51
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Inagaki Y, Ogawa T, Tabata MJ, Nagata Y, Watanabe R, Kawamoto T, Moriyama K, Tanaka T. Identification of OPN3 as associated with non-syndromic oligodontia in a Japanese population. J Hum Genet 2021; 66:769-775. [PMID: 33611338 DOI: 10.1038/s10038-021-00903-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 11/09/2022]
Abstract
Tooth agenesis is one of the most frequent congenital abnormalities found in the maxillofacial region. Oligodontia, a severe form of tooth agenesis, occurs as an isolated anomaly or as a syndromic feature. We performed whole exome sequencing analyses to identify causative mutation in a Japanese family with three affected individuals with non-syndromic oligodontia. After variant filtering procedures and validation by Sanger sequencing, we identified one missense mutation (c.668 C > T, p.Gly223Asp) in OPN3 at 1q43, encoding a photosensitive G-protein-coupled receptor (GPCR) expressed in various tissues including brain, liver, and adipose. This mutation was predicted to be pathogenic in silico and was not found in the public databases. We further examined 48 genetically unrelated cases by targeted sequencing of the OPN3 gene region and found one additional missense variant in this gene (c.768 C > T, p.Met256Ile) that was also predicted to be pathogenic. Localization of OPN3 protein by immunohistochemical analysis using mouse embryo revealed its specific expression in the tooth gems from bud to bell stages and their surrounding tissues. These results indicated that OPN3 was involved in non-syndromic oligodontia, which has made an anchoring point for clinical application including DNA diagnostics.
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Affiliation(s)
- Yumi Inagaki
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takuya Ogawa
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Makoto J Tabata
- Section of Biostructural Science, Department of Hard Tissue Engineering, Graduate School of Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuki Nagata
- BioResource Research Center, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryo Watanabe
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tatsuo Kawamoto
- Division of Orofacial Functions and Orthodontics, Department of Health Improvement, Kyushu Dental University, Fukuoka, Japan
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan. .,BioResource Research Center, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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52
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Choi EH, Daruwalla A, Suh S, Leinonen H, Palczewski K. Retinoids in the visual cycle: role of the retinal G protein-coupled receptor. J Lipid Res 2021; 62:100040. [PMID: 32493732 PMCID: PMC7910522 DOI: 10.1194/jlr.tr120000850] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
Driven by the energy of a photon, the visual pigments in rod and cone photoreceptor cells isomerize 11-cis-retinal to the all-trans configuration. This photochemical reaction initiates the signal transduction pathway that eventually leads to the transmission of a visual signal to the brain and leaves the opsins insensitive to further light stimulation. For the eye to restore light sensitivity, opsins require recharging with 11-cis-retinal. This trans-cis back conversion is achieved through a series of enzymatic reactions composing the retinoid (visual) cycle. Although it is evident that the classical retinoid cycle is critical for vision, the existence of an adjunct pathway for 11-cis-retinal regeneration has been debated for many years. Retinal pigment epithelium (RPE)-retinal G protein-coupled receptor (RGR) has been identified previously as a mammalian retinaldehyde photoisomerase homologous to retinochrome found in invertebrates. Using pharmacological, genetic, and biochemical approaches, researchers have now established the physiological relevance of the RGR in 11-cis-retinal regeneration. The photoisomerase activity of RGR in the RPE and Müller glia explains how the eye can remain responsive in daylight. In this review, we will focus on retinoid metabolism in the eye and visual chromophore regeneration mediated by RGR.
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Affiliation(s)
- Elliot H Choi
- Department of Ophthalmology, Gavin Herbert Eye Institute, Center for Translational Vision Research, University of California, Irvine, CA, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.
| | - Anahita Daruwalla
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA; Departments of Physiology and Biophysics, and Chemistry, University of California, Irvine, CA, USA
| | - Susie Suh
- Department of Ophthalmology, Gavin Herbert Eye Institute, Center for Translational Vision Research, University of California, Irvine, CA, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Henri Leinonen
- Department of Ophthalmology, Gavin Herbert Eye Institute, Center for Translational Vision Research, University of California, Irvine, CA, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, Center for Translational Vision Research, University of California, Irvine, CA, USA; Departments of Physiology and Biophysics, and Chemistry, University of California, Irvine, CA, USA.
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53
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Kline JM, Heusinkveld LE, Taranto E, Martin CB, Tomasi AG, Hsu IJ, Cho K, Khillan JS, Murphy PM, Pontejo SM. Structural and functional analysis of Ccr1l1, a Rodentia-restricted eosinophil-selective chemokine receptor homologue. J Biol Chem 2021; 296:100373. [PMID: 33548230 PMCID: PMC7949164 DOI: 10.1016/j.jbc.2021.100373] [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: 09/16/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 11/25/2022] Open
Abstract
Mouse Ccr1l1 (Ccr1-like 1) encodes an orphan G-protein-coupled receptor (GPCR) with the highest homology to the inflammatory and highly promiscuous chemokine receptors Ccr1 and Ccr3 (70 and 50% amino acid identity, respectively). Ccr1l1 was first cloned in 1995, yet current knowledge of this putative chemokine receptor is limited to its gene organization and chromosomal localization. Here we report that Ccr1l1 is a Rodentia-specific gene selectively expressed in eosinophils. However, eosinophil phenotypes, development, and responsiveness to chemokines were all normal in naïve Ccr1l1 knockout mice. We demonstrate for the first time that recombinant Ccr1l1 is expressed on the plasma membrane of transfected cells and contains an extracellular N terminus and an intracellular C terminus, consistent with GPCR topology. Using receptor internalization, β-arrestin recruitment, calcium flux, and chemotaxis assays, we excluded all 37 available mouse chemokines, including Ccr1 ligands, and two viral chemokines as Ccr1l1 ligands, and demonstrated that mouse Ccr1, but not Ccr1l1, exhibits constitutive signaling activity. However, sequence analysis and structural modeling revealed that Ccr1l1 is well equipped to act as a classical signaling GPCR, with N-terminal sulfotyrosines as the only signaling and chemokine-binding determinant absent in Ccr1l1. Hereof, we show that a sulfatable N-terminal Ccr1 Y18 residue is essential for chemotaxis and calcium responses induced by Ccl3 and Ccl9/10, but substituting the corresponding Ccr1l1 F19 residue with tyrosine failed to confer responsiveness to Ccr1 ligands. Although Ccr1l1 remains an extreme outlier in the chemokine receptor family, our study supports that it might respond to unidentified mouse chemokine ligands in eosinophil-driven immune responses.
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Affiliation(s)
- Jaclyn M Kline
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lauren E Heusinkveld
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eleanor Taranto
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Clare B Martin
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandra G Tomasi
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Isabel J Hsu
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyoungin Cho
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jaspal S Khillan
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sergio M Pontejo
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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Chawla U, Perera SMDC, Fried SDE, Eitel AR, Mertz B, Weerasinghe N, Pitman MC, Struts AV, Brown MF. Activation of the G‐Protein‐Coupled Receptor Rhodopsin by Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202003342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | | | - Steven D. E. Fried
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Blake Mertz
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Michael C. Pitman
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Andrey V. Struts
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russia
| | - Michael F. Brown
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
- Department of Physics University of Arizona Tucson AZ 85721 USA
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55
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Slater O, Miller B, Kontoyianni M. Decoding Protein-protein Interactions: An Overview. Curr Top Med Chem 2021; 20:855-882. [PMID: 32101126 DOI: 10.2174/1568026620666200226105312] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
Abstract
Drug discovery has focused on the paradigm "one drug, one target" for a long time. However, small molecules can act at multiple macromolecular targets, which serves as the basis for drug repurposing. In an effort to expand the target space, and given advances in X-ray crystallography, protein-protein interactions have become an emerging focus area of drug discovery enterprises. Proteins interact with other biomolecules and it is this intricate network of interactions that determines the behavior of the system and its biological processes. In this review, we briefly discuss networks in disease, followed by computational methods for protein-protein complex prediction. Computational methodologies and techniques employed towards objectives such as protein-protein docking, protein-protein interactions, and interface predictions are described extensively. Docking aims at producing a complex between proteins, while interface predictions identify a subset of residues on one protein that could interact with a partner, and protein-protein interaction sites address whether two proteins interact. In addition, approaches to predict hot spots and binding sites are presented along with a representative example of our internal project on the chemokine CXC receptor 3 B-isoform and predictive modeling with IP10 and PF4.
