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Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angew Chem Int Ed Engl 2018; 57:3048-3053. [DOI: 10.1002/anie.201708889] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/20/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Zahra Shamsi
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Plant Biology, Center for Biophysics & Quantitative Biology, National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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52
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Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201708889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Zahra Shamsi
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Plant Biology, Center for Biophysics & Quantitative Biology, National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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53
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Xu B, Vasile S, Østergaard S, Paulsson JF, Pruner J, Åqvist J, Wulff BS, Gutiérrez-de-Terán H, Larhammar D. Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y 2 Receptor. Mol Pharmacol 2018; 93:323-334. [PMID: 29367257 DOI: 10.1124/mol.117.110627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/19/2018] [Indexed: 11/22/2022] Open
Abstract
Understanding the agonist-receptor interactions in the neuropeptide Y (NPY)/peptide YY (PYY) signaling system is fundamental for the design of novel modulators of appetite regulation. We report here the results of a multidisciplinary approach to elucidate the binding mode of the native peptide agonist PYY to the human Y2 receptor, based on computational modeling, peptide chemistry and in vitro pharmacological analyses. The preserved binding orientation proposed for full-length PYY and five analogs, truncated at the amino terminus, explains our pharmacological results where truncations of the N-terminal proline helix showed little effect on peptide affinity. This was followed by receptor mutagenesis to investigate the roles of several receptor positions suggested by the modeling. As a complement, PYY-(3-36) analogs were synthesized with modifications at different positions in the common PYY/NPY C-terminal fragment (32TRQRY36-amide). The results were assessed and interpreted by molecular dynamics and Free Energy Perturbation (FEP) simulations of selected mutants, providing a detailed map of the interactions of the PYY/NPY C-terminal fragment with the transmembrane cavity of the Y2 receptor. The amidated C-terminus would be stabilized by polar interactions with Gln2886.55 and Tyr2195.39, while Gln1303.32 contributes to interactions with Q34 in the peptide and T32 is close to the tip of TM7 in the receptor. This leaves the core, α-helix of the peptide exposed to make potential interactions with the extracellular loops. This model agrees with most experimental data available for the Y2 system and can be used as a basis for optimization of Y2 receptor agonists.
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Affiliation(s)
- Bo Xu
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Silvana Vasile
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Søren Østergaard
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Johan F Paulsson
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Jasna Pruner
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Johan Åqvist
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Birgitte S Wulff
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Hugo Gutiérrez-de-Terán
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Dan Larhammar
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
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54
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Ito S, Iwaki M, Sugita S, Abe-Yoshizumi R, Iwata T, Inoue K, Kandori H. Unique Hydrogen Bonds in Membrane Protein Monitored by Whole Mid-IR ATR Spectroscopy in Aqueous Solution. J Phys Chem B 2017; 122:165-170. [PMID: 29215887 DOI: 10.1021/acs.jpcb.7b11064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein function is coupled to its structural changes, for which stimulus-induced difference Fourier-transform infrared (FTIR) spectroscopy is a powerful method. By optimizing the attenuated total reflection (ATR)-FTIR analysis on sodium-pumping rhodopsin KR2 in aqueous solution, we first measured the accurate difference spectra upon sodium binding in the whole IR region (4000-1000 cm-1). The new spectral window allows the analysis of not only the fingerprint region (1800-1000 cm-1) but also the hydrogen-bonding donor region (4000-1800 cm-1), revealing an unusually strong hydrogen bond of Tyr located in the sodium binding site of KR2. Progress in ATR-FTIR difference spectroscopy provides an approach to investigating stimulus-induced structural changes of membrane proteins under physiological aqueous conditions.
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Affiliation(s)
| | | | | | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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55
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Dupré C, Bruno O, Bonnaud A, Giganti A, Nosjean O, Legros C, Boutin JA. Assessments of cellular melatonin receptor signaling pathways: β-arrestin recruitment, receptor internalization, and impedance variations. Eur J Pharmacol 2017; 818:534-544. [PMID: 29154938 DOI: 10.1016/j.ejphar.2017.11.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/03/2017] [Accepted: 11/13/2017] [Indexed: 12/30/2022]
Abstract
Melatonin receptors belong to the family of G-protein coupled receptors. Agonist-induced receptor activation is terminated with the recruitment of β-arrestin, which leads to receptor internalization. Furthermore, agonist binding induces a shift in cellular shape that translates into a change in the electric impedance of the cell. In the present study, we employed engineered cells to study these internalization-related processes in the context of the two melatonin receptors, MT1 and MT2. To assess these three receptor internalization-related functions and validate the results, we employed four classical ligands of melatonin receptors: the natural agonist melatonin; the super-agonist 2-iodo-melatonin and the two antagonists luzindole and 4-phenyl-2-propionamidotetralin. The assessments confirmed the nature of the agonistic ligands but showed that 4-phenyl-2-propionamidotetralin, a described antagonist, is a biased partial agonist at MT2 with poorer affinity for MT1. The methods are now available to be applied to any receptor system for which multiple signaling pathways must be evaluated for new molecules.
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Affiliation(s)
- Clémence Dupré
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France
| | - Olivier Bruno
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France
| | - Anne Bonnaud
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France
| | - Adeline Giganti
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France
| | - Céline Legros
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 125, Chemin De Ronde, 78290 Croissy-sur-Seine, France.
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56
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Thangappan J, Madan B, Wu S, Lee SG. Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor. Sci Rep 2017; 7:15205. [PMID: 29123217 PMCID: PMC5680341 DOI: 10.1038/s41598-017-15513-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/27/2017] [Indexed: 01/19/2023] Open
Abstract
Joint-based descriptor is a new level of macroscopic descriptor for protein structure using joints of secondary structures as a basic element. Here, we propose how the joint-based descriptor can be applied to examine the conformational distances or differences of transmembrane (TM) proteins. Specifically, we performed three independent studies that measured the global and conformational distances between GPCR A family and its related structures. First, the conformational distances of GPCR A family and other 7TM proteins were evaluated. This provided the information on the distant and close families or superfamilies to GPCR A family and permitted the identification of conserved local conformations. Second, computational models of GPCR A family proteins were validated, which enabled us to estimate how much they reproduce the native conformation of GPCR A proteins at global and local conformational level. Finally, the conformational distances between active and inactive states of GPCR proteins were estimated, which identified the difference of local conformation. The proposed macroscopic joint-based approach is expected to allow us to investigate structural features, evolutionary relationships, computational models and conformational changes of TM proteins in a more simplistic manner.
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Affiliation(s)
- Jayaraman Thangappan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea
| | - Bharat Madan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea
| | - Sangwook Wu
- Department of Physics, Pukyong National University, Busan, 608-737, Republic of Korea.
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea.
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57
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Bhattacharya A, Brea RJ, Devaraj NK. De novo vesicle formation and growth: an integrative approach to artificial cells. Chem Sci 2017; 8:7912-7922. [PMID: 29619165 PMCID: PMC5858084 DOI: 10.1039/c7sc02339a] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/13/2017] [Indexed: 12/22/2022] Open
Abstract
The assembly of synthetic membranes provides a powerful tool to reconstruct the structure and function of living cells.
The assembly of artificial cells provides a novel strategy to reconstruct life's functions and shed light on how life emerged on Earth and possibly elsewhere. A major challenge to the development of artificial cells is the establishment of simple methodologies to mimic native membrane generation. An ambitious strategy is the bottom-up approach, which aims to systematically control the assembly of highly ordered membrane architectures with defined functionality. This perspective will cover recent advances and the current state-of-the-art of minimal lipid architectures that can faithfully reconstruct the structure and function of living cells. Specifically, we will overview work related to the de novo formation and growth of biomimetic membranes. These studies give us a deeper understanding of the nature of living systems and bring new insights into the origin of cellular life.
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Affiliation(s)
- Ahanjit Bhattacharya
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , CA 92093 , USA .
| | - Roberto J Brea
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , CA 92093 , USA .
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , CA 92093 , USA .
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58
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Fierro F, Suku E, Alfonso-Prieto M, Giorgetti A, Cichon S, Carloni P. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis. Front Mol Biosci 2017; 4:63. [PMID: 28932739 PMCID: PMC5592726 DOI: 10.3389/fmolb.2017.00063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany
| | - Eda Suku
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Biotechnology, University of VeronaVerona, Italy
| | - Sven Cichon
- Institute of Neuroscience and Medicine INM-1, Forschungszentrum JülichJülich, Germany.,Institute for Human Genetics, Department of Genomics, Life&Brain Center, University of BonnBonn, Germany.,Division of Medical Genetics, Department of Biomedicine, University of BaselBasel, Switzerland
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule AachenAachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National UniversityHanoi, Vietnam
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59
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Lupala CS, Rasaeifar B, Gomez-Gutierrez P, Perez JJ. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling. J Biomol Struct Dyn 2017; 36:2436-2448. [PMID: 28728517 DOI: 10.1080/07391102.2017.1357503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.
