784, South Korea
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Yan L, Holleran BJ, Lavigne P, Escher E, Guillemette G, Leduc R. Analysis of transmembrane domains 1 and 4 of the human angiotensin II AT1 receptor by cysteine-scanning mutagenesis. J Biol Chem 2009; 285:2284-93. [PMID: 19940150 DOI: 10.1074/jbc.m109.077180] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The octapeptide hormone angiotensin II (AngII) exerts a wide variety of cardiovascular effects through the activation of the AT(1) receptor, which belongs to the G protein-coupled receptor superfamily. Like other G protein-coupled receptors, the AT(1) receptor possesses seven transmembrane domains that provide structural support for the formation of the ligand-binding pocket. Here, we investigated the role of the first and fourth transmembrane domains (TMDs) in the formation of the binding pocket of the human AT(1) receptor using the substituted-cysteine accessibility method. Each residue within the Phe-28((1.32))-Ile-53((1.57)) fragment of TMD1 and Leu-143((4.40))-Phe-170((4.67)) fragment of TMD4 was mutated, one at a time, to a cysteine. The resulting mutant receptors were expressed in COS-7 cells, which were subsequently treated with the charged sulfhydryl-specific alkylating agent methanethiosulfonate ethylammonium (MTSEA). This treatment led to a significant reduction in the binding affinity of TMD1 mutants M30C((1.34))-AT(1) and T33C((1.37))-AT(1) and TMD4 mutant V169C((4.66))-AT(1). Although this reduction in binding of the TMD1 mutants was maintained when examined in a constitutively active receptor (N111G-AT(1)) background, we found that V169C((4.66))-AT(1) remained unaffected when treated with MTSEA compared with untreated in this context. Moreover, the complete loss of binding observed for R167C((4.64))-AT(1) was restored upon treatment with MTSEA. Our results suggest that the extracellular portion of TMD1, particularly residues Met-30((1.34)) and Thr-33((1.37)), as well as residues Arg-167((4.64)) and Val-169((4.66)) at the junction of TMD4 and the second extracellular loop, are important binding determinants within the AT(1) receptor binding pocket but that these TMDs undergo very little movement, if at all, during the activation process.
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Affiliation(s)
- Liping Yan
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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Improved retinal function in a mouse model of dominant retinitis pigmentosa following AAV-delivered gene therapy. Mol Ther 2009; 17:593-9. [PMID: 19174761 DOI: 10.1038/mt.2008.301] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Mutational heterogeneity represents one of the greatest barriers impeding the progress toward the clinic of gene therapies for many dominantly inherited disorders. A general strategy of gene suppression in conjunction with replacement has been proposed to overcome this mutational heterogeneity. In the current study, various aspects of this strategy are explored for a dominant form of the retinal degeneration, retinitis pigmentosa (RP), caused by mutations in the rhodopsin gene (RHO-adRP). While > 200 mutations have been identified in rhodopsin (RHO), in principle, suppression and replacement may be employed to provide a single mutation-independent therapeutic for this form of the disorder. In the study we demonstrate in a transgenic mouse simulating human RHO-adRP that RNA interference-based suppression, together with gene replacement utilizing the endogenous mouse gene as the replacement, provides significant benefit as evaluated by electroretinography (ERG). Moreover, this is mirrored histologically by preservation of photoreceptors. AAV-based vectors were utilized for in vivo delivery of the therapy to the target cell type, the photoreceptors. The results demonstrate that RNAi-based mutation-independent suppression and replacement can provide benefit for RHO-adRP and promote the therapeutic approach as potentially beneficial for other autosomal dominantly inherited disorders.
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Morris MB, Dastmalchi S, Church WB. Rhodopsin: structure, signal transduction and oligomerisation. Int J Biochem Cell Biol 2008; 41:721-4. [PMID: 18692154 DOI: 10.1016/j.biocel.2008.04.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2008] [Revised: 04/05/2008] [Accepted: 04/07/2008] [Indexed: 12/15/2022]
Abstract
Rhodopsin was the first G protein-coupled receptor (GPCR) for which a high-resolution crystal structure was obtained. Several crystal structures have now been solved representing different activation states of the receptor. These structures, together with those from lower resolution techniques (e.g. electron microscopy), shed light on the stepwise process by which energy from an extracellular photon is transduced across the membrane to the intracellular compartment thereby activating signalling mechanisms responsible for very low-level light detection. Controversy remains in several areas including: (i) transmembrane helix movements responsible for the transduction process, (ii) the stoichiometry of coupling to G proteins and their mode of activation, (iii) the role, if any, of receptor oligomerisation and (iv) the suitability of using structures of this GPCR as templates for modelling the structures of other GPCRs, and their mechanisms of activation.
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Affiliation(s)
- Michael B Morris
- Bosch Institute, School of Medical Sciences, University of Sydney, NSW 2006, Australia.