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Affiliation(s)
- Olivia Slater
- Department of Pharmaceutical Sciences, Southern Illinois University, Edwardsville, IL 62026, United States
| | - Bethany Miller
- Department of Pharmaceutical Sciences, Southern Illinois University, Edwardsville, IL 62026, United States
| | - Maria Kontoyianni
- Department of Pharmaceutical Sciences, Southern Illinois University, Edwardsville, IL 62026, United States
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56
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Schafer CT, Shumate A, Farrens DL. Novel fluorescent GPCR biosensor detects retinal equilibrium binding to opsin and active G protein and arrestin signaling conformations. J Biol Chem 2020; 295:17486-17496. [PMID: 33453993 DOI: 10.1074/jbc.ra120.014631] [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: 05/29/2020] [Revised: 09/25/2020] [Indexed: 01/14/2023] Open
Abstract
Rhodopsin is a canonical class A photosensitive G protein-coupled receptor (GPCR), yet relatively few pharmaceutical agents targeting this visual receptor have been identified, in part due to the unique characteristics of its light-sensitive, covalently bound retinal ligands. Rhodopsin becomes activated when light isomerizes 11-cis-retinal into an agonist, all-trans-retinal (ATR), which enables the receptor to activate its G protein. We have previously demonstrated that, despite being covalently bound, ATR can display properties of equilibrium binding, yet how this is accomplished is unknown. Here, we describe a new approach for both identifying compounds that can activate and attenuate rhodopsin and testing the hypothesis that opsin binds retinal in equilibrium. Our method uses opsin-based fluorescent sensors, which directly report the formation of active receptor conformations by detecting the binding of G protein or arrestin fragments that have been fused onto the receptor's C terminus. We show that these biosensors can be used to monitor equilibrium binding of the agonist, ATR, as well as the noncovalent binding of β-ionone, an antagonist for G protein activation. Finally, we use these novel biosensors to observe ATR release from an activated, unlabeled receptor and its subsequent transfer to the sensor in real time. Taken together, these data support the retinal equilibrium binding hypothesis. The approach we describe should prove directly translatable to other GPCRs, providing a new tool for ligand discovery and mutant characterization.
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Affiliation(s)
- Christopher T Schafer
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA.
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57
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Kozlova MI, Bushmakin IM, Belyaeva JD, Shalaeva DN, Dibrova DV, Cherepanov DA, Mulkidjanian AY. Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1518-1542. [PMID: 33705291 DOI: 10.1134/s0006297920120056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
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Affiliation(s)
- M I Kozlova
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - I M Bushmakin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - J D Belyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D N Shalaeva
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany.
| | - D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D A Cherepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - A Y Mulkidjanian
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
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58
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Chawla U, Perera SMDC, Fried SDE, Eitel AR, Mertz B, Weerasinghe N, Pitman MC, Struts AV, Brown MF. Activation of the G-Protein-Coupled Receptor Rhodopsin by Water. Angew Chem Int Ed Engl 2020; 60:2288-2295. [PMID: 32596956 DOI: 10.1002/anie.202003342] [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: 03/05/2020] [Revised: 05/28/2020] [Indexed: 12/31/2022]
Abstract
Visual rhodopsin is an important archetype for G-protein-coupled receptors, which are membrane proteins implicated in cellular signal transduction. Herein, we show experimentally that approximately 80 water molecules flood rhodopsin upon light absorption to form a solvent-swollen active state. An influx of mobile water is necessary for activating the photoreceptor, and this finding is supported by molecular dynamics (MD) simulations. Combined force-based measurements involving osmotic and hydrostatic pressure indicate the expansion occurs by changes in cavity volumes, together with greater hydration in the active metarhodopsin-II state. Moreover, we discovered that binding and release of the C-terminal helix of transducin is coupled to hydration changes as may occur in visual signal amplification. Hydration-dehydration explains signaling by a dynamic allosteric mechanism, in which the soft membrane matter (lipids and water) has a pivotal role in the catalytic G-protein cycle.
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Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Steven D E Fried
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Anna R Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake Mertz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael C Pitman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA
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59
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Vogel A, Bosse M, Gauglitz M, Wistuba S, Schmidt P, Kaiser A, Gurevich VV, Beck-Sickinger AG, Hildebrand PW, Huster D. The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation. Molecules 2020; 25:E5489. [PMID: 33255213 PMCID: PMC7727705 DOI: 10.3390/molecules25235489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 01/08/2023] Open
Abstract
We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.
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Affiliation(s)
- Alexander Vogel
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Mathias Bosse
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Marcel Gauglitz
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Sarah Wistuba
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Vsevolod V. Gurevich
- Vanderbilt University Medical Center, 2200 Pierce Avenue, Nashville, TN 37232, USA;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Peter W. Hildebrand
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
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60
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Yang LK, Tao YX. Alanine Scanning Mutagenesis of the DRYxxI Motif and Intracellular Loop 2 of Human Melanocortin-4 Receptor. Int J Mol Sci 2020; 21:ijms21207611. [PMID: 33076233 PMCID: PMC7589821 DOI: 10.3390/ijms21207611] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) is a member of the G-protein-coupled receptor (GPCR) superfamily, which has been extensively studied in obesity pathogenesis due to its critical role in regulating energy homeostasis. Both the Gs-cAMP and ERK1/2 cascades are known as important intracellular signaling pathways initiated by the MC4R. The DRYxxI motif at the end of transmembrane domain 3 and the intracellular loop 2 (ICL2) are thought to be crucial for receptor function in several GPCRs. To study the functions of this domain in MC4R, we performed alanine-scanning mutagenesis on seventeen residues. We showed that one residue was critical for receptor cell surface expression. Eight residues were important for ligand binding. Mutations of three residues impaired Gs-cAMP signaling without changing the binding properties. Investigation on constitutive activities of all the mutants in the cAMP pathway revealed that six residues were involved in constraining the receptor in inactive states and five residues were important for receptor activation in the absence of an agonist. In addition, mutations of four residues impaired the ligand-stimulated ERK1/2 signaling pathway without affecting the binding properties. We also showed that some mutants were biased to the Gs-cAMP or ERK1/2 signaling pathway. In summary, we demonstrated that the DRYxxI motif and ICL2 were important for MC4R function.
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61
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Structure-Function Analyses of Human Bitter Taste Receptors-Where Do We Stand? Molecules 2020; 25:molecules25194423. [PMID: 32993119 PMCID: PMC7582848 DOI: 10.3390/molecules25194423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The finding that bitter taste receptors are expressed in numerous tissues outside the oral cavity and fulfill important roles in metabolic regulation, innate immunity and respiratory control, have made these receptors important targets for drug discovery. Efficient drug discovery depends heavily on detailed knowledge on structure-function-relationships of the target receptors. Unfortunately, experimental structures of bitter taste receptors are still lacking, and hence, the field relies mostly on structures obtained by molecular modeling combined with functional experiments and point mutageneses. The present article summarizes the current knowledge on the structure–function relationships of human bitter taste receptors. Although these receptors are difficult to express in heterologous systems and their homology with other G protein-coupled receptors is very low, detailed information are available at least for some of these receptors.
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Structural Complexity and Plasticity of Signaling Regulation at the Melanocortin-4 Receptor. Int J Mol Sci 2020; 21:ijms21165728. [PMID: 32785054 PMCID: PMC7460885 DOI: 10.3390/ijms21165728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
The melanocortin-4 receptor (MC4R) is a class A G protein-coupled receptor (GPCR), essential for regulation of appetite and metabolism. Pathogenic inactivating MC4R mutations are the most frequent cause of monogenic obesity, a growing medical and socioeconomic problem worldwide. The MC4R mediates either ligand-independent or ligand-dependent signaling. Agonists such as α-melanocyte-stimulating hormone (α-MSH) induce anorexigenic effects, in contrast to the endogenous inverse agonist agouti-related peptide (AgRP), which causes orexigenic effects by suppressing high basal signaling activity. Agonist action triggers the binding of different subtypes of G proteins and arrestins, leading to concomitant induction of diverse intracellular signaling cascades. An increasing number of experimental studies have unraveled molecular properties and mechanisms of MC4R signal transduction related to physiological and pathophysiological aspects. In addition, the MC4R crystal structure was recently determined at 2.75 Å resolution in an inactive state bound with a peptide antagonist. Underpinned by structural homology models of MC4R complexes simulating a presumably active-state conformation compared to the structure of the inactive state, we here briefly summarize the current understanding and key players involved in the MC4R switching process between different activity states. Finally, these perspectives highlight the complexity and plasticity in MC4R signaling regulation and identify gaps in our current knowledge.