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Affiliation(s)
- Cecylia S Lupala
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
| | - Bahareh Rasaeifar
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
| | - Patricia Gomez-Gutierrez
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
| | - Juan J Perez
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
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60
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Prosser RS, Ye L, Pandey A, Orazietti A. Activation processes in ligand-activated G protein-coupled receptors: A case study of the adenosine A 2A receptor. Bioessays 2017; 39. [PMID: 28787091 DOI: 10.1002/bies.201700072] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we review concepts related to an ensemble description of G-protein-coupled receptors (GPCRs). The ensemble is characterized by both inactive and active states, whose equilibrium populations and exchange rates depend sensitively on ligand, environment, and allosteric factors. This review focuses on the adenosine A2 receptor (A2A R), a prototypical class A GPCR. 19 F Nuclear Magnetic Resonance (NMR) studies show that apo A2A R is characterized by a broad ensemble of conformers, spanning inactive to active states, and resembling states defined earlier for rhodopsin. In keeping with ideas associated with a conformational selection mechanism, addition of agonist serves to allosterically restrict the overall degrees of freedom at the G protein binding interface and bias both states and functional dynamics to facilitate G protein binding and subsequent activation. While the ligand does not necessarily "induce" activation, it does bias sampling of states, increase the cooperativity of the activation process and thus, the lifetimes of functional activation intermediates, while restricting conformational dynamics to that needed for activation.
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Affiliation(s)
- R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Libin Ye
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada
| | - Aditya Pandey
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada
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61
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Rana S, Sahoo AR, Majhi BK. Structural complexes of the agonist, inverse agonist and antagonist bound C5a receptor: insights into pharmacology and signaling. MOLECULAR BIOSYSTEMS 2017; 12:1586-99. [PMID: 26978009 DOI: 10.1039/c6mb00031b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The C5a receptor (C5aR) is a pharmacologically important G-protein coupled receptor (GPCR) that interacts with (h)C5a, by recruiting both the "orthosteric" sites (site1 at the N-terminus and site2 at the ECS, extra cellular surface) on C5aR in a two site-binding model. However, the complex pharmacological landscape and the distinguishing chemistry operating either at the "orthosteric" site1 or at the functionally important "orthosteric" site2 of C5aR are still not clear, which greatly limits the understanding of C5aR pharmacology. One of the major bottlenecks is the lack of an experimental structure or a refined model structure of C5aR with appropriately defined active sites. The study attempts to understand the pharmacology at the "orthosteric" site2 of C5aR rationally by generating a highly refined full-blown model structure of C5aR through advanced molecular modeling techniques, and further subjecting it to automated docking and molecular dynamics (MD) studies in the POPC bilayer. The first series of structural complexes of C5aR respectively bound to a linear native peptide agonist ((h)C5a-CT), a small molecule inverse agonist (NDT) and a cyclic peptide antagonist (PMX53) are reported, apparently establishing the unique pharmacological landscape of the "orthosteric" site2, which also illustrates an energetically distinct but coherent competitive chemistry ("cation-π" vs. "π-π" interactions) involved in distinguishing the established ligands known for targeting the "orthosteric" site2 of C5aR. Over a total of 1 μs molecular dynamics (MD) simulation in the POPC bilayer, it is evidenced that while the agonist prefers a "cation-π" interaction, the inverse agonist prefers a "cogwheel/L-shaped" interaction in contrast to the "edge-to-face/T-shaped" type π-π interactions demonstrated by the antagonist by engaging the F275(7.28) of the C5aR. In the absence of a NMR or crystallographically guided model structure of C5aR, the computational model complexes not only provide valuable insights for understanding the C5aR pharmacology, but also emerge as a promising platform for the design and discovery of future potential drug candidates targeting the (h)C5a-C5aR signaling axes.
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Affiliation(s)
- Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 751007, India.
| | - Amita Rani Sahoo
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 751007, India.
| | - Bharat Kumar Majhi
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 751007, India.
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62
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Lee Y, Basith S, Choi S. Recent Advances in Structure-Based Drug Design Targeting Class A G Protein-Coupled Receptors Utilizing Crystal Structures and Computational Simulations. J Med Chem 2017; 61:1-46. [PMID: 28657745 DOI: 10.1021/acs.jmedchem.6b01453] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) represent the largest and most physiologically important integral membrane protein family, and these receptors respond to a wide variety of physiological and environmental stimuli. GPCRs are among the most critical therapeutic targets for numerous human diseases, and approximately one-third of the currently marketed drugs target this receptor family. The recent breakthroughs in GPCR structural biology have significantly contributed to our understanding of GPCR function, ligand binding, and pharmacological action as well as to the design of new drugs. This perspective highlights the latest advances in GPCR structures with a focus on the receptor-ligand interactions of each receptor family in class A nonrhodopsin GPCRs as well as the structural features for their activation, biased signaling, and allosteric mechanisms. The current state-of-the-art methodologies of structure-based drug design (SBDD) approaches in the GPCR research field are also discussed.
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Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
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63
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Abstract
The Reggio group has constructed computer models of the inactive and G-protein-activated states of the cannabinoid CB1 and CB2 receptors, as well as, several orphan receptors that recognize a subset of cannabinoid compounds, including GPR55 and GPR18. These models have been used to design ligands, mutations, and covalent labeling studies. The resultant second-generation models have been used to design ligands with improved affinity, efficacy, and subtype selectivity. Herein, we provide a guide for the development of GPCR models using the most recent orphan receptor studied in our lab, GPR3. GPR3 is an orphan receptor that belongs to the Class A family of G-protein-coupled receptors. It shares high sequence similarity with GPR6, GPR12, the lysophospholipid receptors, and the cannabinoid receptors. GPR3 is predominantly expressed in mammalian brain and oocytes and it is known as a Gαs-coupled receptor activated constitutively in cells. GPR3 represents a possible target for the treatment of different pathological conditions such as Alzheimer's disease, oocyte maturation, or neuropathic pain. However, the lack of potent and selective GPR3 ligands is delaying the exploitation of this promising therapeutic target. In this context, we aim to develop a homology model that helps us to elucidate the structural determinants governing ligand-receptor interactions at GPR3. In this chapter, we detail the methods and rationale behind the construction of the GPR3 active-and inactive-state models. These homology models will enable the rational design of novel ligands, which may serve as research tools for further understanding of the biological role of GPR3.
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Affiliation(s)
- Paula Morales
- University of North Carolina at Greensboro, Greensboro, NC, United States.
| | - Dow P Hurst
- University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Patricia H Reggio
- University of North Carolina at Greensboro, Greensboro, NC, United States
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64
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Cunningham MR, Aungraheeta R, Mundell SJ. Pathophysiological consequences of receptor mistraffic: Tales from the platelet P2Y 12 receptor. Mol Cell Endocrinol 2017; 449:74-81. [PMID: 28212842 DOI: 10.1016/j.mce.2017.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/12/2022]
Abstract
Genetic variations in G protein-coupled receptor (GPCR) genes can disrupt receptor function in a wide variety of human genetic diseases, including platelet bleeding disorders. Platelets are critical for haemostasis with inappropriate platelet activation leading to the development of arterial thrombosis, which can result in heart attack and stroke whilst decreased platelet activity is associated with an increased risk of bleeding. GPCRs expressed on the surface of platelets play key roles in regulating platelet activity and therefore function. Receptors include purinergic receptors (P2Y1 and P2Y12), proteinase-activated receptor (PAR1 and PAR4) and thromboxane receptors (TPα), among others. Pharmacological blockade of these receptors forms a powerful therapeutic tool in the treatment and prevention of arterial thrombosis. With the advance of genomic technologies, there has been a substantial increase in the identification of naturally occurring rare and common GPCR variants. These variants include single-nucleotide polymorphisms (SNPs) and insertion or deletions that have the potential to alter GPCR expression or function. A number of defects in platelet GPCRs that disrupt receptor function have now been characterized in patients with mild bleeding disorders. This review will focus on rare, function-disrupting variants of platelet GPCRs with particular emphasis upon mutations in the P2Y12 receptor gene that affect receptor traffic to modulate platelet function. Further this review will outline how the identification and characterization of function-disrupting GPCR mutations provides an essential link in translating our detailed understanding of receptor traffic and function in cell line studies into relevant human biological systems.
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Affiliation(s)
- Margaret R Cunningham
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, UK
| | - Riyaad Aungraheeta
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK
| | - Stuart J Mundell
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK.
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65
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Woolley MJ, Conner AC. Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family. Mol Cell Endocrinol 2017; 449:3-11. [PMID: 27899324 DOI: 10.1016/j.mce.2016.11.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/02/2016] [Accepted: 11/24/2016] [Indexed: 11/16/2022]
Abstract
The extracellular loops (ECLs) of G protein-coupled receptors (GPCRs) can bind directly to docked orthosteric or allosteric ligands, they can contain transient contact points for ligand entry into the transmembrane (TM) bundle and they can regulate the activation of the receptor signalling pathways. Of the three ECLs, ECL2 is the largest and most structurally diverse reflecting its functional importance. This has been shown through biochemical techniques and has been supported by the many subsequent crystal structures of GPCRs bound to both agonists and antagonists. ECL2 shares common structural features between (and sometimes across) receptor sub-families and can facilitate ligand entry to the TM core or act directly as a surface of the ligand-binding pocket. Structural similarities seem to underpin common binding mechanisms; however, where these exist, variations in primary sequence ensure ligand-binding specificity. This review will compare current understanding of the structural themes and main functional roles of ECL2 in ligand binding, activation and regulation of the major families of GPCRs.
