1
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Wang J, Koirala K, Do HN, Miao Y. PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations. J Phys Chem B 2024; 128:7332-7340. [PMID: 39041172 DOI: 10.1021/acs.jpcb.4c02047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Predicting protein-peptide interactions is crucial for understanding peptide binding processes and designing peptide drugs. However, traditional computational modeling approaches face challenges in accurately predicting peptide-protein binding structures due to the slow dynamics and high flexibility of the peptides. Here, we introduce a new workflow termed "PepBinding" for predicting peptide binding structures, which combines peptide docking, all-atom enhanced sampling simulations using the Peptide Gaussian accelerated Molecular Dynamics (Pep-GaMD) method, and structural clustering. PepBinding has been demonstrated on seven distinct model peptides. In peptide docking using HPEPDOCK, the peptide backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures ranged from 3.8 to 16.0 Å, corresponding to the medium to inaccurate quality models according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. The Pep-GaMD simulations performed for only 200 ns significantly improved the docking models, resulting in five medium and two acceptable quality models. Therefore, PepBinding is an efficient workflow for predicting peptide binding structures and is publicly available at https://github.com/MiaoLab20/PepBinding.
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Affiliation(s)
- Jinan Wang
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kushal Koirala
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hung N Do
- Computational Biology Program, Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yinglong Miao
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
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2
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Batebi H, Pérez-Hernández G, Rahman SN, Lan B, Kamprad A, Shi M, Speck D, Tiemann JKS, Guixà-González R, Reinhardt F, Stadler PF, Papasergi-Scott MM, Skiniotis G, Scheerer P, Kobilka BK, Mathiesen JM, Liu X, Hildebrand PW. Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor. Nat Struct Mol Biol 2024:10.1038/s41594-024-01334-2. [PMID: 38867113 DOI: 10.1038/s41594-024-01334-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by promoting guanine nucleotide exchange. Here, we investigate the coupling of G proteins with GPCRs and describe the events that ultimately lead to the ejection of GDP from its binding pocket in the Gα subunit, the rate-limiting step during G-protein activation. Using molecular dynamics simulations, we investigate the temporal progression of structural rearrangements of GDP-bound Gs protein (Gs·GDP; hereafter GsGDP) upon coupling to the β2-adrenergic receptor (β2AR) in atomic detail. The binding of GsGDP to the β2AR is followed by long-range allosteric effects that significantly reduce the energy needed for GDP release: the opening of α1-αF helices, the displacement of the αG helix and the opening of the α-helical domain. Signal propagation to the Gs occurs through an extended receptor interface, including a lysine-rich motif at the intracellular end of a kinked transmembrane helix 6, which was confirmed by site-directed mutagenesis and functional assays. From this β2AR-GsGDP intermediate, Gs undergoes an in-plane rotation along the receptor axis to approach the β2AR-Gsempty state. The simulations shed light on how the structural elements at the receptor-G-protein interface may interact to transmit the signal over 30 Å to the nucleotide-binding site. Our analysis extends the current limited view of nucleotide-free snapshots to include additional states and structural features responsible for signaling and G-protein coupling specificity.
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Affiliation(s)
- Hossein Batebi
- Universität Leipzig, Medizinische Fakultät, Institut für Medizinische Physik und Biophysik, Leipzig, Germany
- Freie Universität Berlin, Fachbereich Physik, Berlin, Germany
| | - Guillermo Pérez-Hernández
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Sabrina N Rahman
- University of Copenhagen, Department of Drug Design and Pharmacology, Copenhagen, Denmark
| | - Baoliang Lan
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Antje Kamprad
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Berlin, Germany
| | - Mingyu Shi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - David Speck
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Berlin, Germany
| | - Johanna K S Tiemann
- Universität Leipzig, Medizinische Fakultät, Institut für Medizinische Physik und Biophysik, Leipzig, Germany
- Novozymes A/S, Lyngby, Denmark
| | - Ramon Guixà-González
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Franziska Reinhardt
- Universität Leipzig, Department of Computer Science, Bioinformatics, Leipzig, Germany
| | - Peter F Stadler
- Universität Leipzig, Department of Computer Science, Bioinformatics, Leipzig, Germany
| | - Makaía M Papasergi-Scott
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick Scheerer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Berlin, Germany
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesper M Mathiesen
- University of Copenhagen, Department of Drug Design and Pharmacology, Copenhagen, Denmark
| | - Xiangyu Liu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Peter W Hildebrand
- Universität Leipzig, Medizinische Fakultät, Institut für Medizinische Physik und Biophysik, Leipzig, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
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3
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Determinants of Neutral Antagonism and Inverse Agonism in the β 2-Adrenergic Receptor. J Chem Inf Model 2024; 64:2045-2057. [PMID: 38447156 DOI: 10.1021/acs.jcim.3c01763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Free-energy profiles for the activation/deactivation of the β2-adrenergic receptor (ADRB2) with neutral antagonist and inverse agonist ligands have been determined with well-tempered multiple-walker (MW) metadynamics simulations. The inverse agonists carazolol and ICI118551 clearly favor single inactive conformational minima in both the binary and ternary ligand-receptor-G-protein complexes, in accord with the inverse-agonist activity of the ligands. The behavior of neutral antagonists is more complex, as they seem also to affect the recruitment of the G-protein. The results are analyzed in terms of the conformational states of the well-known microswitches that have been proposed as indicators of receptor activity.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04107 Leipzig, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, United Kingdom
- Swiss Bioinformatics Institute, CH1206 Geneva, Switzerland
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
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4
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Ham D, Inoue A, Xu J, Du Y, Chung KY. Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq. Commun Biol 2024; 7:362. [PMID: 38521872 PMCID: PMC10960872 DOI: 10.1038/s42003-024-06056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.
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Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Shenzhen Futian Biomedical Innovation R&D Center, the Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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5
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Daly C, Guseinov AA, Hahn H, Wright A, Tikhonova IG, Thomsen ARB, Plouffe B. β-Arrestin-dependent and -independent endosomal G protein activation by the vasopressin type 2 receptor. eLife 2023; 12:RP87754. [PMID: 37855711 PMCID: PMC10586804 DOI: 10.7554/elife.87754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
The vasopressin type 2 receptor (V2R) is an essential G protein-coupled receptor (GPCR) in renal regulation of water homeostasis. Upon stimulation, the V2R activates Gαs and Gαq/11, which is followed by robust recruitment of β-arrestins and receptor internalization into endosomes. Unlike canonical GPCR signaling, the β-arrestin association with the V2R does not terminate Gαs activation, and thus, Gαs-mediated signaling is sustained while the receptor is internalized. Here, we demonstrate that this V2R ability to co-interact with G protein/β-arrestin and promote endosomal G protein signaling is not restricted to Gαs, but also involves Gαq/11. Furthermore, our data imply that β-arrestins potentiate Gαs/Gαq/11 activation at endosomes rather than terminating their signaling. Surprisingly, we found that the V2R internalizes and promote endosomal G protein activation independent of β-arrestins to a minor degree. These new observations challenge the current model of endosomal GPCR signaling and suggest that this event can occur in both β-arrestin-dependent and -independent manners.