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63
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Nonaka Y, Hanai S, Katayama K, Imai H, Kandori H. Unique Retinal Binding Pocket of Primate Blue-Sensitive Visual Pigment. Biochemistry 2020; 59:2602-2607. [PMID: 32567852 DOI: 10.1021/acs.biochem.0c00394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The visual pigments of humans contain 11-cis retinal as the chromophore of light perception, and its photoisomerization to the all-trans form initiates visual excitation in our eyes. It is well-known that three isomeric states of retinal (11-cis, all-trans, and 9-cis) are in photoequilibrium at very low temperatures such as 77 K. Here we report the lack of formation of the 9-cis form in monkey blue (MB) at 77 K, as revealed by light-induced difference Fourier transform infrared spectroscopy. This indicates that the chromophore binding pocket of MB does not accommodate the 9-cis form, even though it accommodates the all-trans form by twisting the chromophore. Mutation of the blue-specific tyrosine at position 265 to tryptophan, which is highly conserved in other animal rhodopsins, led to formation of the 9-cis form in MB, suggesting that Y265 is one of the determinants of the unique photochemistry in blue pigments. We also found that 9-cis retinal does not bind to MB opsin, implying that the chromophore binding pocket does not accommodate the 9-cis form at physiological temperature. The unique property of MB is discussed on the basis of the results presented here.
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Affiliation(s)
- Yuki Nonaka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shunpei Hanai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - 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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64
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Jaeger K, Bruenle S, Weinert T, Guba W, Muehle J, Miyazaki T, Weber M, Furrer A, Haenggi N, Tetaz T, Huang CY, Mattle D, Vonach JM, Gast A, Kuglstatter A, Rudolph MG, Nogly P, Benz J, Dawson RJP, Standfuss J. Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7. Cell 2020; 178:1222-1230.e10. [PMID: 31442409 PMCID: PMC6709783 DOI: 10.1016/j.cell.2019.07.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/19/2019] [Accepted: 07/12/2019] [Indexed: 11/15/2022]
Abstract
The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer.
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Affiliation(s)
- Kathrin Jaeger
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Steffen Bruenle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Wolfgang Guba
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jonas Muehle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI; Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Takuya Miyazaki
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland; Chugai Pharmaceutical Co., Ltd., Research Division, Kamakura Research Labs, Kamakura, Kanagawa, Japan
| | - Martin Weber
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Noemi Haenggi
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Tim Tetaz
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Chia-Ying Huang
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Daniel Mattle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI; Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jean-Marie Vonach
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Alain Gast
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- 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
| | - Przemyslaw Nogly
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Joerg Benz
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, 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.
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI.
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65
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Grahl A, Abiko LA, Isogai S, Sharpe T, Grzesiek S. A high-resolution description of β 1-adrenergic receptor functional dynamics and allosteric coupling from backbone NMR. Nat Commun 2020; 11:2216. [PMID: 32371991 PMCID: PMC7200737 DOI: 10.1038/s41467-020-15864-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by extra- and intracellular ligands occurs via modulation of complex conformational equilibria, but their exact kinetic details and underlying atomic mechanisms are unknown. Here we quantified these dynamic equilibria in the β1-adrenergic receptor in its apo form and seven ligand complexes using 1H/15N NMR spectroscopy. We observe three major exchanging conformations: an inactive conformation (Ci), a preactive conformation (Cp) and an active conformation (Ca), which becomes fully populated in a ternary complex with a G protein mimicking nanobody. The Ci ↔ Cp exchange occurs on the microsecond scale, the Cp ↔ Ca exchange is slower than ~5 ms and only occurs in the presence of two highly conserved tyrosines (Y5.58, Y7.53), which stabilize the active conformation of TM6. The Cp→Ca chemical shift changes indicate a pivoting motion of the entire TM6 that couples the effector site to the orthosteric ligand pocket. Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by ligands occurs via modulation of complex conformational equilibria. Here authors quantify these equilibria and their dynamics in the β1-adrenergic receptor in its apo form and seven ligand complexes using NMR.
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Affiliation(s)
- Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Shin Isogai
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Core Facility, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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66
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Pritchard AB, Kanai SM, Krock B, Schindewolf E, Oliver-Krasinski J, Khalek N, Okashah N, Lambert NA, Tavares ALP, Zackai E, Clouthier DE. Loss-of-function of Endothelin receptor type A results in Oro-Oto-Cardiac syndrome. Am J Med Genet A 2020; 182:1104-1116. [PMID: 32133772 PMCID: PMC7202054 DOI: 10.1002/ajmg.a.61531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 01/14/2023]
Abstract
Craniofacial morphogenesis is regulated in part by signaling from the Endothelin receptor type A (EDNRA). Pathogenic variants in EDNRA signaling pathway components EDNRA, GNAI3, PCLB4, and EDN1 cause Mandibulofacial Dysostosis with Alopecia (MFDA), Auriculocondylar syndrome (ARCND) 1, 2, and 3, respectively. However, cardiovascular development is normal in MFDA and ARCND individuals, unlike Ednra knockout mice. One explanation may be that partial EDNRA signaling remains in MFDA and ARCND, as mice with reduced, but not absent, EDNRA signaling also lack a cardiovascular phenotype. Here we report an individual with craniofacial and cardiovascular malformations mimicking the Ednra -/- mouse phenotype, including a distinctive micrognathia with microstomia and a hypoplastic aortic arch. Exome sequencing found a novel homozygous missense variant in EDNRA (c.1142A>C; p.Q381P). Bioluminescence resonance energy transfer assays revealed that this amino acid substitution in helix 8 of EDNRA prevents recruitment of G proteins to the receptor, abrogating subsequent receptor activation by its ligand, Endothelin-1. This homozygous variant is thus the first reported loss-of-function EDNRA allele, resulting in a syndrome we have named Oro-Oto-Cardiac Syndrome. Further, our results illustrate that EDNRA signaling is required for both normal human craniofacial and cardiovascular development, and that limited EDNRA signaling is likely retained in ARCND and MFDA individuals. This work illustrates a straightforward approach to identifying the functional consequence of novel genetic variants in signaling molecules associated with malformation syndromes.
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Affiliation(s)
- Amanda Barone Pritchard
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley M Kanai
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bryan Krock
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Nahla Khalek
- Center for Fetal Diagnosis and Treatment, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Najeah Okashah
- Department of Pharmacology and Toxicology, Medical College of Georgia-Augusta University, Augusta, Georgia, USA
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia-Augusta University, Augusta, Georgia, USA
| | - Andre L P Tavares
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elaine Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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67
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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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68
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Gao Y, Erickson JW, Cerione RA, Ramachandran S. Purification of the Rhodopsin-Transducin Complex for Structural Studies. Methods Mol Biol 2020; 2009:307-315. [PMID: 31152413 DOI: 10.1007/978-1-4939-9532-5_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
G protein-coupled receptors (GPCRs) comprise the largest family of transmembrane receptors and are targets for over 30% of all drugs on the market. Structural information of GPCRs and more importantly that of the complex between GPCRs and their signaling partner heterotrimeric G proteins is of great importance. Here we present a method for the large-scale purification of the rhodopsin-transducin complex, the GPCR-G protein signaling complex in visual phototransduction, directly from their native retinal membrane using native proteins purified from bovine retinae. Formation of the complex on native membrane is orchestrated in part by the proper engagement of lipid-modified rhodopsin and transducin (i.e., palmitoylation of the rhodopsin C-terminus, myristoylation and farnesylation of the αT and γ1, respectively). The resulting complex is of high purity and stability and has proved suitable for further biophysical and structural studies. The methods described here should be applicable to other recombinantly expressed receptors from insect cells or mamalian cells by forming stable, functional complexes directly on purified cell membranes.
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Affiliation(s)
- Yang Gao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Jon W Erickson
- Departments of Chemistry and Chemical Biology and Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Richard A Cerione
- Departments of Chemistry and Chemical Biology and Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sekar Ramachandran
- Departments of Chemistry and Chemical Biology and Molecular Medicine, Cornell University, Ithaca, NY, USA.
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69
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Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding. J Chem Theory Comput 2020; 16:1834-1842. [PMID: 31972074 DOI: 10.1021/acs.jctc.9b01035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Energetic contributions at the single-residue level for retinal-opsin interactions in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but antisymmetric to some extent. Fourteen residues were identified to be major players in retinal relaxation along a plausible pathway from bathorhodopsin to the blue-shifted intermediate, which is in good agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.