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Affiliation(s)
- Michael J Woolley
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alex C Conner
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.
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66
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Cai Y, Liu Y, Culhane KJ, DeVree BT, Yang Y, Sunahara RK, Yan ECY. Purification of family B G protein-coupled receptors using nanodiscs: Application to human glucagon-like peptide-1 receptor. PLoS One 2017; 12:e0179568. [PMID: 28609478 PMCID: PMC5469476 DOI: 10.1371/journal.pone.0179568] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/31/2017] [Indexed: 12/16/2022] Open
Abstract
Family B G protein-coupled receptors (GPCRs) play vital roles in hormone-regulated homeostasis. They are drug targets for metabolic diseases, including type 2 diabetes and osteoporosis. Despite their importance, the signaling mechanisms for family B GPCRs at the molecular level remain largely unexplored due to the challenges in purification of functional receptors in sufficient amount for biophysical characterization. Here, we purified the family B GPCR human glucagon-like peptide-1 (GLP-1) receptor (GLP1R), whose agonists, e.g. exendin-4, are used for the treatment of type 2 diabetes mellitus. The receptor was expressed in HEK293S GnTl- cells using our recently developed protocol. The protocol incorporates the receptor into the native-like lipid environment of reconstituted high density lipoprotein (rHDL) particles, also known as nanodiscs, immediately after the membrane solubilization step followed by chromatographic purification, minimizing detergent contact with the target receptor to reduce denaturation and prolonging stabilization of receptor in lipid bilayers without extra steps of reconstitution. This method yielded purified GLP1R in nanodiscs that could bind to GLP-1 and exendin-4 and activate Gs protein. This nanodisc purification method can potentially be a general strategy to routinely obtain purified family B GPCRs in the 10s of microgram amounts useful for spectroscopic analysis of receptor functions and activation mechanisms.
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Affiliation(s)
- Yingying Cai
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Yuting Liu
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Kelly J. Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Brian T. DeVree
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yang Yang
- Nanobiology Institute, Yale University, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Roger K. Sunahara
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
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Dantas de Araujo A, Wu C, Wu KC, Reid RC, Durek T, Lim J, Fairlie DP. Europium-Labeled Synthetic C3a Protein as a Novel Fluorescent Probe for Human Complement C3a Receptor. Bioconjug Chem 2017; 28:1669-1676. [DOI: 10.1021/acs.bioconjchem.7b00132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Aline Dantas de Araujo
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Chongyang Wu
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert C. Reid
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Durek
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular
Bioscience, ‡Australian Research Council Centre of Excellence in Advanced Molecular
Imaging, Institute for Molecular Bioscience, and §Centre for Inflammation Disease Research, The University of Queensland, Brisbane, Queensland 4072, Australia
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68
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Schmidt D, Gunera J, Baker JG, Kolb P. Similarity- and Substructure-Based Development of β 2-Adrenergic Receptor Ligands Based on Unusual Scaffolds. ACS Med Chem Lett 2017; 8:481-485. [PMID: 28523097 DOI: 10.1021/acsmedchemlett.6b00363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/27/2017] [Indexed: 11/30/2022] Open
Abstract
The β2-adrenergic receptor (β2AR) is a G protein-coupled receptor (GPCR) and a well-explored target. Here, we report the discovery of 13 ligands, ten of which are novel, of this particular GPCR. They have been identified by similarity- and substructure-based searches using multiple ligands, which were described in an earlier study, as starting points. Of note, two of the molecules used as queries here distinguish themselves from other β2AR antagonists by their unique scaffold. The molecules described in this work allow us to explore the ligand space around the previously reported molecules in greater detail, leading to insights into their structure-activity relationship. We also report experimental binding and selectivity data and putative binding modes for the novel molecules.
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Affiliation(s)
- Denis Schmidt
- Department
of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg
6, 35032 Marburg, Germany
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jakub Gunera
- Department
of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Jillian G. Baker
- Cell
Signalling, School of Life Science, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
| | - Peter Kolb
- Department
of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg
6, 35032 Marburg, Germany
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69
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Hinz L, Ahles A, Ruprecht B, Küster B, Engelhardt S. Two serines in the distal C-terminus of the human ß1-adrenoceptor determine ß-arrestin2 recruitment. PLoS One 2017; 12:e0176450. [PMID: 28472170 PMCID: PMC5417508 DOI: 10.1371/journal.pone.0176450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 04/11/2017] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) undergo phosphorylation at several intracellular residues by G protein-coupled receptor kinases. The resulting phosphorylation pattern triggers arrestin recruitment and receptor desensitization. The exact sites of phosphorylation and their function remained largely unknown for the human β1-adrenoceptor (ADRB1), a key GPCR in adrenergic signal transduction and the target of widely used drugs such as β-blockers. The present study aimed to identify the intracellular phosphorylation sites in the ADRB1 and to delineate their function. The human ADRB1 was expressed in HEK293 cells and its phosphorylation pattern was determined by mass spectrometric analysis before and after stimulation with a receptor agonist. We identified a total of eight phosphorylation sites in the receptor's third intracellular loop and C-terminus. Analyzing the functional relevance of individual sites using phosphosite-deficient receptor mutants we found phosphorylation of the ADRB1 at Ser461/Ser462 in the distal part of the C-terminus to determine β-arrestin2 recruitment and receptor internalization. Our data reveal the phosphorylation pattern of the human ADRB1 and the site that mediates recruitment of β-arrestin2.
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Affiliation(s)
- Laura Hinz
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
| | - Andrea Ahles
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
- * E-mail: (AA); (SE)
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Center for Protein Science Munich (CIPSM), Freising, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Center for Protein Science Munich (CIPSM), Freising, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- * E-mail: (AA); (SE)
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70
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Rovati GE, Capra V, Shaw VS, Malik RU, Sivaramakrishnan S, Neubig RR. The DRY motif and the four corners of the cubic ternary complex model. Cell Signal 2017; 35:16-23. [PMID: 28347873 DOI: 10.1016/j.cellsig.2017.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/24/2017] [Indexed: 12/14/2022]
Abstract
Recent structural data on GPCRs using a variety of spectroscopic approaches suggest that GPCRs adopt a dynamic conformational landscape, with ligands stabilizing subsets of these states to activate one or more downstream signaling effectors. A key outstanding question posed by this emerging dynamic structural model of GPCRs is what states, active, inactive, or intermediate are captured by the numerous crystal structures of GPCRs complexed with a variety of agonists, partial agonists, and antagonists. In the early nineties the discovery of inverse agonists and constitutive activity led to the idea that the active receptor state (R⁎) is an intrinsic property of the receptor itself rather than of the RG complex, eventually leading to the formulation of the cubic ternary complex model (CTC). Here, by a careful analysis of a series of data obtained with a number of mutants of the highly conserved E/DRY motif, we show evidences for the existence of all the receptor states theorized by the CTC, four 'uncoupled (R, R⁎ and HR and HR⁎), and, consequently four 'coupled' (RG, R⁎G, HRG and HR⁎G). The E/DRY motif located at the cytosolic end of transmembrane helix III of Class A GPCRs has been widely studied and analyzed because it forms a network of interactions believed to lock receptors in the inactive conformation (R), and, thus, to play a key role in receptor activation. Our conclusions are supported by recent crystal and NMR spectra, as well as by results obtained with two prototypical GPCRs using a new FRET technology that de-couples G protein binding to the receptor from signal transduction. Thus, despite its complexity and limitations, we propose that the CTC is a useful framework to reconcile pharmacological, biochemical and structural data.
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Affiliation(s)
- G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
| | - Valérie Capra
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy; Department of Health Science, University of Milan, Milano, Italy.
| | - Vincent S Shaw
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Rabia U Malik
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Richard R Neubig
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA.
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71
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Brea RJ, Cole CM, Lyda BR, Ye L, Prosser RS, Sunahara RK, Devaraj NK. In Situ Reconstitution of the Adenosine A 2A Receptor in Spontaneously Formed Synthetic Liposomes. J Am Chem Soc 2017; 139:3607-3610. [PMID: 28263576 DOI: 10.1021/jacs.6b12830] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cell transmembrane receptors play a key role in the detection of environmental stimuli and control of intracellular communication. G protein-coupled receptors constitute the largest transmembrane protein family involved in cell signaling. However, current methods for their functional reconstitution in biomimetic membranes remain both challenging and limited in scope. Herein, we describe the spontaneous reconstitution of adenosine A2A receptor (A2AR) during the de novo formation of synthetic liposomes via native chemical ligation. The approach takes advantage of a nonenzymatic and chemoselective method to rapidly generate A2AR embedded phospholiposomes from receptor solubilized in n-dodecyl-β-d-maltoside analogs. In situ lipid synthesis for protein reconstitution technology proceeds in the absence of dialysis and/or detergent absorbents, and A2AR assimilation into synthetic liposomes can be visualized by microscopy and probed by radio-ligand binding.