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Affiliation(s)
- Carole Daly
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University BelfastBelfastUnited Kingdom
| | | | - Hyunggu Hahn
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
- NYU Pain Research Center, New York University College of DentistryNew YorkUnited States
| | - Adam Wright
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University BelfastBelfastUnited Kingdom
| | | | - Alex Rojas Bie Thomsen
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
- NYU Pain Research Center, New York University College of DentistryNew YorkUnited States
| | - Bianca Plouffe
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University BelfastBelfastUnited Kingdom
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6
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Daly C, Guseinov AA, Hahn H, Wright A, Tikhonova IG, Thomsen ARB, Plouffe B. β-arrestin-dependent and -independent endosomal G protein activation by the vasopressin type 2 receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535208. [PMID: 37034816 PMCID: PMC10081317 DOI: 10.1101/2023.04.01.535208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The vasopressin type 2 receptor (V2R) is an essential GPCR in renal regulation of water homeostasis. Upon stimulation, the V2R activates Gαs and Gαq/11, which is followed by robust recruitment of β-arrestins and receptor internalization into endosomes. Unlike canonical GPCR signaling, the β-arrestin association with the V2R does not terminate Gαs activation, and thus, Gαs-mediated signaling is sustained while the receptor is internalized. Here, we demonstrate that this V2R ability to co-interact with G protein/β-arrestin and promote endosomal G protein signaling is not restricted to Gαs, but also involves Gαq/11. Furthermore, our data implies that β-arrestins potentiate Gαs/Gαq/11 activation at endosomes rather than terminating their signaling. Surprisingly, we found that the V2R internalizes and promote endosomal G protein activation independent of β-arrestins to a minor degree. These new observations challenge the current model of endosomal GPCR signaling and suggest that this event can occur in both β-arrestin-dependent and -independent manners.
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Affiliation(s)
- Carole Daly
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | | | - Hyunggu Hahn
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, USA
- NYU Pain Research Center, New York University College of Dentistry, New York, USA
| | - Adam Wright
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | | | - Alex Rojas Bie Thomsen
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, USA
- NYU Pain Research Center, New York University College of Dentistry, New York, USA
| | - Bianca Plouffe
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
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7
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Seufert F, Chung YK, Hildebrand PW, Langenhan T. 7TM domain structures of adhesion GPCRs: what's new and what's missing? Trends Biochem Sci 2023; 48:726-739. [PMID: 37349240 DOI: 10.1016/j.tibs.2023.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Adhesion-type G protein-coupled receptors (aGPCRs) have long resisted approaches to resolve the structural details of their heptahelical transmembrane (7TM) domains. Single-particle cryogenic electron microscopy (cryo-EM) has recently produced aGPCR 7TM domain structures for ADGRD1, ADGRG1, ADGRG2, ADGRG3, ADGRG4, ADGRG5, ADGRF1, and ADGRL3. We review the unique properties, including the position and conformation of their activating tethered agonist (TA) and signaling motifs within the 7TM bundle, that the novel structures have helped to identify. We also discuss questions that the kaleidoscope of novel aGPCR 7TM domain structures have left unanswered. These concern the relative positions, orientations, and interactions of the 7TM and GPCR autoproteolysis-inducing (GAIN) domains with one another. Clarifying their interplay remains an important goal of future structural studies on aGPCRs.
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Affiliation(s)
- Florian Seufert
- Institute of Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Yin Kwan Chung
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany; Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Tobias Langenhan
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany.
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8
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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9
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Jang W, Lu S, Xu X, Wu G, Lambert NA. The role of G protein conformation in receptor-G protein selectivity. Nat Chem Biol 2023; 19:687-694. [PMID: 36646958 PMCID: PMC10238660 DOI: 10.1038/s41589-022-01231-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/22/2022] [Indexed: 01/17/2023]
Abstract
G protein-coupled receptors (GPCRs) selectively activate at least one of the four families of heterotrimeric G proteins, but the mechanism of coupling selectivity remains unclear. Structural studies emphasize structural complementarity of GPCRs and nucleotide-free G proteins, but selectivity is likely to be determined by transient intermediate-state complexes that exist before nucleotide release. Here we study coupling to nucleotide-decoupled G protein variants that can adopt conformations similar to receptor-bound G proteins without releasing nucleotide, and are therefore able to bypass intermediate-state complexes. We find that selectivity is degraded when nucleotide release is not required for GPCR-G protein complex formation, to the extent that most GPCRs interact with most nucleotide-decoupled G proteins. These findings demonstrate the absence of absolute structural incompatibility between noncognate receptor-G protein pairs, and are consistent with the hypothesis that transient intermediate states are partly responsible for coupling selectivity.
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Affiliation(s)
- Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA.
| | - Sumin Lu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Xin Xu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Guangyu Wu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA.
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10
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Gusach A, García-Nafría J, Tate CG. New insights into GPCR coupling and dimerisation from cryo-EM structures. Curr Opin Struct Biol 2023; 80:102574. [PMID: 36963163 PMCID: PMC10423944 DOI: 10.1016/j.sbi.2023.102574] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/01/2023] [Accepted: 02/19/2023] [Indexed: 03/26/2023]
Abstract
Over the past three years (2020-2022) more structures of GPCRs have been determined than in the previous twenty years (2000-2019), primarily of GPCR complexes that are large enough for structure determination by single-particle cryo-EM. This review will present some structural highlights that have advanced our molecular understanding of promiscuous G protein coupling, how a G protein receptor kinase and β-arrestins couple to GPCRs, and GPCR dimerisation. We will also discuss advances in the use of gene fusions, nanobodies, and Fab fragments to facilitate the structure determination of GPCRs in the inactive state that, on their own, are too small for structure determination by single-particle cryo-EM.
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Affiliation(s)
- Anastasiia Gusach
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 2QH, UK. https://twitter.com/GusachAnastasia
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain. https://twitter.com/JGarciaNafria
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 2QH, UK.
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11
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Papasergi-Scott MM, Kwarcinski FE, Yu M, Panova O, Ovrutsky AM, Skiniotis G, Tall GG. Structures of Ric-8B in complex with Gα protein folding clients reveal isoform specificity mechanisms. Structure 2023; 31:553-564.e7. [PMID: 36931277 PMCID: PMC10164081 DOI: 10.1016/j.str.2023.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
Mammalian Ric-8 proteins act as chaperones to regulate the cellular abundance of heterotrimeric G protein α subunits. The Ric-8A isoform chaperones Gαi/o, Gα12/13, and Gαq/11 subunits, while Ric-8B acts on Gαs/olf subunits. Here, we determined cryoelectron microscopy (cryo-EM) structures of Ric-8B in complex with Gαs and Gαolf, revealing isoform differences in the relative positioning and contacts between the C-terminal α5 helix of Gα within the concave pocket formed by Ric-8 α-helical repeat elements. Despite the overall architectural similarity with our earlier structures of Ric-8A complexed to Gαq and Gαi1, Ric-8B distinctly accommodates an extended loop found only in Gαs/olf proteins. The structures, along with results from Ric-8 protein thermal stability assays and cell-based Gαolf folding assays, support a requirement for the Gα C-terminal region for binding specificity, and highlight that multiple structural elements impart specificity for Ric-8/G protein binding.