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Affiliation(s)
- Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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70
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Chen TY, Li X, Hung CH, Bahudhanapati H, Tan J, Kass DJ, Zhang Y. The relaxin family peptide receptor 1 (RXFP1): An emerging player in human health and disease. Mol Genet Genomic Med 2020; 8:e1194. [PMID: 32100955 PMCID: PMC7196478 DOI: 10.1002/mgg3.1194] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Background Relaxin/relaxin family peptide receptor 1 (RXFP1) signaling is important for both normal physiology and disease. Strong preclinical evidence supports relaxin as a potent antifibrotic molecule. However, relaxin‐based therapy failed in clinical trial in patients with systemic sclerosis. We and others have discovered that aberrant expression of RXFP1 may contribute to the abnormal relaxin/RXFP1 signaling in different diseases. Reduced RXFP1 expression and alternative splicing transcripts with potential functional consequences have been observed in fibrotic tissues. A relative decrease in RXFP1 expression in fibrotic tissues—specifically lung and skin—may explain a potential insensitivity to relaxin. In addition, receptor dimerization also plays important roles in relaxin/RXFP1 signaling. Methods This review describes the tissue specific expression, characteristics of the splicing variants, and homo/heterodimerization of RXFP1 in both normal physiological function and human diseases. We discuss the potential implications of these molecular features for developing therapeutics to restore relaxin/RXFP1 signaling and to harness relaxin's potential antifibrotic effects. Results Relaxin/RXFP1 signaling is important in both normal physiology and in human diseases. Reduced expression of RXFP1 in fibrotic lung and skin tissues surrenders both relaxin/RXFP1 signaling and their responsiveness to exogenous relaxin treatments. Alternative splicing and receptor dimerization are also important in regulating relaxin/RXFP1 signaling. Conclusions Understanding the molecular mechanisms that drive aberrant expression of RXFP1 in disease and the functional roles of alternative splicing and receptor dimerization will provide insight into therapeutic targets that may restore the relaxin responsiveness of fibrotic tissues.
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Affiliation(s)
- Ting-Yun Chen
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.,Institute of Allied Health Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Xiaoyun Li
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ching-Hsia Hung
- Institute of Allied Health Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Harinath Bahudhanapati
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiangning Tan
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel J Kass
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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71
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Jing M, Zhang Y, Wang H, Li Y. G-protein-coupled receptor-based sensors for imaging neurochemicals with high sensitivity and specificity. J Neurochem 2019; 151:279-288. [PMID: 31419844 PMCID: PMC6819231 DOI: 10.1111/jnc.14855] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 01/02/2023]
Abstract
Neurotransmitters and neuromodulators are key neurochemicals that mediate cell-cell communication, maintain the body's homeostasis, and control a wide range of biological processes. Thus, dysregulation of neurochemical signaling is associated with a range of psychiatric disorders and neurological diseases. Understanding the physiological and pathophysiological functions of neurochemicals, particularly in complex biological systems in vivo, requires tools that can probe their dynamics with high sensitivity and specificity. Recently, genetically encoded fluorescent sensors for visualizing specific neurochemicals were developed by coupling neurochemical-sensing G-protein-coupled receptors (GPCRs) with a circular-permutated fluorescent protein. These GPCR-based sensors can monitor the dynamics of neurochemicals in behaving animals with high spatiotemporal resolution. Here, we review recent progress regarding the development and application of GPCR-based sensors for imaging neurochemicals, and we discuss future perspectives.
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Affiliation(s)
- Miao Jing
- Chinese Institute for Brain Research, Beijing, China
| | - Yajun Zhang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
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72
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Wang F, Zhou B. Quantitative structure-activity relationship models for bitter-tasting tripeptides based on integrated descriptors. Struct Chem 2019. [DOI: 10.1007/s11224-019-01432-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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73
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Imamoto Y, Kojima K, Oka T, Maeda R, Shichida Y. Conformational Differences among Metarhodopsin I, Metarhodopsin II, and Opsin Probed by Wide-Angle X-ray Scattering. J Phys Chem B 2019; 123:9134-9142. [PMID: 31580080 DOI: 10.1021/acs.jpcb.9b08311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the photoproducts of vertebrate rhodopsin, only metarhodopsin II (Meta-II) preferentially adopts the active structure in which transmembrane helices are rearranged. Light-induced helical rearrangement of rhodopsin in membrane-embedded form was directly monitored by wide-angle X-ray scattering (WAXS) using nanodiscs. The change in the WAXS curve for the formation of Meta-II was characterized by a peak at 0.2 Å-1 and a valley at 0.6 Å-1, which were not observed in metarhodopsin I and opsin. However, acid-induced active opsin (Opsin*) showed a 0.2 Å-1 peak, but no 0.6 Å-1 valley. Analyses using the model structures based on the crystal structures of dark state and Meta-II suggest that the outward movement of helix VI occurred in Opsin*. However, the displaced helices III and V in Meta-II resulting from the disruption of cytoplasmic ionic lock were restored in Opsin*, which is likely to destabilize the G-protein-activating structure of opsin.
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Affiliation(s)
- Yasushi Imamoto
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Keiichi Kojima
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | | | - Ryo Maeda
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Yoshinori Shichida
- Research Organization for Science and Technology , Ritsumeikan University , Kusatsu , Shiga 525-8577 , Japan
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74
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Abstract
Sphingosine-1-phosphate (S1P) is a lipidic mediator in mammals that functions either as a second messenger or as a ligand. In the latter case, it is transported by its HDL-associated apoM carrier and circulated in blood where it binds to specific S1P receptors on cell membranes and induces downstream reactions. Although S1P signaling pathways are essential for many biological processes, they are poorly understood at the molecular level. Here, the solved crystal structures of the S1P1 receptor were used to evaluate molecular dynamics (MD) simulations to generate greater detailed molecular insights into the mechanism of S1P signaling. The MD simulations provided observations at the coarse-grained and atomic levels indicating that S1P may access the receptor binding pocket directly from solvents. Lifting of the bulky N-terminal cap region of the receptor precedes initial S1P binding. Glu1213.29 guides S1P penetration, and together with Arg2927.34 is responsible for the stabilization of S1P in the binding pocket, which is consistent with experimental predictions. The complete binding of S1P is followed by receptor activation, wherein Trp2696.48 moves toward the transmembrane helix (TM) 7, resulting in the formation of an enhanced hydrogen bond network in the lower region of TM7. The distance between TM3 and TM6 is subsequently increased, resulting in the opening of the intracellular binding pocket that enables G protein binding. Further analysis of the force distribution network in the receptor yielded a detailed molecular understanding of the signal transmission network that is activated upon agonist binding.
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75
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Botta J, Bibic L, Killoran P, McCormick PJ, Howell LA. Design and development of stapled transmembrane peptides that disrupt the activity of G-protein-coupled receptor oligomers. J Biol Chem 2019; 294:16587-16603. [PMID: 31467080 PMCID: PMC6851324 DOI: 10.1074/jbc.ra119.009160] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/08/2019] [Indexed: 12/23/2022] Open
Abstract
Membrane proteins can associate into larger complexes. Examples include receptor tyrosine complexes, ion channels, transporters, and G protein–coupled receptors (GPCRs). For the latter, there is abundant evidence indicating that GPCRs assemble into complexes, through both homo- and heterodimerization. However, the tools for studying and disrupting these complexes, GPCR or otherwise, are limited. Here, we have developed stabilized interference peptides for this purpose. We have previously reported that tetrahydrocannabinol-mediated cognitive impairment arises from homo- or heterooligomerization between the GPCRs cannabinoid receptor type 1 (CB1R) and 5-hydroxytryptamine 2A (5-HT2AR) receptors. Here, to disrupt this interaction through targeting CB1–5-HT2A receptor heteromers in HEK293 cells and using an array of biochemical techniques, including calcium and cAMP measurements, bimolecular fluorescence complementation assays, and CD-based helicity assessments, we developed a NanoLuc binary technology (NanoBiT)-based reporter assay to screen a small library of aryl-carbon–stapled transmembrane-mimicking peptides produced by solid-phase peptide synthesis. We found that these stapling peptides have increased α-helicity and improved proteolytic resistance without any loss of disrupting activity in vitro, suggesting that this approach may also have utility in vivo. In summary, our results provide proof of concept for using NanoBiT to study membrane protein complexes and for stabilizing disrupting peptides to target such membrane complexes through hydrocarbon-mediated stapling. We propose that these peptides could be developed to target previously undruggable GPCR heteromers.