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Affiliation(s)
- Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Christian M Cole
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Brent R Lyda
- Department of Pharmacology, University of California, San Diego , La Jolla, California 92093, United States
| | - Libin Ye
- Department of Chemistry, University of Toronto , Mississauga, Ontario L5L 1C6, Canada
| | - R Scott Prosser
- Department of Chemistry, University of Toronto , Mississauga, Ontario L5L 1C6, Canada
| | - Roger K Sunahara
- Department of Pharmacology, University of California, San Diego , La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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72
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Ho TT, Nguyen JT, Liu J, Stanczak P, Thompson AA, Yan YG, Chen J, Allerston CK, Dillard CL, Xu H, Shoger NJ, Cameron JS, Massari ME, Aertgeerts K. Method for rapid optimization of recombinant GPCR protein expression and stability using virus-like particles. Protein Expr Purif 2017; 133:41-49. [PMID: 28263854 DOI: 10.1016/j.pep.2017.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/24/2017] [Accepted: 03/01/2017] [Indexed: 10/20/2022]
Abstract
Recent innovative approaches to stabilize and crystallize GPCRs have resulted in an unprecedented breakthrough in GPCR crystal structures as well as application of the purified receptor protein in biophysical and biochemical ligand binding assays. However, the protein optimization process to enable these technologies is lengthy and requires iterative overexpression, solubilization, purification and functional analysis of tens to hundreds of protein variants. Here, we report a new and versatile method to screen in parallel hundreds of GPCR variants in HEK293 produced virus-like particles (VLPs) for protein yield, stability, functionality and ligand binding. This approach reduces the time and resources during GPCR construct optimization by eliminating lengthy protein solubilization and purification steps and by its adaptability to many binding assay formats (label or label-free detection). We exemplified the robustness of our VLP method by screening 210 GALR3-VLP variants in a radiometric agonist-based binding assay and a subset of 88 variants in a label-free antagonist-based assay. The resulting GALR3 agonist or antagonist stabilizing variants were then further used for recombinant protein expression in transfected insect cells. The final purified protein variants were successfully immobilized on a biosensor chip and used in a surface plasmon resonance binding assay.
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Affiliation(s)
- Thao T Ho
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Jasmine T Nguyen
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Juping Liu
- Department of Preclinical Development, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Pawel Stanczak
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Aaron A Thompson
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Yingzhuo G Yan
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Jasmine Chen
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Charles K Allerston
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Charles L Dillard
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Hao Xu
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Nicholas J Shoger
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Jill S Cameron
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Mark E Massari
- Department of Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
| | - Kathleen Aertgeerts
- Department of Structural Biology, Dart Neuroscience, 12278 Scripps Summit Drive, San Diego, CA 92131, USA.
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73
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Ponzoni L, Rossetti G, Maggi L, Giorgetti A, Carloni P, Micheletti C. Unifying view of mechanical and functional hotspots across class A GPCRs. PLoS Comput Biol 2017; 13:e1005381. [PMID: 28158180 PMCID: PMC5315405 DOI: 10.1371/journal.pcbi.1005381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 02/17/2017] [Accepted: 01/25/2017] [Indexed: 01/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors’ functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. The biological functionality of several receptors and enzymes depends on their capability to sustain large-scale structural fluctuations and adopt different conformational states in response to ligand binding. This is the case for G protein-coupled receptors (GPCRs), the largest superfamily of signaling proteins in mammals and a primary pharmaceutical target. To better understand the functional dynamics of GPCRs, we have analysed the inter-residue distance variations across the available structures for several receptors of the rhodopsin-like family (class A). We first reconstructed the network of mechanical, rigid-like couplings between nearby amino acids and then identified those acting as dynamical/mechanical hubs. These were the sites whose virtual removal led to a significant softening of the overall mechanical network. After validating the biological relevance of these sites by comparison against known key functional sites, we singled out those regions which emerge as prominent mechanical hubs and yet have an otherwise still unknown functional role. The most relevant of such novel putative functional sites, which could be probed by mutagenesis experiments, is at interface of two transmembrane helices and we expect it to be crucial for assisting GPCRs conformational response to agonist binding.
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Affiliation(s)
| | - Giulia Rossetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- JSC: Division Computational Science – Simulation Laboratory Biology – Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich, Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- * E-mail: (LP); (GR)
| | - Luca Maggi
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
| | - Alejandro Giorgetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
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74
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Kleinau G, Worth CL, Kreuchwig A, Biebermann H, Marcinkowski P, Scheerer P, Krause G. Structural-Functional Features of the Thyrotropin Receptor: A Class A G-Protein-Coupled Receptor at Work. Front Endocrinol (Lausanne) 2017; 8:86. [PMID: 28484426 PMCID: PMC5401882 DOI: 10.3389/fendo.2017.00086] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
The thyroid-stimulating hormone receptor (TSHR) is a member of the glycoprotein hormone receptors, a sub-group of class A G-protein-coupled receptors (GPCRs). TSHR and its endogenous ligand thyrotropin (TSH) are of essential importance for growth and function of the thyroid gland and proper function of the TSH/TSHR system is pivotal for production and release of thyroid hormones. This receptor is also important with respect to pathophysiology, such as autoimmune (including ophthalmopathy) or non-autoimmune thyroid dysfunctions and cancer development. Pharmacological interventions directly targeting the TSHR should provide benefits to disease treatment compared to currently available therapies of dysfunctions associated with the TSHR or the thyroid gland. Upon TSHR activation, the molecular events conveying conformational changes from the extra- to the intracellular side of the cell across the membrane comprise reception, conversion, and amplification of the signal. These steps are highly dependent on structural features of this receptor and its intermolecular interaction partners, e.g., TSH, antibodies, small molecules, G-proteins, or arrestin. For better understanding of signal transduction, pathogenic mechanisms such as autoantibody action and mutational modifications or for developing new pharmacological strategies, it is essential to combine available structural data with functional information to generate homology models of the entire receptor. Although so far these insights are fragmental, in the past few decades essential contributions have been made to investigate in-depth the involved determinants, such as by structure determination via X-ray crystallography. This review summarizes available knowledge (as of December 2016) concerning the TSHR protein structure, associated functional aspects, and based on these insights we suggest several receptor complex models. Moreover, distinct TSHR properties will be highlighted in comparison to other class A GPCRs to understand the molecular activation mechanisms of this receptor comprehensively. Finally, limitations of current knowledge and lack of information are discussed highlighting the need for intensified efforts toward TSHR structure elucidation.
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Affiliation(s)
- Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
- Group Protein X-Ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany
| | | | - Annika Kreuchwig
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
| | | | - Patrick Scheerer
- Group Protein X-Ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany
| | - Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
- *Correspondence: Gerd Krause,
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Bourque K, Pétrin D, Sleno R, Devost D, Zhang A, Hébert TE. Distinct Conformational Dynamics of Three G Protein-Coupled Receptors Measured Using FlAsH-BRET Biosensors. Front Endocrinol (Lausanne) 2017; 8:61. [PMID: 28439254 PMCID: PMC5383666 DOI: 10.3389/fendo.2017.00061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/21/2017] [Indexed: 12/30/2022] Open
Abstract
A number of studies have profiled G protein-coupled receptor (GPCR) conformation using fluorescent biaresenical hairpin binders (FlAsH) as acceptors for BRET or FRET. These conformation-sensitive biosensors allow reporting of movements occurring on the intracellular surface of a receptor to investigate mechanisms of receptor activation and function. Here, we generated eight FlAsH-BRET-based biosensors within the sequence of the β2-adrenergic receptor (β2AR) and compared agonist-induced responses to the angiotensin II receptor type I (AT1R) and the prostaglandin F2α receptor (FP). Although all three receptors had FlAsH-binding sequences engineered into the third intracellular loops and carboxyl-terminal domain, both the magnitude and kinetics of the BRET responses to ligand were receptor-specific. Biosensors in ICL3 of both the AT1R and FP responded robustly when stimulated with their respective full agonists as opposed to the β2AR where responses in the third intracellular loop were weak and transient when engaged by isoproterenol. C-tail sensors responses were more robust in the β2AR and AT1R but not in FP. Even though GPCRs share the heptahelical topology and are expressed in the same cellular background, different receptors have unique conformational fingerprints.
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Affiliation(s)
- Kyla Bourque
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Rory Sleno
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Dominic Devost
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Alice Zhang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Terence E. Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
- *Correspondence: Terence E. Hébert,
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76
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Rial D, Morató X, Real JI, Gonçalves FQ, Stagljar I, Pereira FC, Fernández-Dueñas V, Cunha RA, Ciruela F. Parkinson's disease-associated GPR37 receptor regulates cocaine-mediated synaptic depression in corticostriatal synapses. Neurosci Lett 2016; 638:162-166. [PMID: 28007645 DOI: 10.1016/j.neulet.2016.12.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/11/2016] [Accepted: 12/13/2016] [Indexed: 11/15/2022]
Abstract
GPR37 is an orphan G protein-coupled receptor highly expressed in the brain. The precise function of GPR37 is still unknown, but a number of evidences indicate it modulates the dopaminergic system. Here, we aimed to determine the role of GPR37 on the control of cocaine-mediated electrophysiological effects (synaptic transmission and short-term plasticity) in corticostriatal synapses. Accordingly, we evaluated basal synaptic transmission and paired-pulse stimulation (PPS) in wild-type and GPR37KO mice slices. Regardless of the genotype, a low concentration of cocaine (2μM) did not modify basal synaptic transmission. Conversely, a higher dose of cocaine (30μM) decreased synaptic transmission in both genotypes, although with different intensities: approximately 30% in slices from wild-type mice and 45% in slices from GPR37-KO mice. On the other hand, no differences in PPS ratio were observed between wild-type and GPR37-KO cocaine-treated mice. Overall, our data suggest that GPR37 is involved in cocaine-induced modification of basal synaptic transmission without modifying cocaine effects in short-term plasticity.