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Affiliation(s)
- Makaía M Papasergi-Scott
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Frank E Kwarcinski
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Maiya Yu
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ann M Ovrutsky
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Gregory G Tall
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
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12
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Han J, Zhang J, Nazarova AL, Bernhard SM, Krumm BE, Zhao L, Lam JH, Rangari VA, Majumdar S, Nichols DE, Katritch V, Yuan P, Fay JF, Che T. Ligand and G-protein selectivity in the κ-opioid receptor. Nature 2023; 617:417-425. [PMID: 37138078 PMCID: PMC10172140 DOI: 10.1038/s41586-023-06030-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
The κ-opioid receptor (KOR) represents a highly desirable therapeutic target for treating not only pain but also addiction and affective disorders1. However, the development of KOR analgesics has been hindered by the associated hallucinogenic side effects2. The initiation of KOR signalling requires the Gi/o-family proteins including the conventional (Gi1, Gi2, Gi3, GoA and GoB) and nonconventional (Gz and Gg) subtypes. How hallucinogens exert their actions through KOR and how KOR determines G-protein subtype selectivity are not well understood. Here we determined the active-state structures of KOR in a complex with multiple G-protein heterotrimers-Gi1, GoA, Gz and Gg-using cryo-electron microscopy. The KOR-G-protein complexes are bound to hallucinogenic salvinorins or highly selective KOR agonists. Comparisons of these structures reveal molecular determinants critical for KOR-G-protein interactions as well as key elements governing Gi/o-family subtype selectivity and KOR ligand selectivity. Furthermore, the four G-protein subtypes display an intrinsically different binding affinity and allosteric activity on agonist binding at KOR. These results provide insights into the actions of opioids and G-protein-coupling specificity at KOR and establish a foundation to examine the therapeutic potential of pathway-selective agonists of KOR.
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Affiliation(s)
- Jianming Han
- Department of Anesthesiology, Washington University in St Louis, St Louis, MO, USA
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St Louis and Washington University School of Medicine, St Louis, MO, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St Louis, MO, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Antonina L Nazarova
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Sarah M Bernhard
- Department of Anesthesiology, Washington University in St Louis, St Louis, MO, USA
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St Louis and Washington University School of Medicine, St Louis, MO, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Lei Zhao
- Department of Anesthesiology, Washington University in St Louis, St Louis, MO, USA
| | - Jordy Homing Lam
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Vipin A Rangari
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St Louis and Washington University School of Medicine, St Louis, MO, USA
| | - Susruta Majumdar
- Department of Anesthesiology, Washington University in St Louis, St Louis, MO, USA
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St Louis and Washington University School of Medicine, St Louis, MO, USA
- Washington University Pain Center, Washington University in St Louis, St Louis, MO, USA
| | - David E Nichols
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St Louis, MO, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan F Fay
- Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, USA.
| | - Tao Che
- Department of Anesthesiology, Washington University in St Louis, St Louis, MO, USA.
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St Louis and Washington University School of Medicine, St Louis, MO, USA.
- Washington University Pain Center, Washington University in St Louis, St Louis, MO, USA.
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13
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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14
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Kossoń P, Dyniewicz J, Lipiński PFJ, Matalińska J, Misicka A, Bojarski AJ, Mordalski S. Gα i-derived peptide binds the µ-opioid receptor. Pharmacol Rep 2023; 75:465-473. [PMID: 36840824 DOI: 10.1007/s43440-023-00457-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) transduce external stimuli into the cell by G proteins via an allosteric mechanism. Agonist binding to the receptor stimulates GDP/GTP exchange within the heterotrimeric G protein complex, whereas recent structures of GPCR-G protein complexes revealed that the H5, S1 and S2 domains of Gα are involved in binding the active receptor, earlier studies showed that a short peptide analog derived from the C-terminus (H5) of the G protein transducin (Gt) is sufficient to stabilize rhodopsin in an active form. METHODS We have used Molecular Dynamics simulations along with biological evaluation by means of radio-ligand binding assay to study the interactions between Gαi-derived peptide (G-peptide) and the µ-opioid receptor (µOR). RESULTS Here, we show that a Gαi-derived peptide of 12 amino acids binds the µ-opioid receptor and acts as an allosteric modulator. The Gαi-derived peptide increases µOR affinity for its agonist morphine in a dose-dependent way. CONCLUSIONS These results indicate that the GPCR-Gα peptide interaction observed so far for only rhodopsin can be extrapolated to µOR. In addition, we show that the C-terminal peptide of the Gαi subunit is sufficient to stabilize the active conformation of the receptor. Our approach opens the possibility to investigate the GPCR-G protein interface with peptide modification.
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Affiliation(s)
- Piotr Kossoń
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Jolanta Dyniewicz
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 313-343, Kraków, Poland
| | - Stefan Mordalski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 313-343, Kraków, Poland.
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15
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Leemann S, Kleinlogel S. Functional optimization of light-activatable Opto-GPCRs: Illuminating the importance of the proximal C-terminus in G-protein specificity. Front Cell Dev Biol 2023; 11:1053022. [PMID: 36936685 PMCID: PMC10014536 DOI: 10.3389/fcell.2023.1053022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction: G-protein coupled receptors (GPCRs) are the largest family of human receptors that transmit signals from natural ligands and pharmaceutical drugs into essentially every physiological process. One main characteristic of G-protein coupled receptors is their ability to specifically couple with different families of G-proteins, thereby triggering specific downstream signaling pathways. While an abundance of structural information is available on G-protein coupled receptorn interactions with G-proteins, little is known about the G-protein coupled receptor domains functionally mediating G-protein specificity, in particular the proximal C-terminus, the structure which cannot be predicted with high confidentiality due to its flexibility. Methods: In this study, we exploited OptoGPCR chimeras between lightgated G-protein coupled receptors (opsins) and ligand-gated G-protein coupled receptors to systematically investigate the involvement of the C-terminus steering G-protein specificity. We employed rhodopsin-beta2-adrenoceptor and melanopsin-mGluR6 chimeras in second messenger assays and developed structural models of the chimeras. Results: We discovered a dominant role of the proximal C-terminus, dictating G-protein selectivity in the melanopsin-mGluR6 chimera, whereas it is the intracellular loop 3, which steers G-protein tropism in the rhodopsin-beta2-adrenoceptor. From the functional results and structural predictions, melanopsin and mGluR6 use a different mechanism to bovine rhodopsin and b2AR to couple to a selective G-protein. Discussion: Collectively, this work adds knowledge to the G-protein coupled receptor domains mediating G-protein selectivity, ultimately paving the way to optogenetically elicited specific G-protein signaling on demand.
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16
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Selçuk B, Erol I, Durdağı S, Adebali O. Evolutionary association of receptor-wide amino acids with G protein-coupling selectivity in aminergic GPCRs. Life Sci Alliance 2022; 5:5/10/e202201439. [PMID: 35613896 PMCID: PMC9133432 DOI: 10.26508/lsa.202201439] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Evolutionary analyses of aminergic G protein–coupled receptors reveal receptor-wide potential determinants of G protein–coupling selectivity. G protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (Gs, Gi, Gq, and G12/13), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Herein, we performed extensive phylogenetic analysis and identified specifically conserved residues for the aminergic receptors having similar coupling profiles. By integrating our methodology of differential evolutionary conservation of G protein–specific amino acids with structural analyses, we identified specific activation networks for Gs, Gi1, Go, and Gq. To validate that these networks could determine coupling selectivity we further analyzed Gs-specific activation network and its association with Gs selectivity. Through molecular dynamics simulations, we showed that previously uncharacterized Glycine at position 7x41 plays an important role in receptor activation and it may determine Gs coupling selectivity by facilitating a larger TM6 movement. Finally, we gathered our results into a comprehensive model of G protein selectivity called “sequential switches of activation” describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms, and G protein contact.