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Affiliation(s)
- Joaquín Botta
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom.,School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Lucka Bibic
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Patrick Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Peter J McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Lesley A Howell
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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76
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Abstract
The evolutionary process that occurs when a species colonizes a new environment provides an opportunity to explore the mechanisms underlying genetic adaptation, which is essential knowledge for understanding evolution and the maintenance of biodiversity. Atlantic herring has an estimated total breeding stock of about 1 trillion (1012) and has colonized the brackish Baltic Sea within the last 10,000 y. Minute genetic differentiation between Atlantic and Baltic herring populations at selectively neutral loci combined with this rapid adaptation to a new environment facilitated the identification of hundreds of loci underlying ecological adaptation. A major question in the field of evolutionary biology is to what extent such an adaptive process involves selection of novel mutations with large effects or genetic changes at many loci, each with a small effect on phenotype (i.e., selection on standing genetic variation). Here we show that a missense mutation in rhodopsin (Phe261Tyr) is an adaptation to the red-shifted Baltic Sea light environment. The transition from phenylalanine to tyrosine differs only by the presence of a hydroxyl moiety in the latter, but this results in an up to 10-nm red-shifted light absorbance of the receptor. Remarkably, an examination of the rhodopsin sequences from 2,056 species of fish revealed that the same missense mutation has occurred independently and been selected for during at least 20 transitions between light environments across all fish. Our results provide a spectacular example of convergent evolution and how a single amino acid change can have a major effect on ecological adaptation.
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77
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Shalaeva DN, Cherepanov DA, Galperin MY, Vriend G, Mulkidjanian AY. G protein-coupled receptors of class A harness the energy of membrane potential to increase their sensitivity and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183051. [PMID: 31449800 DOI: 10.1016/j.bbamem.2019.183051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/28/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022]
Abstract
The human genome contains about 700 genes of G protein-coupled receptors (GPCRs) of class A; these seven-helical membrane proteins are the targets of almost half of all known drugs. In the middle of the helix bundle, crystal structures reveal a highly conserved sodium-binding site, which is connected with the extracellular side by a water-filled tunnel. This binding site contains a sodium ion in those GPCRs that are crystallized in their inactive conformations but does not in those GPCRs that are trapped in agonist-bound active conformations. The escape route of the sodium ion upon the inactive-to-active transition and its very direction have until now remained obscure. Here, by modeling the available experimental data, we show that the sodium gradient over the cell membrane increases the sensitivity of GPCRs if their activation is thermodynamically coupled to the sodium ion translocation into the cytoplasm but decreases it if the sodium ion retreats into the extracellular space upon receptor activation. The model quantitatively describes the available data on both activation and suppression of distinct GPCRs by membrane voltage. The model also predicts selective amplification of the signal from (endogenous) agonists if only they, but not their (partial) analogs, induce sodium translocation. Comparative structure and sequence analyses of sodium-binding GPCRs indicate a key role for the conserved leucine residue in the second transmembrane helix (Leu2.46) in coupling sodium translocation to receptor activation. Hence, class A GPCRs appear to harness the energy of the transmembrane sodium potential to increase their sensitivity and selectivity.
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Affiliation(s)
- Daria N Shalaeva
- School of Physics, Osnabrueck University, 49069 Osnabrück, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Dmitry A Cherepanov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; N.N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Russia.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 HP Nijmegen, the Netherlands.
| | - Armen Y Mulkidjanian
- School of Physics, Osnabrueck University, 49069 Osnabrück, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia.
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78
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García-Nafría J, Tate CG. Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development. Annu Rev Pharmacol Toxicol 2019; 60:51-71. [PMID: 31348870 DOI: 10.1146/annurev-pharmtox-010919-023545] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein-coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR-G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR-G protein selectivity, how accessory membrane proteins alter receptor-ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.
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Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; .,Current affiliation: Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopias Avanzadas, University of Zaragoza, 50018 Zaragoza, Spain;
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79
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Abstract
G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to external stimuli. Upon activation by a ligand, the receptor binds to a partner heterotrimeric G protein and promotes exchange of GTP for GDP, leading to dissociation of the G protein into α and βγ subunits that mediate downstream signals. GPCRs can also activate distinct signaling pathways through arrestins. Active states of GPCRs form by small rearrangements of the ligand-binding, or orthosteric, site that are amplified into larger conformational changes. Molecular understanding of the allosteric coupling between ligand binding and G protein or arrestin interaction is emerging from structures of several GPCRs crystallized in inactive and active states, spectroscopic data, and computer simulations. The coupling is loose, rather than concerted, and agonist binding does not fully stabilize the receptor in an active conformation. Distinct intermediates whose populations are shifted by ligands of different efficacies underlie the complex pharmacology of GPCRs.
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Affiliation(s)
- William I Weis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA;
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80
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Itoigawa A, Hayakawa T, Suzuki-Hashido N, Imai H. A natural point mutation in the bitter taste receptor TAS2R16 causes inverse agonism of arbutin in lemur gustation. Proc Biol Sci 2019; 286:20190884. [PMID: 31161904 DOI: 10.1098/rspb.2019.0884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bitter taste enables the detection of potentially harmful substances and is mediated by bitter taste receptors, TAS2Rs, in vertebrates. Few antagonists and inverse agonists of TAS2Rs have been identified, especially natural compounds. TAS2R16s in humans, apes and Old World monkeys (Catarrhini, Anthropoidea) recognize β-glucoside analogues as specific agonists. Here, we investigated responses of TAS2R16 to β-glucosides in non-anthropoid primates, namely lemurs (Lemuriformes, Strepsirrhini). Salicin acted as an agonist on lemur TAS2R16. Arbutin acted as an agonist in the ring-tailed lemur ( Lemur catta) but as an inverse agonist in black lemur ( Eulemur macaco) and black-and-white ruffed lemur ( Varecia variegata). We identified a strepsirrhine-specific amino acid substitution responsible for the inverse agonism of arbutin. In a food preference test, salicin bitterness was inhibited by arbutin in the black lemur. Structural modelling revealed this locus was important for a rearrangement of the intracellular end of transmembrane helix 7 (TM7). Accordingly, arbutin is the first known natural inverse agonist of TAS2Rs, contributing to our understanding of receptor-ligand interactions and the molecular basis of the unique feeding habit diversification in lemurs. Furthermore, the identification of a causal point mutation suggests that TAS2R can acquire functional changes according to feeding habits and environmental conditions.
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Affiliation(s)
- Akihiro Itoigawa
- 1 Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan.,3 Japan Society for the Promotion of Science , Kojimachi, Chiyoda-ku, Tokyo 102-0083 , Japan
| | - Takashi Hayakawa
- 2 Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan.,4 Faculty of Environmental Earth Science, Hokkaido University , N10W5, Kita-ku, Sapporo, Hokkaido 060-0810 , Japan.,5 Japan Monkey Centre , 26 Inuyamakanrin, Inuyama, Aichi 484-0081 , Japan
| | - Nami Suzuki-Hashido
- 3 Japan Society for the Promotion of Science , Kojimachi, Chiyoda-ku, Tokyo 102-0083 , Japan.,6 Chubu University Academy of Emerging Sciences , 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 , Japan
| | - Hiroo Imai
- 1 Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University , 41-2 Kanrin, Inuyama, Aichi 484-8506 , Japan
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81
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Sahu B, Shah S, Prabhudesai K, Contini A, Idicula-Thomas S. Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms. J Mol Graph Model 2019; 89:156-166. [DOI: 10.1016/j.jmgm.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
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82
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Tzoupis H, Nteli A, Platts J, Mantzourani E, Tselios T. Refinement of the gonadotropin releasing hormone receptor I homology model by applying molecular dynamics. J Mol Graph Model 2019; 89:147-155. [DOI: 10.1016/j.jmgm.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
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83
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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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84
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Díaz Ó, Dalton JAR, Giraldo J. Revealing the Mechanism of Agonist-Mediated Cannabinoid Receptor 1 (CB1) Activation and Phospholipid-Mediated Allosteric Modulation. J Med Chem 2019; 62:5638-5654. [DOI: 10.1021/acs.jmedchem.9b00612] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Óscar Díaz
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - James A. R. Dalton
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
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85
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Senapati S, Poma AB, Cieplak M, Filipek S, Park PSH. Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes. Anal Chem 2019; 91:7226-7235. [PMID: 31074606 DOI: 10.1021/acs.analchem.9b00546] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. Force-distance curve-based AFM (FD-AFM) was utilized to directly probe and localize the conformational states of a GPCR within the membrane at nanoscale resolution based on the mechanical properties of the receptor. FD-AFM was applied to rhodopsin, the light receptor and a prototypical GPCR, embedded in native rod outer segment disc membranes from photoreceptor cells of the retina in mice. Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the active state of the receptor has a higher Young's modulus compared to the inactive state of the receptor. Thus, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Differentiating the states based on the Young's modulus allowed for the mapping of the different states within the membrane. Quantifying the active states present in the membrane containing the constitutively active G90D rhodopsin mutant or apoprotein opsin revealed that most receptors adopt an active state. Traditionally, constitutive activity of GPCRs has been described in terms of two-state models where the receptor can achieve only a single active state. FD-AFM data are inconsistent with a two-state model but instead require models that incorporate multiple active states.