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Affiliation(s)
- Daniel Rial
- CNC-Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Xavier Morató
- Unitat de Farmacologia, Departament Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Spain; Institut de Neurosciències, Universitat de Barcelona, Barcelona, Spain
| | - Joana I Real
- CNC-Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Francisco Q Gonçalves
- CNC-Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Igor Stagljar
- Department of Biochemistry and Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada, Canada
| | | | - Víctor Fernández-Dueñas
- Unitat de Farmacologia, Departament Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Spain; Institut de Neurosciències, Universitat de Barcelona, Barcelona, Spain
| | - Rodrigo A Cunha
- CNC-Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Portugal
| | - Francisco Ciruela
- Unitat de Farmacologia, Departament Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Spain; Institut de Neurosciències, Universitat de Barcelona, Barcelona, Spain.
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77
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Génier S, Degrandmaison J, Moreau P, Labrecque P, Hébert TE, Parent JL. Regulation of GPCR expression through an interaction with CCT7, a subunit of the CCT/TRiC complex. Mol Biol Cell 2016; 27:3800-3812. [PMID: 27708139 PMCID: PMC5170604 DOI: 10.1091/mbc.e16-04-0224] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
A direct and functional interaction between a subunit of the CCT/TCP-1 ring complex (TRiC) chaperonin complex and G protein–coupled receptor (GPCRs) is shown. Evidence is provided that distinct nascent GPCRs can undergo alternative folding pathways and that CCT/TRiC is critical in preventing aggregation of some GPCRs and in promoting their proper maturation and expression. Mechanisms that prevent aggregation and promote folding of nascent G protein–coupled receptors (GPCRs) remain poorly understood. We identified chaperonin containing TCP-1 subunit eta (CCT7) as an interacting partner of the β-isoform of thromboxane A2 receptor (TPβ) by yeast two-hybrid screening. CCT7 coimmunoprecipitated with overexpressed TPβ and β2-adrenergic receptor (β2AR) in HEK 293 cells, but also with endogenous β2AR. CCT7 depletion by small interfering RNA reduced total and cell-surface expression of both receptors and caused redistribution of the receptors to juxtanuclear aggresomes, significantly more so for TPβ than β2AR. Interestingly, Hsp90 coimmunoprecipitated with β2AR but virtually not with TPβ, indicating that nascent GPCRs can adopt alternative folding pathways. In vitro pull-down assays showed that both receptors can interact directly with CCT7 through their third intracellular loops and C-termini. We demonstrate that Trp334 in the TPβ C-terminus is critical for the CCT7 interaction and plays an important role in TPβ maturation and cell-surface expression. Of note, introducing a tryptophan in the corresponding position of the TPα isoform confers the CCT7-binding and maturation properties of TPβ. We show that an interaction with a subunit of the CCT/TCP-1 ring complex (TRiC) chaperonin complex is involved in regulating aggregation of nascent GPCRs and in promoting their proper maturation and expression.
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Affiliation(s)
- Samuel Génier
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Jade Degrandmaison
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Pierrick Moreau
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Pascale Labrecque
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Jean-Luc Parent
- Service de Rhumatologie, Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), and Institut de Pharmacologie de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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Hu J, Feng Z, Ma S, Zhang Y, Tong Q, Alqarni MH, Gou X, Xie XQ. Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery. J Chem Inf Model 2016; 56:1152-63. [PMID: 27186994 PMCID: PMC5395206 DOI: 10.1021/acs.jcim.5b00739] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cannabinoid receptor 2 (CB2), a G protein-coupled receptor (GPCR), is a promising target for the treatment of neuropathic pain, osteoporosis, immune system, cancer, and drug abuse. The lack of an experimental three-dimensional CB2 structure has hindered not only the development of studies of conformational differences between the inactive and active CB2 but also the rational discovery of novel functional compounds targeting CB2. In this work, we constructed models of both inactive and active CB2 by homology modeling. Then we conducted two comparative 100 ns molecular dynamics (MD) simulations on the two systems-the active CB2 bound with both the agonist and G protein and the inactive CB2 bound with inverse agonist-to analyze the conformational difference of CB2 proteins and the key residues involved in molecular recognition. Our results showed that the inactive CB2 and the inverse agonist remained stable during the MD simulation. However, during the MD simulations, we observed dynamical details about the breakdown of the "ionic lock" between R131(3.50) and D240(6.30) as well as the outward/inward movements of transmembrane domains of the active CB2 that bind with G proteins and agonist (TM5, TM6, and TM7). All of these results are congruent with the experimental data and recent reports. Moreover, our results indicate that W258(6.48) in TM6 and residues in TM4 (V164(4.56)-L169(4.61)) contribute greatly to the binding of the agonist on the basis of the binding energy decomposition, while residues S180-F183 in extracellular loop 2 (ECL2) may be of importance in recognition of the inverse agonist. Furthermore, pharmacophore modeling and virtual screening were carried out for the inactive and active CB2 models in parallel. Among all 10 hits, two compounds exhibited novel scaffolds and can be used as novel chemical probes for future studies of CB2. Importantly, our studies show that the hits obtained from the inactive CB2 model mainly act as inverse agonist(s) or neutral antagonist(s) at low concentration. Moreover, the hit from the active CB2 model also behaves as a neutral antagonist at low concentration. Our studies provide new insight leading to a better understanding of the structural and conformational differences between two states of CB2 and illuminate the effects of structure on virtual screening and drug design.
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Affiliation(s)
- Jianping Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- College of Chemistry, Leshan Normal University, Leshan, Sichuan 614004, China
- School of Pharmacy and Bioengineering; Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, Sichuan 610106, China
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yu Zhang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qin Tong
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mohammed Hamed Alqarni
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaojun Gou
- School of Pharmacy and Bioengineering; Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, Sichuan 610106, China
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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79
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Munk C, Isberg V, Mordalski S, Harpsøe K, Rataj K, Hauser AS, Kolb P, Bojarski AJ, Vriend G, Gloriam DE. GPCRdb: the G protein-coupled receptor database - an introduction. Br J Pharmacol 2016; 173:2195-207. [PMID: 27155948 PMCID: PMC4919580 DOI: 10.1111/bph.13509] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/18/2016] [Accepted: 04/24/2016] [Indexed: 12/16/2022] Open
Abstract
GPCRs make up the largest family of human membrane proteins and of drug targets. Recent advances in GPCR pharmacology and crystallography have shed new light on signal transduction, allosteric modulation and biased signalling, translating into new mechanisms and principles for drug design. The GPCR database, GPCRdb, has served the community for over 20 years and has recently been extended to include a more multidisciplinary audience. This review is intended to introduce new users to the services in GPCRdb, which meets three overall purposes: firstly, to provide reference data in an integrated, annotated and structured fashion, with a focus on sequences, structures, single‐point mutations and ligand interactions. Secondly, to equip the community with a suite of web tools for swift analysis of structures, sequence similarities, receptor relationships, and ligand target profiles. Thirdly, to facilitate dissemination through interactive diagrams of, for example, receptor residue topologies, phylogenetic relationships and crystal structure statistics. Herein, these services are described for the first time; visitors and guides are provided with good practices for their utilization. Finally, we describe complementary databases cross‐referenced by GPCRdb and web servers with corresponding functionality.
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Affiliation(s)
- C Munk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - V Isberg
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - S Mordalski
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - K Harpsøe
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - K Rataj
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - A S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - P Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - A J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - G Vriend
- Centre for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - D E Gloriam
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Yanai T, Kurosawa A, Nikaido Y, Nakajima N, Saito T, Osada H, Konno A, Hirai H, Takeda S. Identification and molecular docking studies for novel inverse agonists of SREB, super conserved receptor expressed in brain. Genes Cells 2016; 21:717-27. [PMID: 27184081 DOI: 10.1111/gtc.12378] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/18/2016] [Indexed: 11/28/2022]
Abstract
The identification of novel synthetic ligands for G protein-coupled receptors (GPCRs) is important not only for understanding human physiology, but also for the development of novel drugs, especially for orphan GPCRs for which endogenous ligands are unknown. One of the orphan GPCR subfamilies, Super conserved Receptor Expressed in Brain (SREB), consists of GPR27, GPR85 and GPR173 and is expressed in the central nervous system. We report herein the identification of inverse agonists for the SREB family without their agonists. We carried out an in vitro screening of 5472 chemical compounds from the RIKEN NPDepo chemical library. The binding of [(35) S]GTPγS to the GPR173-Gsα fusion protein expressed in Sf9 cells was measured and resulted in the identification of 8 novel GPR173 inverse agonists. The most potent compound showed an IC50 of approximately 8 μm. The identified compounds were also antagonists for other SREB members, GPR27 and GPR85. These results indicated that the SREB family could couple Gs-type G proteins, and SREB-Gsα fusion proteins showed significant constitutive activities. Moreover, a molecular model of GPR173 was constructed using the screening results. The combination of computational and biological methods will provide a unique approach to ligand identification for orphan GPCRs and brain research.