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Affiliation(s)
- Berkay Selçuk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.,Department of Chemistry, Gebze Technical University, Gebze, Turkey
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Ogün Adebali
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey .,TÜBiTAK Research Institute for Fundamental Sciences, Gebze, Turkey
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17
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Zhao L, He X, Jiang H, Cheng X. Computational characterization of transducer recognition of β2 adrenergic receptor. Biochem Biophys Res Commun 2022; 592:67-73. [DOI: 10.1016/j.bbrc.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/02/2022]
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18
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Ahn D, Chung KY. The Conformational Dynamics of Heterotrimeric G Proteins During GPCR-Mediated Activation. Subcell Biochem 2022; 99:271-284. [PMID: 36151379 DOI: 10.1007/978-3-031-00793-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Heterotrimeric G proteins (G proteins) are essential cellular signaling proteins that mediate extracellular signals to achieve various cellular functions. G-protein-coupled receptors (GPCRs) are the major guanine nucleotide exchange factors (GEFs) that induce G proteins to release guanosine diphosphate and rapidly bind to guanosine triphosphate, resulting in G protein activation. G proteins undergo dynamic conformational changes during the activation/inactivation process, and the precise structural mechanism of GPCR-mediated G protein activation is of great interest. Over the last decade, a number of GPCR-G protein complex structures have been identified, yet an understanding of the mechanisms underlying allosteric conformational changes during receptor-mediated G protein activation and GPCR-G protein coupling selectivity is only now emerging. This review discusses recent studies on the dynamic conformational changes of G proteins and provides insight into the structural mechanism of GPCR-mediated G protein activation.
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Affiliation(s)
- Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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19
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Elgeti M, Hubbell WL. DEER Analysis of GPCR Conformational Heterogeneity. Biomolecules 2021; 11:778. [PMID: 34067265 PMCID: PMC8224605 DOI: 10.3390/biom11060778] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent a large class of transmembrane helical proteins which are involved in numerous physiological signaling pathways and therefore represent crucial pharmacological targets. GPCR function and the action of therapeutic molecules are defined by only a few parameters, including receptor basal activity, ligand affinity, intrinsic efficacy and signal bias. These parameters are encoded in characteristic receptor conformations existing in equilibrium and their populations, which are thus of paramount interest for the understanding of receptor (mal-)functions and rational design of improved therapeutics. To this end, the combination of site-directed spin labeling and EPR spectroscopy, in particular double electron-electron resonance (DEER), is exceedingly valuable as it has access to sub-Angstrom spatial resolution and provides a detailed picture of the number and populations of conformations in equilibrium. This review gives an overview of existing DEER studies on GPCRs with a focus on the delineation of structure/function frameworks, highlighting recent developments in data analysis and visualization. We introduce "conformational efficacy" as a parameter to describe ligand-specific shifts in the conformational equilibrium, taking into account the loose coupling between receptor segments observed for different GPCRs using DEER.
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Affiliation(s)
- Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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20
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Ahn D, Ham D, Chung KY. The conformational transition during G protein-coupled receptor (GPCR) and G protein interaction. Curr Opin Struct Biol 2021; 69:117-123. [PMID: 33975155 DOI: 10.1016/j.sbi.2021.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/23/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
The precise structural mechanism of G protein-coupled receptor (GPCR)-G protein coupling has been of significant research interest because it provides fundamental knowledge on cellular signaling and valuable information for GPCR-targeted drug development. Over the last decade, several GPCR-G protein complex structures have been identified. However, these structures are mere snapshots of guanosine diphosphate (GDP)-released stable GPCR-G protein complexes, which have limited the understanding of the allosteric conformational transition during receptor binding to GDP release and the GPCR-G protein coupling selectivity. Recently, deeper insights into the mechanism underlying stepwise conformational changes during GPCR-G protein coupling were obtained using hydrogen/deuterium exchange mass spectrometry, hydroxyl radical footprinting-mass spectrometry, X-ray crystallography, cryoelectron microscopy, and molecular dynamics simulation techniques. This review summarizes these recent developments.
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Affiliation(s)
- Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon, 16419, Republic of Korea.
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21
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Randáková A, Jakubík J. Functionally selective and biased agonists of muscarinic receptors. Pharmacol Res 2021; 169:105641. [PMID: 33951507 DOI: 10.1016/j.phrs.2021.105641] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022]
Abstract
Disruption of cholinergic signalling via muscarinic receptors is associated with various pathologies, like Alzheimer's disease or schizophrenia. Selective muscarinic agonists possess therapeutic potential in the treatment of diabetes, pain or Sjögren's syndrome. The orthosteric binding site of all subtypes of the muscarinic receptor is structurally identical, making the development of affinity-based selective agonists virtually impossible. Some agonists, however, are functionally selective; they activate only a subset of receptors or signalling pathways. Others may stabilise specific conformations of the receptor leading to non-uniform modulation of individual signalling pathways (biased agonists). Functionally selective and biased agonists represent a promising approach for selective activation of individual subtypes of muscarinic receptors. In this work we review chemical structures, receptor binding and agonist-specific conformations of currently known functionally selective and biased muscarinic agonists in the context of their intricate intracellular signalling. Further, we take a perspective on the possible use of biased agonists for tissue and organ-specific activation of muscarinic receptors.
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Affiliation(s)
- Alena Randáková
- Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic.
| | - Jan Jakubík
- Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic.
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22
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Receptor-Arrestin Interactions: The GPCR Perspective. Biomolecules 2021; 11:biom11020218. [PMID: 33557162 PMCID: PMC7913897 DOI: 10.3390/biom11020218] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Arrestins are a small family of four proteins in most vertebrates that bind hundreds of different G protein-coupled receptors (GPCRs). Arrestin binding to a GPCR has at least three functions: precluding further receptor coupling to G proteins, facilitating receptor internalization, and initiating distinct arrestin-mediated signaling. The molecular mechanism of arrestin–GPCR interactions has been extensively studied and discussed from the “arrestin perspective”, focusing on the roles of arrestin elements in receptor binding. Here, we discuss this phenomenon from the “receptor perspective”, focusing on the receptor elements involved in arrestin binding and emphasizing existing gaps in our knowledge that need to be filled. It is vitally important to understand the role of receptor elements in arrestin activation and how the interaction of each of these elements with arrestin contributes to the latter’s transition to the high-affinity binding state. A more precise knowledge of the molecular mechanisms of arrestin activation is needed to enable the construction of arrestin mutants with desired functional characteristics.
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23
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Liu Q, Yang D, Zhuang Y, Croll TI, Cai X, Dai A, He X, Duan J, Yin W, Ye C, Zhou F, Wu B, Zhao Q, Xu HE, Wang MW, Jiang Y. Ligand recognition and G-protein coupling selectivity of cholecystokinin A receptor. Nat Chem Biol 2021; 17:1238-1244. [PMID: 34556862 PMCID: PMC8604728 DOI: 10.1038/s41589-021-00841-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/24/2021] [Indexed: 02/08/2023]
Abstract
Cholecystokinin A receptor (CCKAR) belongs to family A G-protein-coupled receptors and regulates nutrient homeostasis upon stimulation by cholecystokinin (CCK). It is an attractive drug target for gastrointestinal and metabolic diseases. One distinguishing feature of CCKAR is its ability to interact with a sulfated ligand and to couple with divergent G-protein subtypes, including Gs, Gi and Gq. However, the basis for G-protein coupling promiscuity and ligand recognition by CCKAR remains unknown. Here, we present three cryo-electron microscopy structures of sulfated CCK-8-activated CCKAR in complex with Gs, Gi and Gq heterotrimers, respectively. CCKAR presents a similar conformation in the three structures, whereas conformational differences in the 'wavy hook' of the Gα subunits and ICL3 of the receptor serve as determinants in G-protein coupling selectivity. Our findings provide a framework for understanding G-protein coupling promiscuity by CCKAR and uncover the mechanism of receptor recognition by sulfated CCK-8.