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Affiliation(s)
- Subhadip Senapati
- Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Adolfo B Poma
- Institute of Fundamental Technological Research , Polish Academy of Sciences , Pawińskiego 5B , 02-106 Warsaw , Poland.,Institute of Physics , Polish Academy of Sciences , Aleja Lotników 32/46 , 02-668 Warsaw , Poland
| | - Marek Cieplak
- Institute of Physics , Polish Academy of Sciences , Aleja Lotników 32/46 , 02-668 Warsaw , Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre , University of Warsaw , 02-093 Warsaw , Poland
| | - Paul S H Park
- Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , Ohio 44106 , United States
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86
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García-Nafría J, Tate CG. Cryo-EM structures of GPCRs coupled to G s, G i and G o. Mol Cell Endocrinol 2019; 488:1-13. [PMID: 30930094 DOI: 10.1016/j.mce.2019.02.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 01/14/2023]
Abstract
Advances in electron cryo-microscopy (cryo-EM) now permit the structure determination of G protein-coupled receptors (GPCRs) coupled to heterotrimeric G proteins by single-particle imaging. A combination of G protein engineering and the development of antibodies that stabilise the heterotrimeric G protein facilitate the formation of stable GPCR-G protein complexes suitable for structural biology. Structures have been determined of GPCRs coupled to either heterotrimeric G proteins (Gs, Gi or Go) or mini-G proteins (mini-Gs or mini-Go) by single-particle cryo-EM and X-ray crystallography, respectively. This review describes the technical breakthroughs allowing their structure determination and compares the different techniques. In addition, we compare the structures of GPCRs coupled either to Gs, Gi or Go and analyse the contributions of amino acid residues to the GPCR-G protein interface. There is no unique set of interactions that specifies coupling either to Gs, Gi or Go. Instead, there is a common core of interactions between the C-terminal α-helix of the G protein α-subunit and helices H3, H5 and H6 of the receptor. In addition, there are varying degrees of interaction between all the other GPCR helices and intracellular loops to five regions of the α-subunit and four regions of the β-subunit. These data support the contention that there is not a simple linear barcode that defines the specificity of G protein coupling and thus how a G protein couples to a GPCR cannot currently be determined from simply analysing amino acid sequences. Although the overall architecture of GPCR-G protein complexes is conserved, there are significant differences in the molecular details. The number and type of molecular interactions between amino acid residues at the interfaces varies, resulting in subtly different orientation and position of the G protein with respect to the GPCR. This in turn affects the interface surface area that varies between 845 Å2 and 1490 Å2, which could impact upon the lifetime of signalling complexes in the cell.
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Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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87
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Liu X, Xu X, Hilger D, Aschauer P, Tiemann JKS, Du Y, Liu H, Hirata K, Sun X, Guixà-González R, Mathiesen JM, Hildebrand PW, Kobilka BK. Structural Insights into the Process of GPCR-G Protein Complex Formation. Cell 2019; 177:1243-1251.e12. [PMID: 31080070 DOI: 10.1016/j.cell.2019.04.021] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/25/2019] [Accepted: 04/09/2019] [Indexed: 11/17/2022]
Abstract
The crystal structure of the β2-adrenergic receptor (β2AR) bound to the G protein adenylyl cyclase stimulatory G protein (Gs) captured the complex in a nucleotide-free state (β2AR-Gsempty). Unfortunately, the β2AR-Gsempty complex does not provide a clear explanation for G protein coupling specificity. Evidence from several sources suggests the existence of a transient complex between the β2AR and GDP-bound Gs protein (β2AR-GsGDP) that may represent an intermediate on the way to the formation of β2AR-Gsempty and may contribute to coupling specificity. Here we present a structure of the β2AR in complex with the carboxyl terminal 14 amino acids from Gαs along with the structure of the GDP-bound Gs heterotrimer. These structures provide evidence for an alternate interaction between the β2AR and Gs that may represent an intermediate that contributes to Gs coupling specificity.
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Affiliation(s)
- Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Xinyu Xu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Philipp Aschauer
- Institute for Molecular Bioscience, University of Graz, Humboldtstrasse 50/3, 8010 Graz, Austria
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Charité Medical University Berlin, Berlin 10117, Germany; Institute of Medical Physics and Biophysics, Faculty of Medicine, University Leipzig, Leipzig 04107, Germany
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hongtao Liu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5148, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Xiaoou Sun
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ramon Guixà-González
- Institute of Medical Physics and Biophysics, Charité Medical University Berlin, Berlin 10117, Germany
| | - Jesper M Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Charité Medical University Berlin, Berlin 10117, Germany; Institute of Medical Physics and Biophysics, Faculty of Medicine, University Leipzig, Leipzig 04107, Germany
| | - Brian K Kobilka
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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88
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Acúrcio RC, Scomparin A, Satchi‐Fainaro R, Florindo HF, Guedes RC. Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rita C. Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Anna Scomparin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Helena F. Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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89
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Schulte G, Kozielewicz P. Structural insight into Class F receptors - What have we learnt regarding agonist-induced activation? Basic Clin Pharmacol Toxicol 2019; 126 Suppl 6:17-24. [PMID: 30925000 DOI: 10.1111/bcpt.13235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022]
Abstract
Class F receptors, including the ten Frizzleds (FZD1-10 ) and SMO, mediate the effects of WNTs and hedgehog proteins and belong to the superfamily of G protein-coupled receptors (GPCRs). While the recent, high-resolution insight into mechanisms of GPCR activation provides a better understanding of receptor activation in Class A, B and C GPCRs, it remains unclear how Class F receptors bind their ligands, how ligand binding is translated to receptor activation and how signal initiation and specification are achieved. Here, we summarize recent efforts in elucidating Class F receptor structure and activation mechanisms and critically discuss the progress made in this area. A better understanding of the activation mechanisms of Class F receptors is required to engage in mechanism-based and structure-guided drug discovery to exploit the large therapeutic potential of targeting these receptors pharmacologically.
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Affiliation(s)
- Gunnar Schulte
- Section of Receptor Biology & Signaling, Department Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Paweł Kozielewicz
- Section of Receptor Biology & Signaling, Department Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
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90
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Szlenk CT, Gc JB, Natesan S. Does the Lipid Bilayer Orchestrate Access and Binding of Ligands to Transmembrane Orthosteric/Allosteric Sites of G Protein-Coupled Receptors? Mol Pharmacol 2019; 96:527-541. [PMID: 30967440 DOI: 10.1124/mol.118.115113] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/03/2019] [Indexed: 01/08/2023] Open
Abstract
The ligand-binding sites of many G protein-coupled receptors (GPCRs) are situated around and deeply embedded within the central pocket formed by their seven transmembrane-spanning α-helical domains. Generally, these binding sites are assumed accessible to endogenous ligands from the aqueous phase. Recent advances in the structural biology of GPCRs, along with biophysical and computational studies, suggest that amphiphilic and lipophilic molecules may gain access to these receptors by first partitioning into the membrane and then reaching the binding site via lateral diffusion through the lipid bilayer. In addition, several crystal structures of class A and class B GPCRs bound to their ligands offer unprecedented details on the existence of lipid-facing allosteric binding sites outside the transmembrane helices that can only be reached via lipid pathways. The highly organized structure of the lipid bilayer may direct lipophilic or amphiphilic drugs to a specific depth within the bilayer, changing local concentration of the drug near the binding site and affecting its binding kinetics. Additionally, the constraints of the lipid bilayer, including its composition and biophysical properties, may play a critical role in "pre-organizing" ligand molecules in an optimal orientation and conformation to facilitate receptor binding. Despite its clear involvement in molecular recognition processes, the critical role of the membrane in binding ligands to lipid-exposed transmembrane binding sites remains poorly understood and warrants comprehensive investigation. Understanding the mechanistic basis of the structure-membrane interaction relationship of drugs will not only provide useful insights about receptor binding kinetics but will also enhance our ability to take advantage of the apparent membrane contributions when designing drugs that target transmembrane proteins with improved efficacy and safety. In this minireview, we summarize recent structural and computational studies on membrane contributions to binding processes, elucidating both lipid pathways of ligand access and binding mechanisms for several orthosteric and allosteric ligands of class A and class B GPCRs.