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Affiliation(s)
- Toshihiro Yanai
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Aya Kurosawa
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Yoshiaki Nikaido
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Nozomi Nakajima
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Tamio Saito
- Collaboration Promotion Unit, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Ayumu Konno
- Department of Neurophysiology and Neural Repair, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Hirokazu Hirai
- Department of Neurophysiology and Neural Repair, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Shigeki Takeda
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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81
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Gastaldi S, Zamboni M, Bolasco G, Di Segni G, Tocchini-Valentini GP. Analysis of random PCR-originated mutants of the yeast Ste2 and Ste3 receptors. Microbiologyopen 2016; 5:670-86. [PMID: 27150158 PMCID: PMC4985600 DOI: 10.1002/mbo3.361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/01/2016] [Accepted: 03/08/2016] [Indexed: 01/16/2023] Open
Abstract
The G protein-coupled receptors Ste2 and Ste3 bind α- and a-factor, respectively, in Saccharomyces cerevisiae. These receptors share a similar conformation, with seven transmembrane segments, three intracellular loops, a C-terminus tail, and three extracellular loops. However, the amino acid sequences of these two receptors bear no resemblance to each other. Coincidently the two ligands, α- and a-factor, have different sequences. Both receptors activate the same G protein. To identify amino acid residues that are important for signal transduction, the STE2 and STE3 genes were mutagenized by a random PCR-based method. Mutant receptors were analyzed in MATα cells mutated in the ITC1 gene, whose product represses transcription of a-specific genes in MATα. Expression of STE2 or STE3 in these cells results in autocrine activation of the mating pathway, since this strain produces the Ste2 receptor in addition to its specific ligand, α-factor. It also produces a-factor in addition to its specific receptor, Ste3. Therefore, this strain provides a convenient model to analyze mutants of both receptors in the same background. Many hyperactive mutations were found in STE3, whereas none was detected in STE2. This result is consistent with the different strategies that the two genes have adopted to be expressed.
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Affiliation(s)
- Serena Gastaldi
- CNR, Institute of Cell Biology and Neurobiology (IBCN), Monterotondo (Rome), 00015, Italy
| | - Michela Zamboni
- CNR, Institute of Cell Biology and Neurobiology (IBCN), Monterotondo (Rome), 00015, Italy
| | - Giulia Bolasco
- EMBL, European Molecular Biology Laboratory, Monterotondo (Rome), 00015, Italy
| | - Gianfranco Di Segni
- CNR, Institute of Cell Biology and Neurobiology (IBCN), Monterotondo (Rome), 00015, Italy
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Abstract
Protease signaling in cells elicits multiple physiologically important responses via protease-activated receptors (PARs). There are 4 members of this family of G-protein-coupled receptors (PAR1-4). PARs are activated by proteolysis of the N terminus to reveal a tethered ligand. The rate-limiting step of PAR signaling is determined by the efficiency of proteolysis of the N terminus, which is regulated by allosteric binding sites, cofactors, membrane localization, and receptor dimerization. This ultimately controls the initiation of PAR signaling. In addition, these factors also control the cellular response by directing signaling toward G-protein or β-arrestin pathways. PAR1 signaling on endothelial cells is controlled by the activating protease and heterodimerization with PAR2 or PAR3. As a consequence, the genetic and epigenetic control of PARs and their cofactors in physiologic and pathophysiologic conditions have the potential to influence cellular behavior. Recent studies have uncovered polymorphisms that result in PAR4 sequence variants with altered reactivity that interact to influence platelet response. This further demonstrates how interactions within the plasma membrane can control the physiological output. Understanding the structural rearrangement following PAR activation and how PARs are allosterically controlled within the plasma membrane will determine how best to target this family of receptors therapeutically. The purpose of this article is to review how signaling from PARs is influenced by alternative cleavage sites and the physical interactions within the membrane. Going forward, it will be important to relate the altered signaling to the molecular arrangement of PARs in the cell membrane and to determine how these may be influenced genetically.
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83
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Cohen LS, Arshava B, Kauffman S, Mathew E, Fracchiolla KE, Ding FX, Dumont ME, Becker JM, Naider F. Guided reconstitution of membrane protein fragments. Biopolymers 2016; 102:16-29. [PMID: 23897574 DOI: 10.1002/bip.22349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/13/2013] [Accepted: 06/26/2013] [Indexed: 11/12/2022]
Abstract
Structural analysis by NMR of G protein-coupled receptors (GPCRs) has proven to be extremely challenging. To reduce the number of peaks in the NMR spectra by segmentally labeling a GPCR, we have developed a Guided Reconstitution method that includes the use of charged residues and Cys activation to drive heterodimeric disulfide bond formation. Three different cysteine-activating reagents: 5-5'-dithiobis(2-nitrobenzoic acid) [DTNB], 2,2'-dithiobis(5-nitropyridine) [DTNP], and 4,4'-dipyridyl disulfide [4-PDS] were analyzed to determine their efficiency in heterodimer formation at different pHs. Short peptides representing the N-terminal (NT) and C-terminal (CT) regions of the first extracellular loop (EL1) of Ste2p, the Saccharomyces cerevisiae alpha-factor mating receptor, were activated using these reagents and the efficiencies of activation and rates of heterodimerization were analyzed. Activation of NT peptides with DTNP and 4-PDS resulted in about 60% yield, but heterodimerization was rapid and nearly quantitative. Double transmembrane domain protein fragments were biosynthesized and used in Guided Reconstitution reactions. A 102-residue fragment, 2TM-tail [Ste2p(G31-I120C)], was heterodimerized with CT-EL1-tail(DTNP) at pH 4.6 with a yield of ∼75%. A 132-residue fragment, 2TMlong-tail [Ste2p(M1-I120C)], was expressed in both unlabeled and (15)N-labeled forms and used with a peptide comprising the third transmembrane domain, to generate a 180-residue segmentally labeled 3TM protein that was found to be segmentally labeled using [(15)N,(1)H]-HSQC analysis. Our data indicate that the Guided Reconstitution method would be applicable to the segmental labeling of a membrane protein with 3 transmembrane domains and may prove useful in the preparation of an intact reconstituted GPCR for use in biophysical analysis and structure determination.
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Affiliation(s)
- Leah S Cohen
- Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, NY, 10314
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84
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Kumar A, Baumann M, Balbach J. Small Molecule Inhibited Parathyroid Hormone Mediated cAMP Response by N-Terminal Peptide Binding. Sci Rep 2016; 6:22533. [PMID: 26932583 PMCID: PMC4773758 DOI: 10.1038/srep22533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 02/11/2016] [Indexed: 11/30/2022] Open
Abstract
Ligand binding to certain classes of G protein coupled receptors (GPCRs) stimulates the rapid synthesis of cAMP through G protein. Human parathyroid hormone (PTH), a member of class B GPCRs, binds to its receptor via its N–terminal domain, thereby activating the pathway to this secondary messenger inside cells. Presently, GPCRs are the target of many pharmaceuticals however, these drugs target only a small fraction of structurally known GPCRs (about 10%). Coordination complexes are gaining interest due to their wide applications in the medicinal field. In the present studies we explored the potential of a coordination complex of Zn(II) and anthracenyl–terpyridine as a modulator of the parathyroid hormone response. Preferential interactions at the N–terminal domain of the peptide hormone were manifested by suppressed cAMP generation inside the cells. These observations contribute a regulatory component to the current GPCR–cAMP paradigm, where not the receptor itself, but the activating hormone is a target. To our knowledge, this is the first report about a coordination complex modulating GPCR activity at the level of deactivating its agonist. Developing such molecules might help in the control of pathogenic PTH function such as hyperparathyroidism, where control of excess hormonal activity is essentially required.
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Affiliation(s)
- Amit Kumar
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.,Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany
| | - Monika Baumann
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Germany.,Centre for Structure und Dynamics of Proteins (MZP), Martin-Luther-University Halle-Wittenberg, Germany
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85
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Jo M, Jung ST. Engineering therapeutic antibodies targeting G-protein-coupled receptors. Exp Mol Med 2016; 48:e207. [PMID: 26846450 PMCID: PMC4892866 DOI: 10.1038/emm.2015.105] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022] Open
Abstract
G-protein–coupled receptors (GPCRs) are one of the most attractive therapeutic target classes because of their critical roles in intracellular signaling and their clinical relevance to a variety of diseases, including cancer, infection and inflammation. However, high conformational variability, the small exposed area of extracellular epitopes and difficulty in the preparation of GPCR antigens have delayed both the isolation of therapeutic anti-GPCR antibodies as well as studies on the structure, function and biochemical mechanisms of GPCRs. To overcome the challenges in generating highly specific anti-GPCR antibodies with enhanced efficacy and safety, various forms of antigens have been successfully designed and employed for screening with newly emerged systems based on laboratory animal immunization and high-throughput-directed evolution.