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Affiliation(s)
- Qiufeng Liu
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dehua Yang
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Youwen Zhuang
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Tristan I. Croll
- grid.5335.00000000121885934Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Xiaoqing Cai
- grid.9227.e0000000119573309The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Antao Dai
- grid.9227.e0000000119573309The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinheng He
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Jia Duan
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Wanchao Yin
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chenyu Ye
- grid.8547.e0000 0001 0125 2443School of Pharmacy, Fudan University, Shanghai, China
| | - Fulai Zhou
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Beili Wu
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.9227.e0000000119573309CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Qiang Zhao
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - H. Eric Xu
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ming-Wei Wang
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.8547.e0000 0001 0125 2443School of Pharmacy, Fudan University, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.8547.e0000 0001 0125 2443School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yi Jiang
- grid.9227.e0000000119573309The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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24
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Xiao X, Qin M, Zhang F, Su Y, Zhou B, Zhou Z. Understanding the Mechanism of Activation/Deactivation of GLP-1R via Accelerated Molecular Dynamics Simulation. Aust J Chem 2021. [DOI: 10.1071/ch20127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Glucagon-like peptide-1 receptor (GLP-1R), as a member of the class B G protein-coupled receptors (GPCRs), plays a crucial role in regulating blood glucose level signal recognition through its activation. The conformation changes during the activation pathway are of particular importance for its function. To investigate the activation mechanism of GLP-1R, the crystal structures of active and inactive forms are chosen to perform a total of 2 μs of accelerated molecular dynamics (aMD) simulations and 400ns of conventional molecular dynamics (cMD) simulations. With the aid of structural analysis and potential of mean force (PMF) calculations, we reveal the role of different helices in the activation and deactivation process and obtain the intermediate states during activation and deactivation that are difficult to capture in experiments. Protein structure network (PSN) was utilised to clarify the allosteric communication pathways of activation and deactivation and reveal the mechanisms of its activation and deactivation. The results could advance our understanding of the activation mechanism of GLP-1R and the related drug design.
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25
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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26
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Vogel A, Bosse M, Gauglitz M, Wistuba S, Schmidt P, Kaiser A, Gurevich VV, Beck-Sickinger AG, Hildebrand PW, Huster D. The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation. Molecules 2020; 25:E5489. [PMID: 33255213 PMCID: PMC7727705 DOI: 10.3390/molecules25235489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 01/08/2023] Open
Abstract
We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.
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Affiliation(s)
- Alexander Vogel
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Mathias Bosse
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Marcel Gauglitz
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Sarah Wistuba
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Vsevolod V. Gurevich
- Vanderbilt University Medical Center, 2200 Pierce Avenue, Nashville, TN 37232, USA;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany; (A.K.); (A.G.B.-S.)
| | - Peter W. Hildebrand
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; (A.V.); (M.B.); (M.G.); (S.W.); (P.S.)
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27
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Mondal D, Kolev V, Warshel A. Exploring the activation pathway and G i-coupling specificity of the μ-opioid receptor. Proc Natl Acad Sci U S A 2020; 117:26218-26225. [PMID: 33020275 PMCID: PMC7585030 DOI: 10.1073/pnas.2013364117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Understanding the activation mechanism of the μ-opioid receptor (μ-OR) and its selective coupling to the inhibitory G protein (Gi) is vital for pharmaceutical research aimed at finding treatments for the opioid overdose crisis. Many attempts have been made to understand the mechanism of the μ-OR activation, following the elucidation of new crystal structures such as the antagonist- and agonist-bound μ-OR. However, the focus has not been placed on the underlying energetics and specificity of the activation process. An energy-based picture would not only help to explain this coupling but also help to explore why other possible options are not common. For example, one would like to understand why μ-OR is more selective to Gi than a stimulatory G protein (Gs). Our study used homology modeling and a coarse-grained model to generate all of the possible "end states" of the thermodynamic cycle of the activation of μ-OR. The end points were further used to generate reasonable intermediate structures of the receptor and the Gi to calculate two-dimensional free energy landscapes. The results of the landscape calculations helped to propose a plausible sequence of conformational changes in the μ-OR and Gi system and for exploring the path that leads to its activation. Furthermore, in silico alanine scanning calculations of the last 21 residues of the C terminals of Gi and Gs were performed to shed light on the selective binding of Gi to μ-OR. Overall, the present work appears to demonstrate the potential of multiscale modeling in exploring the action of G protein-coupled receptors.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Vesselin Kolev
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
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28
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Conrad M, Söldner CA, Miao Y, Sticht H. Agonist Binding and G Protein Coupling in Histamine H 2 Receptor: A Molecular Dynamics Study. Int J Mol Sci 2020; 21:ijms21186693. [PMID: 32932742 PMCID: PMC7554837 DOI: 10.3390/ijms21186693] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
The histamine H2 receptor (H2R) plays an important role in the regulation of gastric acid secretion. Therefore, it is a main drug target for the treatment of gastroesophageal reflux or peptic ulcer disease. However, there is as of yet no 3D-structural information available hampering a mechanistic understanding of H2R. Therefore, we created a model of the histamine-H2R-Gs complex based on the structure of the ternary complex of the β2-adrenoceptor and investigated the conformational stability of this active GPCR conformation. Since the physiologically relevant motions with respect to ligand binding and conformational changes of GPCRs can only partly be assessed on the timescale of conventional MD (cMD) simulations, we also applied metadynamics and Gaussian accelerated molecular dynamics (GaMD) simulations. A multiple walker metadynamics simulation in combination with cMD was applied for the determination of the histamine binding mode. The preferential binding pose detected is in good agreement with previous data from site directed mutagenesis and provides a basis for rational ligand design. Inspection of the H2R-Gs interface reveals a network of polar interactions that may contribute to H2R coupling selectivity. The cMD and GaMD simulations demonstrate that the active conformation is retained on a μs-timescale in the ternary histamine-H2R-Gs complex and in a truncated complex that contains only Gs helix α5 instead of the entire G protein. In contrast, histamine alone is unable to stabilize the active conformation, which is in line with previous studies of other GPCRs.
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Affiliation(s)
- Marcus Conrad
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Christian A. Söldner
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Yinglong Miao
- Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA;
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany; (M.C.); (C.A.S.)
- Correspondence:
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29
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Kim HR, Xu J, Maeda S, Duc NM, Ahn D, Du Y, Chung KY. Structural mechanism underlying primary and secondary coupling between GPCRs and the Gi/o family. Nat Commun 2020; 11:3160. [PMID: 32572026 PMCID: PMC7308389 DOI: 10.1038/s41467-020-16975-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Heterotrimeric G proteins are categorized into four main families based on their function and sequence, Gs, Gi/o, Gq/11, and G12/13. One receptor can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. However, the precise mechanism underlying different coupling efficiencies is unknown. Here, we study the structural mechanism underlying primary and secondary Gi/o coupling, using the muscarinic acetylcholine receptor type 2 (M2R) as the primary Gi/o-coupling receptor and the β2-adrenergic receptor (β2AR, which primarily couples to Gs) as the secondary Gi/o-coupling receptor. Hydrogen/deuterium exchange mass spectrometry and mutagenesis studies reveal that the engagement of the distal C-terminus of Gαi/o with the receptor differentiates primary and secondary Gi/o couplings. This study suggests that the conserved hydrophobic residue within the intracellular loop 2 of the receptor (residue 34.51) is not critical for primary Gi/o-coupling; however, it might be important for secondary Gi/o-coupling. G protein-coupled receptors (GPCRs) can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. Here authors use hydrogen/deuterium exchange mass spectrometry and mutagenesis to study the structural mechanism underlying primary and secondary Gi/o coupling.