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Affiliation(s)
- Christopher T Szlenk
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Jeevan B Gc
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Senthil Natesan
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
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91
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Biebermann H, Kleinau G, Schnabel D, Bockenhauer D, Wilson LC, Tully I, Kiff S, Scheerer P, Reyes M, Paisdzior S, Gregory JW, Allgrove J, Krude H, Mannstadt M, Gardella TJ, Dattani M, Jüppner H, Grüters A. A New Multisystem Disorder Caused by the Gαs Mutation p.F376V. J Clin Endocrinol Metab 2019; 104:1079-1089. [PMID: 30312418 PMCID: PMC6380466 DOI: 10.1210/jc.2018-01250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/08/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT The α subunit of the stimulatory G protein (Gαs) links numerous receptors to adenylyl cyclase. Gαs, encoded by GNAS, is expressed predominantly from the maternal allele in certain tissues. Thus, maternal heterozygous loss-of-function mutations cause hormonal resistance, as in pseudohypoparathyroidism type Ia, whereas somatic gain-of-function mutations cause hormone-independent endocrine stimulation, as in McCune-Albright syndrome. OBJECTIVE We report two unrelated boys presenting with a new combination of clinical findings that suggest both gain and loss of Gαs function. DESIGN AND SETTING Clinical features were studied and sequencing of GNAS was performed. Signaling capacities of wild-type and mutant Gαs were determined in the presence of different G protein-coupled receptors (GPCRs) under basal and agonist-stimulated conditions. RESULTS Both unrelated patients presented with unexplained hyponatremia in infancy, followed by severe early onset gonadotrophin-independent precocious puberty and skeletal abnormalities. An identical heterozygous de novo variant (c.1136T>G; p.F376V) was found on the maternal GNAS allele in both patients; this resulted in a clinical phenotype that differed from known Gαs-related diseases and suggested gain of function at the vasopressin 2 receptor (V2R) and lutropin/choriogonadotropin receptor (LHCGR), yet increased serum PTH concentrations indicative of impaired proximal tubular PTH1 receptor (PTH1R) function. In vitro studies demonstrated that Gαs-F376V enhanced ligand-independent signaling at the PTH1R, LHCGR, and V2R and, at the same time, blunted ligand-dependent responses. Structural homology modeling suggested mutation-induced modifications at the C-terminal α5 helix of Gαs that are relevant for interaction with GPCRs and signal transduction. CONCLUSIONS The Gαs p.F376V mutation causes a previously unrecognized multisystem disorder.
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Affiliation(s)
- Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography and Signal Transduction, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dirk Schnabel
- Department for Pediatric Endocrinology and Diabetology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Detlef Bockenhauer
- UCL Centre for Nephrology, London, United Kingdom
- Great Ormond Street Hospital for Children, Renal Unit, London, United Kingdom
| | - Louise C Wilson
- Department of Clinical Genetics, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Ian Tully
- Department of Clinical Genetics, University Hospital of Wales, Cardiff, United Kingdom
| | - Sarah Kiff
- Department of Pediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography and Signal Transduction, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Monica Reyes
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sarah Paisdzior
- Institute of Experimental Pediatric Endocrinology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - John W Gregory
- Division of Population Medicine, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jeremy Allgrove
- Department of Pediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mannstadt
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Thomas J Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mehul Dattani
- Department of Pediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom
- Section of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL GOS Institute of Child Health, London, United Kingdom
| | - Harald Jüppner
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Annette Grüters
- Department for Pediatric Endocrinology and Diabetology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- University Hospital Heidelberg, Heidelberg, Germany
- Correspondence and Reprint Requests: Annette Grüters, PhD, Charité-Universitätsmedizin, Department for Pediatric Endocrinology and Diabetes, Mittelallee 8, 13353 Berlin, Germany. E-mail:
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92
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Optical approaches for single-cell and subcellular analysis of GPCR-G protein signaling. Anal Bioanal Chem 2019; 411:4481-4508. [PMID: 30927013 DOI: 10.1007/s00216-019-01774-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 01/05/2023]
Abstract
G protein-coupled receptors (GPCRs), G proteins, and their signaling associates are major signal transducers that control the majority of cellular signaling and regulate key biological functions including immune, neurological, cardiovascular, and metabolic processes. These pathways are targeted by over one-third of drugs on the market; however, the current understanding of their function is limited and primarily derived from cell-destructive approaches providing an ensemble of static, multi-cell information about the status and composition of molecules. Spatiotemporal behavior of molecules involved is crucial to understanding in vivo cell behaviors both in health and disease, and the advent of genetically encoded fluorescence proteins and small fluorophore-based biosensors has facilitated the mapping of dynamic signaling in cells with subcellular acuity. Since we and others have developed optogenetic methods to regulate GPCR-G protein signaling in single cells and subcellular regions using dedicated wavelengths, the desire to develop and adopt optogenetically amenable assays to measure signaling has motivated us to take a broader look at the available optical tools and approaches compatible with measuring single-cell and subcellular GPCR-G protein signaling. Here we review such key optical approaches enabling the examination of GPCR, G protein, secondary messenger, and downstream molecules such as kinase and lipid signaling in living cells. The methods reviewed employ both fluorescence and bioluminescence detection. We not only further elaborate the underlying principles of these sensors but also discuss the experimental criteria and limitations to be considered during their use in single-cell and subcellular signal mapping.
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93
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Falls BA, Zhang Y. Insights into the Allosteric Mechanism of Setmelanotide (RM-493) as a Potent and First-in-Class Melanocortin-4 Receptor (MC4R) Agonist To Treat Rare Genetic Disorders of Obesity through an in Silico Approach. ACS Chem Neurosci 2019; 10:1055-1065. [PMID: 30048591 DOI: 10.1021/acschemneuro.8b00346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human melanocortin-4 receptor (hMC4R) mutations have been implicated as the cause for about 6-8% of all severe obesity cases. Drug-like molecules that are able to rescue the functional activity of mutated receptors are highly desirable to combat genetic obesity among this population of patients. One such molecule is the selective MC4R agonist RM-493 (setmelanotide). While this molecule has been shown to activate mutated receptors with 20-fold higher potency over the endogenous agonist, little is known about its binding mode and how it effectively interacts with hMC4R despite the presence of mutations. In this study, a MC4R homology model was constructed based on the X-ray crystal structure of the adenosine A2A receptor in the active state. Four MC4R mutations commonly found in genetically obese patients and known to effect ligand binding in vitro were introduced into the constructed model. RM-493 was then docked into the wild-type and mutated models in order to better elucidate the possible binding modes for this promising drug candidate and assess how it may be interacting with MC4R to effectively activate receptor polymorphisms. The results reflected the orthosteric interactions of both the endogenous and synthetic ligands with the MC4R, which is supported by the site-directed mutagenesis studies. Meanwhile it helped explain the decremental affinity and potency of these ligands with the receptor polymorphisms. More significantly, our findings indicated that the structural characteristics of RM-493 may allow for enhanced receptor-ligand interactions, particularly through those with the putative allosteric binding sites, which facilitated the ligand to stabilize the active state of native and mutant MC4Rs to maintain reasonably high affinity and potency.