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Affiliation(s)
- Migyeong Jo
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, Korea
| | - Sang Taek Jung
- Department of Bio and Nano Chemistry, Kookmin University, Seoul, Korea
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86
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Yin XJ, Geng CA, Huang XY, Chen H, Ma YB, Chen XL, Sun CL, Yang TH, Zhou J, Zhang XM, Chen JJ. Bioactivity-guided synthesis of tropine derivatives as new agonists for melatonin receptors. RSC Adv 2016. [DOI: 10.1039/c6ra06748d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Twenty-three tropine derivatives as new melatonin receptor (MT1 and MT2) agonists were synthesized and evaluated on HEK293 cells in vitro.
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87
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Laurila E, Ahola A, Hyttinen J, Aalto-Setälä K. Methods for in vitro functional analysis of iPSC derived cardiomyocytes - Special focus on analyzing the mechanical beating behavior. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1864-72. [PMID: 26707468 DOI: 10.1016/j.bbamcr.2015.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 12/09/2015] [Accepted: 12/16/2015] [Indexed: 02/06/2023]
Abstract
A rapidly increasing number of papers describing novel iPSC models for cardiac diseases are being published. To be able to understand the disease mechanisms in more detail, we should also take the full advantage of the various methods for analyzing these cell models. The traditionally and commonly used electrophysiological analysis methods have been recently accompanied by novel approaches for analyzing the mechanical beatingbehavior of the cardiomyocytes. In this review, we provide first a concise overview on the methodology for cardiomyocyte functional analysis and then concentrate on the video microscopy, which provides a promise for a new faster yet reliable method for cardiomyocyte functional analysis. We also show how analysis conditions may affect the results. Development of the methodology not only serves the basic research on the disease models, but could also provide the much needed efficient early phase screening method for cardiac safety toxicology. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.
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Affiliation(s)
- Eeva Laurila
- University of Tampere, BioMediTech and School of Medicine, Tampere, Finland.
| | - Antti Ahola
- Tampere University of Technology, Department of Electronics and Communications Engineering, BioMediTech, Tampere, Finland
| | - Jari Hyttinen
- Tampere University of Technology, Department of Electronics and Communications Engineering, BioMediTech, Tampere, Finland
| | - Katriina Aalto-Setälä
- University of Tampere, BioMediTech and School of Medicine, Tampere, Finland; Heart Hospital, Tampere University Hospital, Tampere, Finland
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88
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The N-terminus of the yeast G protein-coupled receptor Ste2p plays critical roles in surface expression, signaling, and negative regulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:715-24. [PMID: 26707753 DOI: 10.1016/j.bbamem.2015.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/18/2015] [Accepted: 12/15/2015] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) are found in all eukaryotic cells examined to date where they function as membrane-bound proteins that bind a multitude of extracellular ligands to initiate intracellular signal transduction systems controlling cellular physiology. GPCRs have seven heptahelical membrane spanning domains connected by extracellular and intracellular loops with an extracellular N-terminus and an intracellular C-terminus. The N-terminus has been the least studied domain of most GPCRs. The yeast Ste2p protein, the receptor for the thirteen amino acid peptide pheromone α-factor, has been used extensively as a model to study GPCR structure and function. In this study we constructed a number of deletions of the Ste2p N-terminus and uncovered an unexpected function as a negative regulatory domain. We examined the role of the N-terminus in expression, signaling function and ligand-binding properties and found that the residues 11-30 play a critical role in receptor expression on the cell surface. The studies also indicated that residues 2-10 of the N-terminus are involved in negative regulation of signaling as shown by the observation that deletion of these residues enhanced mating and gene induction. Furthermore, our results indicated that the residues 21-30 are essential for optimal signaling. Overall, we propose that the N-terminus of Ste2p plays multiple regulatory roles in controlling receptor function.
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89
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Gustavsson M, Zheng Y, Handel TM. Production of Chemokine/Chemokine Receptor Complexes for Structural Biophysical Studies. Methods Enzymol 2015; 570:233-60. [PMID: 26921949 DOI: 10.1016/bs.mie.2015.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
The development of methods for expression and purification of seven-transmembrane receptors has led to an increase in structural and biophysical data and greatly improved the understanding of receptor structure and function. For chemokine receptors, this has been highlighted by the determination of crystal structures of CXCR4 and CCR5 in complex with small-molecule antagonists, followed recently by two receptor/chemokine complexes; CXCR4 in complex with vMIP-II and US28 in complex with the CX3CL1. However, these studies cover only a few of the many chemokines and chemokine receptors and production of stable receptor/chemokine complexes remains a challenging task. Here, we present a method for producing purified complexes between chemokine receptors and chemokines by coexpression in Sf9 cells. Using the complex between atypical chemokine receptor 3 and its native chemokine CXCL12 as an example, we describe the virus production, protein expression, and purification process as well as reconstitution into different membrane mimics. This method provides an efficient way of producing pure receptor/chemokine complexes and has been used to successfully produce receptor/chemokine complexes for CXC as well as CC receptors.
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Affiliation(s)
- Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Tracy M Handel
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA.
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90
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Advances in Computational Techniques to Study GPCR–Ligand Recognition. Trends Pharmacol Sci 2015; 36:878-890. [DOI: 10.1016/j.tips.2015.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 12/16/2022]
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91
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Affiliation(s)
- Anne Tromelin
- CNRS; UMR6265 Centre des Sciences du Goût et de l'Alimentation; F-21000 Dijon France
- INRA; UMR1324 Centre des Sciences du Goût et de l'Alimentation; F-21000 Dijon France
- Université de Bourgogne; UMR Centre des Sciences du Goût et de l'Alimentation; F-21000 Dijon France
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92
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Abstract
There are many reported examples of small structural modifications to GPCR-targeted ligands leading to major changes in their functional activity, converting agonists into antagonists or vice versa. These shifts in functional activity are often accompanied by negligible changes in binding affinity. The current perspective focuses on outlining and analyzing various approaches that have been used to interconvert GPCR agonists, partial agonists, and antagonists in order to achieve the intended functional activity at a GPCR of therapeutic interest. An improved understanding of specific structural modifications that are likely to alter the functional activity of a GPCR ligand may be of use to researchers designing GPCR-targeted drugs and/or probe compounds, specifically in cases where a particular ligand exhibits good potency but not the preferred functional activity at the GPCR of choice.
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Affiliation(s)
- Peter I Dosa
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota , 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota , 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
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93
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Veya L, Piguet J, Vogel H. Single Molecule Imaging Deciphers the Relation between Mobility and Signaling of a Prototypical G Protein-coupled Receptor in Living Cells. J Biol Chem 2015; 290:27723-35. [PMID: 26363070 DOI: 10.1074/jbc.m115.666677] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Indexed: 01/10/2023] Open
Abstract
Lateral diffusion enables efficient interactions between membrane proteins, leading to signal transmission across the plasma membrane. An open question is how the spatiotemporal distribution of cell surface receptors influences the transmembrane signaling network. Here we addressed this issue by studying the mobility of a prototypical G protein-coupled receptor, the neurokinin-1 receptor, during its different phases of cellular signaling. Attaching a single quantum dot to individual neurokinin-1 receptors enabled us to follow with high spatial and temporal resolution over long time regimes the fate of individual receptors at the plasma membrane. Single receptor trajectories revealed a very heterogeneous mobility distribution pattern with diffusion constants ranging from 0.0005 to 0.1 μm(2)/s comprising receptors freely diffusing and others confined in 100-600-nm-sized membrane domains as well as immobile receptors. A two-dimensional representation of mobility and confinement resolved two major, broadly distributed receptor populations, one showing high mobility and low lateral restriction and the other showing low mobility and high restriction. We found that about 40% of the receptors in the basal state are already confined in membrane domains and are associated with clathrin. After stimulation with an agonist, an additional 30% of receptors became further confined. Using inhibitors of clathrin-mediated endocytosis, we found that the fraction of confined receptors at the basal state depends on the quantity of membrane-associated clathrin and is correlated to a significant decrease of the canonical pathway activity of the receptors. This shows that the high plasticity of receptor mobility is of central importance for receptor homeostasis and fine regulation of receptor activity.