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Affiliation(s)
- Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Jun Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.,Division of Precision Medicine, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
| | - Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, 2001 Longxiang Ave, Shenzhen, Guangdong, 518172, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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30
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Qiao A, Han S, Li X, Li Z, Zhao P, Dai A, Chang R, Tai L, Tan Q, Chu X, Ma L, Thorsen TS, Reedtz-Runge S, Yang D, Wang MW, Sexton PM, Wootten D, Sun F, Zhao Q, Wu B. Structural basis of G s and G i recognition by the human glucagon receptor. Science 2020; 367:1346-1352. [PMID: 32193322 DOI: 10.1126/science.aaz5346] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/11/2020] [Indexed: 12/13/2022]
Abstract
Class B G protein-coupled receptors, an important class of therapeutic targets, signal mainly through the Gs class of heterotrimeric G proteins, although they do display some promiscuity in G protein binding. Using cryo-electron microscopy, we determined the structures of the human glucagon receptor (GCGR) bound to glucagon and distinct classes of heterotrimeric G proteins, Gs or Gi1 These two structures adopt a similar open binding cavity to accommodate Gs and Gi1 The Gs binding selectivity of GCGR is explained by a larger interaction interface, but there are specific interactions that affect Gi more than Gs binding. Conformational differences in the receptor intracellular loops were found to be key selectivity determinants. These distinctions in transducer engagement were supported by mutagenesis and functional studies.
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Affiliation(s)
- Anna Qiao
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo Han
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xinmei Li
- University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhixin Li
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Peishen Zhao
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Antao Dai
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Rulve Chang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Linhua Tai
- University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiuxiang Tan
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaojing Chu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Limin Ma
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | | | - Dehua Yang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ming-Wei Wang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmacy, Fudan University, Shanghai 201203, China.,National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Patrick M Sexton
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Denise Wootten
- School of Pharmacy, Fudan University, Shanghai 201203, China. .,Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Fei Sun
- University of Chinese Academy of Sciences, Beijing 100049, China. .,National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. .,University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. .,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
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31
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Che T, English J, Krumm BE, Kim K, Pardon E, Olsen RHJ, Wang S, Zhang S, Diberto JF, Sciaky N, Carroll FI, Steyaert J, Wacker D, Roth BL. Nanobody-enabled monitoring of kappa opioid receptor states. Nat Commun 2020; 11:1145. [PMID: 32123179 PMCID: PMC7052193 DOI: 10.1038/s41467-020-14889-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 12/22/2022] Open
Abstract
Recent studies show that GPCRs rapidly interconvert between multiple states although our ability to interrogate, monitor and visualize them is limited by a relative lack of suitable tools. We previously reported two nanobodies (Nb39 and Nb6) that stabilize distinct ligand- and efficacy-delimited conformations of the kappa opioid receptor. Here, we demonstrate via X-ray crystallography a nanobody-targeted allosteric binding site by which Nb6 stabilizes a ligand-dependent inactive state. As Nb39 stabilizes an active-like state, we show how these two state-dependent nanobodies can provide real-time reporting of ligand stabilized states in cells in situ. Significantly, we demonstrate that chimeric GPCRs can be created with engineered nanobody binding sites to report ligand-stabilized states. Our results provide both insights regarding potential mechanisms for allosterically modulating KOR with nanobodies and a tool for reporting the real-time, in situ dynamic range of GPCR activity.
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MESH Headings
- Allosteric Site
- Binding Sites
- Biosensing Techniques
- Crystallography, X-Ray
- Cyclic AMP/metabolism
- Dynorphins/chemistry
- Dynorphins/pharmacology
- HEK293 Cells
- Humans
- Luminescent Measurements/methods
- Piperazines/chemistry
- Piperazines/pharmacology
- Piperidines/chemistry
- Piperidines/pharmacology
- Protein Conformation
- Pyrrolidines/chemistry
- Pyrrolidines/pharmacology
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, kappa/agonists
- Receptors, Opioid, kappa/chemistry
- Receptors, Opioid, kappa/genetics
- Receptors, Opioid, kappa/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/metabolism
- Tetrahydroisoquinolines/chemistry
- Tetrahydroisoquinolines/pharmacology
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Affiliation(s)
- Tao Che
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Justin English
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kuglae Kim
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, 1050, Belgium
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Sheng Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shicheng Zhang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey F Diberto
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - F Ivy Carroll
- Research Triangle Institute, Research Triangle Park, Durham, NC, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, 1050, Belgium
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Pharmacological Sciences and Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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Randáková A, Nelic D, Ungerová D, Nwokoye P, Su Q, Doležal V, El-Fakahany EE, Boulos J, Jakubík J. Novel M 2 -selective, G i -biased agonists of muscarinic acetylcholine receptors. Br J Pharmacol 2020; 177:2073-2089. [PMID: 31910288 DOI: 10.1111/bph.14970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND PURPOSE More than 30% of currently marketed medications act via GPCRs. Thus, GPCRs represent one of the most important pharmacotherapeutic targets. In contrast to traditional agonists activating multiple signalling pathways, agonists activating a single signalling pathway represent a new generation of drugs with increased specificity and fewer adverse effects. EXPERIMENTAL APPROACH We have synthesized novel agonists of muscarinic ACh receptors and tested their binding and function (on levels of cAMP and inositol phosphates) in CHO cells expressing individual subtypes of muscarinic receptors, primary cultures of rat aortic smooth muscle cells and suspensions of digested native tissues from rats. Binding of the novel compounds to M2 receptors was modelled in silico. KEY RESULTS Two of the tested new compounds (1-(thiophen-2-ylmethyl)-3,6-dihydro-2H-pyridinium and 1-methyl-1-(thiophen-2-ylmethyl)-3,6-dihydro-2H-pyridinium) only inhibited cAMP synthesis in CHO cells, primary cultures, and native tissues, with selectivity for M2 muscarinic receptors and displaying bias towards the Gi signalling pathway at all subtypes of muscarinic receptors. Molecular modelling revealed interactions with the orthosteric binding site in a way specific for a given agonist followed by agonist-specific changes in the conformation of the receptor. CONCLUSIONS AND IMPLICATIONS The identified compounds may serve as lead structures in the search for novel non-steroidal and non-opioid analgesics acting via M2 and M4 muscarinic receptors with reduced side effects associated with activation of the phospholipase C signalling pathway.