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Matsumoto H, Yoshizawa T. Rhodopsin Regeneration is AcceleratedviaNoncovalent 11-cisRetinalOpsin ComplexA Role of Retinal Binding Pocket of Opsin. Photochem Photobiol 2008; 84:985-9. [DOI: 10.1111/j.1751-1097.2008.00338.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Martinelli A, Tuccinardi T. Molecular modeling of adenosine receptors: new results and trends. Med Res Rev 2008; 28:247-77. [PMID: 17492754 DOI: 10.1002/med.20106] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Adenosine is a ubiquitous neuromodulator, which carries out its biological task by stimulating four cell surface receptors (A(1), A(2A), A(2B), and A(3)). Adenosine receptors (ARs) are members of the superfamily of G protein-coupled receptors (GPCRs). Their discovery opened up new avenues for potential drug treatment of a variety of conditions such as asthma, neurodegenerative disorders, chronic inflammatory diseases, and many other physiopathological states that are believed to be associated with changes in adenosine levels. Knowledge of the 3D structure of ARs could be of great help in the task of understanding their function and in the rational design of specific ligands. However, since GPCRs are membrane-bound proteins, high-resolution structural characterization is still an extremely difficult task. For this reason, great importance has been placed on molecular modeling studies and, particularly in the last few years, on homology modeling (HM) techniques. The publication of the first high-resolution crystal structure for bovine rhodopsin (bRh), a GPCR superfamily member, provides the option of utilizing HM to generate 3D models based on detailed structural information. In this review we report, analyze, and compare the main experimental data, computational HM procedures and validation methods used for ARs, describing in detail the most successful results.
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Affiliation(s)
- Adriano Martinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy.
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Dastmalchi S, Church WB, Morris MB. Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. BMC Bioinformatics 2008; 9 Suppl 1:S14. [PMID: 18315845 PMCID: PMC2259415 DOI: 10.1186/1471-2105-9-s1-s14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background G protein-coupled receptors (GPCRs) are abundant, activate complex signalling and represent the targets for up to ~60% of pharmaceuticals but there is a paucity of structural data. Bovine rhodopsin is the first GPCR for which high-resolution structures have been completed but significant variations in structure are likely to exist among the GPCRs. Because of this, considerable effort has been expended on developing in silico tools for refining structures of individual GPCRs. We have developed REPIMPS, a modification of the inverse-folding software Profiles-3D, to assess and predict the rotational orientation and vertical position of helices within the helix bundle of individual GPCRs. We highlight the value of the method by applying it to the Baldwin GPCR template but the method can, in principle, be applied to any low- or high-resolution membrane protein template or structure. Results 3D models were built for transmembrane helical segments of 493 GPCRs based on the Baldwin template, and the models were then scored using REPIMPS and Profiles-3D. The compatibility scores increased significantly using REPIMPS because it takes into account the physicochemical properties of the (lipid) environment surrounding the helix bundle. The arrangement of helices in the helix bundle of the 493 models was then altered systematically by rotating the individual helices. For most GPCRs in the set, changes in the rotational position of one or more helices resulted in significant improvement in the compatibility scores. In particular, for most GPCRs, a rotation of helix VII by 240–300° resulted in improved scores. Bovine rhodopsin modelled using this method showed 3.31 Å RMSD to its crystal structure for 198 Cα atom pairs, suggesting the utility of the method even when starting with idealised structures such as the Baldwin template. Conclusion We have developed an in silico tool which can be used to test the validity of, and refine, models of GPCRs with respect to helix rotation and vertical position based on the physicochemical properties of amino acids and the surrounding environment. The method can be applied to any multi-pass membrane protein and potentially can be used in combination with other high-throughput methodologies to generate and refine models of membrane proteins.
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Affiliation(s)
- Siavoush Dastmalchi
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz 51664, Iran.
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Thompson MD, Cole DEC, Jose PA. Pharmacogenomics of G protein-coupled receptor signaling: insights from health and disease. Methods Mol Biol 2008; 448:77-107. [PMID: 18370232 DOI: 10.1007/978-1-59745-205-2_6] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification and characterization of the processes of G protein-coupled receptor (GPCR) activation and inactivation have refined not only the study of the GPCRs but also the genomics of many accessory proteins necessary for these processes. This has accelerated progress in understanding the fundamental mechanisms involved in GPCR structure and function, including receptor transport to the membrane, ligand binding, activation and inactivation by GRK-mediated (and other) phosphorylation. The catalog of G(s)alpha and Gbeta subunit polymorphisms that result in complex phenotypes has complemented the effort to catalog the GPCRs and their variants. The study of the genomics of GPCR accessory proteins has also provided insight into pathways of disease, such as the contributions of regulator of G protein signaling (RGS) protein to hypertension and activator of G protein signaling (AGS) proteins to the response to hypoxia. In the case of the G protein-coupled receptor kinases (GRKs), identified originally in the retinal tissues that converge on rhodopsin, proteins such as GRK4 have been identified that have been subsequently associated with hypertension. Here, we review the structure and function of GPCR and associated proteins in the context of the gene families that encode them and the genetic disorders associated with their altered function. An understanding of the pharmacogenomics of GPCR signaling provides the basis for examining the GPCRs disrupted in monogenic disease and the pharmacogenetics of a given receptor system.
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Affiliation(s)
- Miles D Thompson
- Department of Laboratory Medicine and Pathobiology, Banting Institute, University of Toronto, Toronto, Ontario, Canada
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Mancia F, Hendrickson WA. Expression of recombinant G-protein coupled receptors for structural biology. MOLECULAR BIOSYSTEMS 2007; 3:723-34. [PMID: 17882334 DOI: 10.1039/b713558k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Filippo Mancia
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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