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Affiliation(s)
- Bethany A. Falls
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23298, United States
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23298, United States
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94
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Ognjenović J, Grisshammer R, Subramaniam S. Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies. Annu Rev Biomed Eng 2019; 21:395-415. [PMID: 30892930 DOI: 10.1146/annurev-bioeng-060418-052453] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In recent years, cryo electron microscopy (cryo-EM) technology has been transformed with the development of better instrumentation, direct electron detectors, improved methods for specimen preparation, and improved software for data analysis. Analyses using single-particle cryo-EM methods have enabled determination of structures of proteins with sizes smaller than 100 kDa and resolutions of ∼2 Å in some cases. The use of electron tomography combined with subvolume averaging is beginning to allow the visualization of macromolecular complexes in their native environment in unprecedented detail. As a result of these advances, solutions to many intractable challenges in structural and cell biology, such as analysis of highly dynamic soluble and membrane-embedded protein complexes or partially ordered protein aggregates, are now within reach. Recent reports of structural studies of G protein-coupled receptors, spliceosomes, and fibrillar specimens illustrate the progress that has been made using cryo-EM methods, and are the main focus of this review.
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Affiliation(s)
- Jana Ognjenović
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20814, USA; ,
| | - Reinhard Grisshammer
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20814, USA; ,
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada;
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95
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Gurevich VV, Gurevich EV. The structural basis of the arrestin binding to GPCRs. Mol Cell Endocrinol 2019; 484:34-41. [PMID: 30703488 PMCID: PMC6377262 DOI: 10.1016/j.mce.2019.01.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/04/2019] [Accepted: 01/17/2019] [Indexed: 12/12/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of signaling proteins targeted by more clinically used drugs than any other protein family. GPCR signaling via G proteins is quenched (desensitized) by the phosphorylation of the active receptor by specific GPCR kinases (GRKs) followed by tight binding of arrestins to active phosphorylated receptors. Thus, arrestins engage two types of receptor elements: those that contain GRK-added phosphates and those that change conformation upon activation. GRKs attach phosphates to serines and threonines in the GPCR C-terminus or any one of the cytoplasmic loops. In addition to these phosphates, arrestins engage the cavity that appears between trans-membrane helices upon receptor activation and several other non-phosphorylated elements. The residues that bind GPCRs are localized on the concave side of both arrestin domains. Arrestins undergo a global conformational change upon receptor binding (become activated). Arrestins serve as important hubs of cellular signaling, emanating from activated GPCRs and receptor-independent.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
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96
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Chen Y, Liu T, Xi Q, Jia W, Yin D, Wang X. A Computational Approach to the Study of the Binding Mode of S1P1R Agonists Based on the Active-Like Receptor Model. J Chem Inf Model 2019; 59:1624-1633. [DOI: 10.1021/acs.jcim.8b00764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yonghui Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Tianqi Liu
- Department of Medicinal Chemistry, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Qiumu Xi
- Department of Medicinal Chemistry, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Wenqiang Jia
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Dali Yin
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
- Department of Medicinal Chemistry, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
| | - Xiaojian Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
- Department of Medicinal Chemistry, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, P.R. China
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97
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Edward Zhou X, Melcher K, Eric Xu H. Structural biology of G protein-coupled receptor signaling complexes. Protein Sci 2019; 28:487-501. [PMID: 30311978 PMCID: PMC6371222 DOI: 10.1002/pro.3526] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors that mediate numerous cell signaling pathways, and are targets of more than one-third of clinical drugs. Thanks to the advancement of novel structural biology technologies, high-resolution structures of GPCRs in complex with their signaling transducers, including G-protein and arrestin, have been determined. These 3D complex structures have significantly improved our understanding of the molecular mechanism of GPCR signaling and provided a structural basis for signaling-biased drug discovery targeting GPCRs. Here we summarize structural studies of GPCR signaling complexes with G protein and arrestin using rhodopsin as a model system, and highlight the key features of GPCR conformational states in biased signaling including the sequence motifs of receptor TM6 that determine selective coupling of G proteins, and the phosphorylation codes of GPCRs for arrestin recruitment. We envision the future of GPCR structural biology not only to solve more high-resolution complex structures but also to show stepwise GPCR signaling complex assembly and disassembly and dynamic process of GPCR signal transduction.
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Affiliation(s)
- X. Edward Zhou
- Center for Cancer and Cell Biology, Innovation and Integration ProgramVan Andel Research InstituteGrand RapidsMichigan
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Innovation and Integration ProgramVan Andel Research InstituteGrand RapidsMichigan
| | - H. Eric Xu
- Center for Cancer and Cell Biology, Innovation and Integration ProgramVan Andel Research InstituteGrand RapidsMichigan
- Key Laboratory of Receptor Research, VARI‐SIMM Center, Center for Structure and Function of Drug TargetsShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
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98
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Gurevich VV, Gurevich EV. GPCR Signaling Regulation: The Role of GRKs and Arrestins. Front Pharmacol 2019; 10:125. [PMID: 30837883 PMCID: PMC6389790 DOI: 10.3389/fphar.2019.00125] [Citation(s) in RCA: 330] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
Every animal species expresses hundreds of different G protein-coupled receptors (GPCRs) that respond to a wide variety of external stimuli. GPCRs-driven signaling pathways are involved in pretty much every physiological function and in many pathologies. Therefore, GPCRs are targeted by about a third of clinically used drugs. The signaling of most GPCRs via G proteins is terminated by the phosphorylation of active receptor by specific kinases (GPCR kinases, or GRKs) and subsequent binding of arrestin proteins, that selectively recognize active phosphorylated receptors. In addition, GRKs and arrestins play a role in multiple signaling pathways in the cell, both GPCR-initiated and receptor-independent. Here we focus on the mechanisms of GRK- and arrestin-mediated regulation of GPCR signaling, which includes homologous desensitization and redirection of signaling to additional pathways by bound arrestins.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
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99
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Katayama K, Gulati S, Ortega JT, Alexander NS, Sun W, Shenouda MM, Palczewski K, Jastrzebska B. Specificity of the chromophore-binding site in human cone opsins. J Biol Chem 2019; 294:6082-6093. [PMID: 30770468 DOI: 10.1074/jbc.ra119.007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The variable composition of the chromophore-binding pocket in visual receptors is essential for vision. The visual phototransduction starts with the cis-trans isomerization of the retinal chromophore upon absorption of photons. Despite sharing the common 11-cis-retinal chromophore, rod and cone photoreceptors possess distinct photochemical properties. Thus, a detailed molecular characterization of the chromophore-binding pocket of these receptors is critical to understanding the differences in the photochemistry of vision between rods and cones. Unlike for rhodopsin (Rh), the crystal structures of cone opsins remain to be determined. To obtain insights into the specific chromophore-protein interactions that govern spectral tuning in human visual pigments, here we harnessed the unique binding properties of 11-cis-6-membered-ring-retinal (11-cis-6mr-retinal) with human blue, green, and red cone opsins. To unravel the specificity of the chromophore-binding pocket of cone opsins, we applied 11-cis-6mr-retinal analog-binding analyses to human blue, green, and red cone opsins. Our results revealed that among the three cone opsins, only blue cone opsin can accommodate the 11-cis-6mr-retinal in its chromophore-binding pocket, resulting in the formation of a synthetic blue pigment (B6mr) that absorbs visible light. A combination of primary sequence alignment, molecular modeling, and mutagenesis experiments revealed the specific amino acid residue 6.48 (Tyr-262 in blue cone opsins and Trp-281 in green and red cone opsins) as a selectivity filter in human cone opsins. Altogether, the results of our study uncover the molecular basis underlying the binding selectivity of 11-cis-6mr-retinal to the cone opsins.
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Affiliation(s)
- Kota Katayama
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Life Science and Applied Chemistry, Showa-ku, Nagoya 466-8555, Japan; OptoBio Technology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
| | - Joseph T Ortega
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nathan S Alexander
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106
| | - Marina M Shenouda
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697; Polgenix Inc., Cleveland, Ohio 44106.
| | - Beata Jastrzebska
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
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100
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Advances in Engineering and Application of Optogenetic Indicators for Neuroscience. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9030562] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Our ability to investigate the brain is limited by available technologies that can record biological processes in vivo with suitable spatiotemporal resolution. Advances in optogenetics now enable optical recording and perturbation of central physiological processes within the intact brains of model organisms. By monitoring key signaling molecules noninvasively, we can better appreciate how information is processed and integrated within intact circuits. In this review, we describe recent efforts engineering genetically-encoded fluorescence indicators to monitor neuronal activity. We summarize recent advances of sensors for calcium, potassium, voltage, and select neurotransmitters, focusing on their molecular design, properties, and current limitations. We also highlight impressive applications of these sensors in neuroscience research. We adopt the view that advances in sensor engineering will yield enduring insights on systems neuroscience. Neuroscientists are eager to adopt suitable tools for imaging neural activity in vivo, making this a golden age for engineering optogenetic indicators.
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