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Affiliation(s)
- Alena Randáková
- Department of Neurochemistry, Institute of Physiology CAS, Prague, Czech Republic
| | - Dominik Nelic
- Department of Neurochemistry, Institute of Physiology CAS, Prague, Czech Republic
| | - Dana Ungerová
- Department of Neurochemistry, Institute of Physiology CAS, Prague, Czech Republic
| | - Peter Nwokoye
- Department of Physical Sciences, Barry University, Miami Shores, Florida
| | - Qiwen Su
- Department of Physical Sciences, Barry University, Miami Shores, Florida
| | - Vladimír Doležal
- Department of Neurochemistry, Institute of Physiology CAS, Prague, Czech Republic
| | - Esam E El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, Minnesota
| | - John Boulos
- Department of Physical Sciences, Barry University, Miami Shores, Florida
| | - Jan Jakubík
- Department of Neurochemistry, Institute of Physiology CAS, Prague, Czech Republic
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Maeda S, Qu Q, Robertson MJ, Skiniotis G, Kobilka BK. Structures of the M1 and M2 muscarinic acetylcholine receptor/G-protein complexes. Science 2019; 364:552-557. [PMID: 31073061 DOI: 10.1126/science.aaw5188] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
Muscarinic acetylcholine receptors are G protein-coupled receptors that respond to acetylcholine and play important signaling roles in the nervous system. There are five muscarinic receptor subtypes (M1R to M5R), which, despite sharing a high degree of sequence identity in the transmembrane region, couple to different heterotrimeric GTP-binding proteins (G proteins) to transmit signals. M1R, M3R, and M5R couple to the Gq/ 11 family, whereas M2R and M4R couple to the Gi/ o family. Here, we present and compare the cryo-electron microscopy structures of M1R in complex with G11 and M2R in complex with GoA The M1R-G11 complex exhibits distinct features, including an extended transmembrane helix 5 and carboxyl-terminal receptor tail that interacts with G protein. Detailed analysis of these structures provides a framework for understanding the molecular determinants of G-protein coupling selectivity.
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Affiliation(s)
- Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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Hildebrand PW, Rose AS, Tiemann JK. Bringing Molecular Dynamics Simulation Data into View. Trends Biochem Sci 2019; 44:902-913. [DOI: 10.1016/j.tibs.2019.06.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 12/14/2022]
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Wang J, Alekseenko A, Kozakov D, Miao Y. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. Front Mol Biosci 2019; 6:112. [PMID: 31737642 PMCID: PMC6835073 DOI: 10.3389/fmolb.2019.00112] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/09/2019] [Indexed: 01/31/2023] Open
Abstract
Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology, and oncology. However, it is challenging to predict peptide-protein binding with conventional computational modeling approaches, due to slow dynamics and high peptide flexibility. Here, we present a prototype of the approach which combines global peptide docking using ClusPro PeptiDock and all-atom enhanced simulations using Gaussian accelerated molecular dynamics (GaMD). For three distinct model peptides, the lowest backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures obtained from PeptiDock were 3.3–4.8 Å, being medium quality predictions according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6–2.7 Å, yielding two high quality (sub-angstrom) and one medium quality models. Furthermore, the GaMD simulations identified important low-energy conformational states and revealed the mechanism of peptide binding to the target proteins. Therefore, PeptiDock+GaMD is a promising approach for exploring peptide-protein interactions.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Andrey Alekseenko
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Dima Kozakov
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
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36
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Rutigliano G, Bräunig J, Del Grande C, Carnicelli V, Masci I, Merlino S, Kleinau G, Tessieri L, Pardossi S, Paisdzior S, Dell'Osso L, Biebermann H, Zucchi R. Non-Functional Trace Amine-Associated Receptor 1 Variants in Patients With Mental Disorders. Front Pharmacol 2019; 10:1027. [PMID: 31572197 PMCID: PMC6753877 DOI: 10.3389/fphar.2019.01027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The G protein–coupled receptor (GPCR) trace amine-associated receptor 1 (TAAR1) is expressed across brain areas involved in emotions, reward and cognition, and modulates monoaminergic and glutamatergic neurotransmissions. TAAR1 is stimulated with nanomolar affinity by 3-iodothyronamine (T1AM), an endogenous messenger considered a novel branch of thyroid hormone signaling. The human gene for TAAR1 maps to locus 6q23, within a region associated with major mental disorders. Materials and Methods: We screened a cohort of patients with major mental disorders (n = 104) and a group of healthy controls (n = 130) for TAAR1 variants. HEK293 cells were transiently transfected with: i) wild-type TAAR1 and ii) mutated TAAR1, either in homozygous or heterozygous state. Cell surface expression and Gs/adenylyl cyclase activation upon administration of β-phenylethylamine (PEA), T1AM, and RO5166017, were assessed. Results: We detected 13 missense variants in TAAR1 coding region, with a significant enrichment in patients as compared to healthy controls (11 vs. 1, 1 variant in both groups, p < 0.01). In silico analysis identified four dysfunctional variants, all in patients. Three of these—R23C, Y131C, and C263R—were functionally characterized. In cells co-transfected with wild-type and mutated TAAR1, we observed a significant reduction of cell surface expression. In heterozygosity, the three TAAR1 variants substantially dampened Gs signaling in response to PEA, and, more robustly, to T1AM. Co-stimulation with PEA and RO5166017 did not yield any improvement in Gs signaling. R23C, Y131C, and C263R are rare in the general population and map in functionally important highly conserved positions across TAAR1 orthologous and paralogous genes. Conclusions: Our findings suggest that disruptions of TAAR1 activity may be relevant to the pathophysiology of mental disorders, thereby providing a promising target for novel psychopharmacological interventions.