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Affiliation(s)
- Luc Veya
- From the Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Joachim Piguet
- From the Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Horst Vogel
- From the Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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94
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Jastrzebska B, Chen Y, Orban T, Jin H, Hofmann L, Palczewski K. Disruption of Rhodopsin Dimerization with Synthetic Peptides Targeting an Interaction Interface. J Biol Chem 2015; 290:25728-44. [PMID: 26330551 DOI: 10.1074/jbc.m115.662684] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/06/2022] Open
Abstract
Although homo- and heterodimerizations of G protein-coupled receptors (GPCRs) are well documented, GPCR monomers are able to assemble in different ways, thus causing variations in the interactive interface between receptor monomers among different GPCRs. Moreover, the functional consequences of this phenomenon, which remain to be clarified, could be specific for different GPCRs. Synthetic peptides derived from transmembrane (TM) domains can interact with a full-length GPCR, blocking dimer formation and affecting its function. Here we used peptides corresponding to TM helices of bovine rhodopsin (Rho) to investigate the Rho dimer interface and functional consequences of its disruption. Incubation of Rho with TM1, TM2, TM4, and TM5 peptides in rod outer segment (ROS) membranes shifted the resulting detergent-solubilized protein migration through a gel filtration column toward smaller molecular masses with a reduced propensity for dimer formation in a cross-linking reaction. Binding of these TM peptides to Rho was characterized by both mass spectrometry and a label-free assay from which dissociation constants were calculated. A BRET (bioluminescence resonance energy transfer) assay revealed that the physical interaction between Rho molecules expressed in membranes of living cells was blocked by the same four TM peptides identified in our in vitro experiments. Although disruption of the Rho dimer/oligomer had no effect on the rates of G protein activation, binding of Gt to the activated receptor stabilized the dimer. However, TM peptide-induced disruption of dimer/oligomer decreased receptor stability, suggesting that Rho supramolecular organization could be essential for ROS stabilization and receptor trafficking.
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Affiliation(s)
- Beata Jastrzebska
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965
| | - Yuanyuan Chen
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965
| | - Tivadar Orban
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965
| | - Hui Jin
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965
| | - Lukas Hofmann
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965
| | - Krzysztof Palczewski
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965
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95
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Topiol S, Sabio M. The role of experimental and computational structural approaches in 7TM drug discovery. Expert Opin Drug Discov 2015. [DOI: 10.1517/17460441.2015.1072166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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96
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Hofmann L, Palczewski K. Advances in understanding the molecular basis of the first steps in color vision. Prog Retin Eye Res 2015; 49:46-66. [PMID: 26187035 DOI: 10.1016/j.preteyeres.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
Abstract
Serving as one of our primary environmental inputs, vision is the most sophisticated sensory system in humans. Here, we present recent findings derived from energetics, genetics and physiology that provide a more advanced understanding of color perception in mammals. Energetics of cis-trans isomerization of 11-cis-retinal accounts for color perception in the narrow region of the electromagnetic spectrum and how human eyes can absorb light in the near infrared (IR) range. Structural homology models of visual pigments reveal complex interactions of the protein moieties with the light sensitive chromophore 11-cis-retinal and that certain color blinding mutations impair secondary structural elements of these G protein-coupled receptors (GPCRs). Finally, we identify unsolved critical aspects of color tuning that require future investigation.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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97
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Ul-Haq Z, Saeed M, Halim SA, Khan W. 3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing. PLoS One 2015; 10:e0122223. [PMID: 25860348 PMCID: PMC4393300 DOI: 10.1371/journal.pone.0122223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 02/19/2015] [Indexed: 11/24/2022] Open
Abstract
Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1). This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein.
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Affiliation(s)
- Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Maria Saeed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Sobia Ahsan Halim
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Waqasuddin Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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98
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Preti D, Baraldi PG, Moorman AR, Borea PA, Varani K. History and perspectives of A2A adenosine receptor antagonists as potential therapeutic agents. Med Res Rev 2015; 35:790-848. [PMID: 25821194 DOI: 10.1002/med.21344] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Growing evidence emphasizes that the purine nucleoside adenosine plays an active role as a local regulator in different pathologies. Adenosine is a ubiquitous nucleoside involved in various physiological and pathological functions by stimulating A1 , A2A , A2B , and A3 adenosine receptors (ARs). At the present time, the role of A2A ARs is well known in physiological conditions and in a variety of pathologies, including inflammatory tissue damage and neurodegenerative disorders. In particular, the use of selective A2A antagonists has been reported to be potentially useful in the treatment of Parkinson's disease (PD). In this review, A2A AR signal transduction pathways, together with an analysis of the structure-activity relationships of A2A antagonists, and their corresponding pharmacological roles and therapeutic potential have been presented. The initial results from an emerging polypharmacological approach are also analyzed. This approach is based on the optimization of the affinity and/or functional activity of the examined compounds toward multiple targets, such as A1 /A2A ARs and monoamine oxidase-B (MAO-B), both closely implicated in the pathogenesis of PD.
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Affiliation(s)
- Delia Preti
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Pier Giovanni Baraldi
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121, Ferrara, Italy
| | | | - Pier Andrea Borea
- Section of Pharmacology, Department of Medical Science, University of Ferrara, 44121, Ferrara, Italy
| | - Katia Varani
- Section of Pharmacology, Department of Medical Science, University of Ferrara, 44121, Ferrara, Italy
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99
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Gurbel PA, Kuliopulos A, Tantry US. G-protein-coupled receptors signaling pathways in new antiplatelet drug development. Arterioscler Thromb Vasc Biol 2015; 35:500-12. [PMID: 25633316 DOI: 10.1161/atvbaha.114.303412] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Platelet G-protein-coupled receptors influence platelet function by mediating the response to various agonists, including ADP, thromboxane A2, and thrombin. Blockade of the ADP receptor, P2Y12, in combination with cyclooxygenase-1 inhibition by aspirin has been among the most widely used pharmacological strategies to reduce cardiovascular event occurrence in high-risk patients. The latter dual pathway blockade strategy is one of the greatest advances in the field of cardiovascular medicine. In addition to P2Y12, the platelet thrombin receptor, protease activated receptor-1, has also been recently targeted for inhibition. Blockade of protease activated receptor-1 has been associated with reduced thrombotic event occurrence when added to a strategy using P2Y12 and cyclooxygenase-1 inhibition. At this time, the relative contributions of these G-protein-coupled receptor signaling pathways to in vivo thrombosis remain incompletely defined. The observation of treatment failure in ≈10% of high-risk patients treated with aspirin and potent P2Y12 inhibitors provides the rationale for targeting novel pathways mediating platelet function. Targeting intracellular signaling downstream from G-protein-coupled receptor receptors with phosphotidylionisitol 3-kinase and Gq inhibitors are among the novel strategies under investigation to prevent arterial ischemic event occurrence. Greater understanding of the mechanisms of G-protein-coupled receptor-mediated signaling may allow the tailoring of antiplatelet therapy.
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Affiliation(s)
- Paul A Gurbel
- From the Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, MD (P.A.G., U.S.T.); and Center for Hemostasis and Thrombosis Research, Tufts Medical Center, Boston, MA (A.K.).
| | - Athan Kuliopulos
- From the Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, MD (P.A.G., U.S.T.); and Center for Hemostasis and Thrombosis Research, Tufts Medical Center, Boston, MA (A.K.)
| | - Udaya S Tantry
- From the Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, MD (P.A.G., U.S.T.); and Center for Hemostasis and Thrombosis Research, Tufts Medical Center, Boston, MA (A.K.)
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100
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Jones ML, Norman JE, Morgan NV, Mundell SJ, Lordkipanidzé M, Lowe GC, Daly ME, Simpson MA, Drake S, Watson SP, Mumford AD. Diversity and impact of rare variants in genes encoding the platelet G protein-coupled receptors. Thromb Haemost 2015; 113:826-37. [PMID: 25567036 PMCID: PMC4510585 DOI: 10.1160/th14-08-0679] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022]
Abstract
Platelet responses to activating agonists are influenced by common population variants within or near G protein-coupled receptor (GPCR) genes that affect receptor activity. However, the impact of rare GPCR gene variants is unknown. We describe the rare single nucleotide variants (SNVs) in the coding and splice regions of 18 GPCR genes in 7,595 exomes from the 1,000-genomes and Exome Sequencing Project databases and in 31 cases with inherited platelet function disorders (IPFDs). In the population databases, the GPCR gene target regions contained 740 SNVs (318 synonymous, 410 missense, 7 stop gain and 6 splice region) of which 70 % had global minor allele frequency (MAF) < 0.05 %. Functional annotation using six computational algorithms, experimental evidence and structural data identified 156/740 (21 %) SNVs as potentially damaging to GPCR function, most commonly in regions encoding the transmembrane and C-terminal intracellular receptor domains. In 31 index cases with IPFDs (Gi-pathway defect n=15; secretion defect n=11; thromboxane pathway defect n=3 and complex defect n=2) there were 256 SNVs in the target regions of 15 stimulatory platelet GPCRs (34 unique; 12 with MAF< 1 % and 22 with MAF≥ 1 %). These included rare variants predicting R122H, P258T and V207A substitutions in the P2Y12 receptor that were annotated as potentially damaging, but only partially explained the platelet function defects in each case. Our data highlight that potentially damaging variants in platelet GPCR genes have low individual frequencies, but are collectively abundant in the population. Potentially damaging variants are also present in pedigrees with IPFDs and may contribute to complex laboratory phenotypes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Andrew D Mumford
- Dr. A. D. Mumford, University of Bristol, Level 7 Bristol Royal Infirmary, Bristol, BS2 8HW, United Kingdom, Tel.: +44 117 3423152, Fax: +44 117 3424036, E-mail
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