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Affiliation(s)
- Grazia Rutigliano
- Scuola Superiore Sant'Anna, Pisa, Italy.,National Research Council (CNR), Institute of Clinical Physiology (IFC), Pisa, Italy
| | - Julia Bräunig
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute für Experimentelle Pädiatrische Endokrinology, Berlin, Germany
| | - Claudia Del Grande
- Department of Clinical and Experimental Medicine, Section of Psychiatry, University of Pisa, Pisa, Italy
| | | | - Isabella Masci
- Department of Clinical and Experimental Medicine, Section of Psychiatry, University of Pisa, Pisa, Italy
| | - Sergio Merlino
- Department of Clinical and Experimental Medicine, Section of Psychiatry, University of Pisa, Pisa, Italy
| | - Gunnar Kleinau
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | | | | | - Sarah Paisdzior
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute für Experimentelle Pädiatrische Endokrinology, Berlin, Germany
| | - Liliana Dell'Osso
- Department of Clinical and Experimental Medicine, Section of Psychiatry, University of Pisa, Pisa, Italy
| | - Heike Biebermann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute für Experimentelle Pädiatrische Endokrinology, Berlin, Germany
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37
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Wang J, Miao Y. Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors. J Phys Chem B 2019; 123:6462-6473. [PMID: 31283874 DOI: 10.1021/acs.jpcb.9b04867] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coupling between G-protein-coupled receptors (GPCRs) and the G proteins is a key step in cellular signaling. Despite extensive experimental and computational studies, the mechanism of specific GPCR-G protein coupling remains poorly understood. This has greatly hindered effective drug design of GPCRs that are primary targets of ∼1/3 of currently marketed drugs. Here, we have employed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method to decipher the mechanism of the GPCR-G protein interactions. Adenosine receptors (ARs) were used as model systems based on very recently determined cryo-EM structures of the A1AR and A2AAR coupled with the Gi and Gs proteins, respectively. Changing the Gi protein to the Gs led to increased fluctuations in the A1AR and agonist adenosine (ADO), while agonist 5'-N-ethylcarboxamidoadenosine (NECA) binding in the A2AAR could be still stabilized upon changing the Gs protein to the Gi. Free energy calculations identified one stable low-energy conformation for each of the A1AR-Gi and A2AAR-Gs complexes as in the cryo-EM structures, similarly for the A2AAR-Gi complex. In contrast, the ADO agonist and Gs protein sampled multiple conformations in the A1AR-Gs system. GaMD simulations thus indicated that the A1AR preferred to couple with the Gi protein to the Gs, while the A2AAR could couple with both the Gs and Gi proteins, being highly consistent with experimental findings of the ARs. More importantly, detailed analysis of the atomic simulations showed that the specific AR-G protein coupling resulted from remarkably complementary residue interactions at the protein interface, involving mainly the receptor transmembrane 6 helix and the Gα α5 helix and α4-β6 loop. In summary, the GaMD simulations have provided unprecedented insights into the dynamic mechanism of specific GPCR-G protein interactions at an atomistic level.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66047 , United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66047 , United States
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38
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Sandhu M, Touma AM, Dysthe M, Sadler F, Sivaramakrishnan S, Vaidehi N. Conformational plasticity of the intracellular cavity of GPCR-G-protein complexes leads to G-protein promiscuity and selectivity. Proc Natl Acad Sci U S A 2019; 116:11956-11965. [PMID: 31138704 PMCID: PMC6575595 DOI: 10.1073/pnas.1820944116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While the dynamics of the intracellular surface in agonist-stimulated GPCRs is well studied, the impact of GPCR dynamics on G-protein selectivity remains unclear. Here, we combine molecular dynamics simulations with live-cell FRET and secondary messenger measurements, for 21 GPCR-G-protein combinations, to advance a dynamic model of the GPCR-G-protein interface. Our data show C terminus peptides of Gαs, Gαi, and Gαq proteins assume a small ensemble of unique orientations when coupled to their cognate GPCRs, similar to the variations observed in 3D structures of GPCR-G-protein complexes. The noncognate G proteins interface with latent intracellular GPCR cavities but dissociate due to weak and unstable interactions. Three predicted mutations in β2-adrenergic receptor stabilize binding of noncognate Gαq protein in its latent cavity, allowing promiscuous signaling through both Gαs and Gαq in a dose-dependent manner. This demonstrates that latent GPCR cavities can be evolved, by design or nature, to tune G-protein selectivity, giving insights to pluridimensional GPCR signaling.
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Affiliation(s)
- Manbir Sandhu
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Anja M Touma
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| | - Matthew Dysthe
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| | - Fredrik Sadler
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| | - Nagarajan Vaidehi
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010;
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
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39
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Abstract
G protein-coupled receptors (GPCRs) regulate a wide variety of important cellular processes and are targeted by a large fraction of approved drugs. GPCRs signal by activating heterotrimeric G proteins and must couple to a select subset of G proteins to produce appropriate intracellular responses. It is not known how GPCRs select G proteins, but it is generally accepted that the Gα subunit C terminus is the primary G protein determinant of coupling selectivity. We systematically studied coupling of GPCRs to four families of G proteins and chimeras with C terminal regions that were exchanged between families. We uncovered rules for coupling selectivity and found that different GPCRs can recognize different features of the same G protein for selective coupling. G protein-coupled receptors (GPCRs) activate four families of heterotrimeric G proteins, and individual receptors must select a subset of G proteins to produce appropriate cellular responses. Although the precise mechanisms of coupling selectivity are uncertain, the Gα subunit C terminus is widely believed to be the primary determinant recognized by cognate receptors. Here, we directly assess coupling between 14 representative GPCRs and 16 Gα subunits, including one wild-type Gα subunit from each of the four families and 12 chimeras with exchanged C termini. We use a sensitive bioluminescence resonance energy transfer (BRET) assay that provides control over both ligand and nucleotide binding, and allows direct comparison across G protein families. We find that the Gs- and Gq-coupled receptors we studied are relatively promiscuous and always couple to some extent to Gi1 heterotrimers. In contrast, Gi-coupled receptors are more selective. Our results with Gα subunit chimeras show that the Gα C terminus is important for coupling selectivity, but no more so than the Gα subunit core. The relative importance of the Gα subunit core and C terminus is highly variable and, for some receptors, the Gα core is more important for selective coupling than the C terminus. Our results suggest general rules for GPCR-G protein coupling and demonstrate that the critical G protein determinants of selectivity vary widely, even for different receptors that couple to the same G protein.
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40
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Seyedabadi M, Ghahremani MH, Albert PR. Biased signaling of G protein coupled receptors (GPCRs): Molecular determinants of GPCR/transducer selectivity and therapeutic potential. Pharmacol Ther 2019; 200:148-178. [PMID: 31075355 DOI: 10.1016/j.pharmthera.2019.05.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023]
Abstract
G protein coupled receptors (GPCRs) convey signals across membranes via interaction with G proteins. Originally, an individual GPCR was thought to signal through one G protein family, comprising cognate G proteins that mediate canonical receptor signaling. However, several deviations from canonical signaling pathways for GPCRs have been described. It is now clear that GPCRs can engage with multiple G proteins and the line between cognate and non-cognate signaling is increasingly blurred. Furthermore, GPCRs couple to non-G protein transducers, including β-arrestins or other scaffold proteins, to initiate additional signaling cascades. Receptor/transducer selectivity is dictated by agonist-induced receptor conformations as well as by collateral factors. In particular, ligands stabilize distinct receptor conformations to preferentially activate certain pathways, designated 'biased signaling'. In this regard, receptor sequence alignment and mutagenesis have helped to identify key receptor domains for receptor/transducer specificity. Furthermore, molecular structures of GPCRs bound to different ligands or transducers have provided detailed insights into mechanisms of coupling selectivity. However, receptor dimerization, compartmentalization, and trafficking, receptor-transducer-effector stoichiometry, and ligand residence and exposure times can each affect GPCR coupling. Extrinsic factors including cell type or assay conditions can also influence receptor signaling. Understanding these factors may lead to the development of improved biased ligands with the potential to enhance therapeutic benefit, while minimizing adverse effects. In this review, evidence for ligand-specific GPCR signaling toward different transducers or pathways is elaborated. Furthermore, molecular determinants of biased signaling toward these pathways and relevant examples of the potential clinical benefits and pitfalls of biased ligands are discussed.
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Affiliation(s)
- Mohammad Seyedabadi
- Department of Pharmacology, School of Medicine, Bushehr University of Medical Sciences, Iran; Education Development Center, Bushehr University of Medical Sciences, Iran
| | | | - Paul R Albert
- Ottawa Hospital Research Institute, Neuroscience, University of Ottawa, Canada.
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41
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Yuan S, Dahoun T, Brugarolas M, Pick H, Filipek S, Vogel H. Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds. Commun Biol 2019; 2:141. [PMID: 31044166 PMCID: PMC6478719 DOI: 10.1038/s42003-019-0384-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
The mammalian olfactory system uses hundreds of specialized G-protein-coupled olfactory receptors (ORs) to discriminate a nearly unlimited number of odorants. Cognate agonists of most ORs have not yet been identified and potential non-olfactory processes mediated by ORs are unknown. Here, we used molecular modeling, fingerprint interaction analysis and molecular dynamics simulations to show that the binding pocket of the prototypical olfactory receptor Olfr73 is smaller, but more flexible, than binding pockets of typical non-olfactory G-protein-coupled receptors. We extended our modeling to virtual screening of a library of 1.6 million compounds against Olfr73. Our screen predicted 25 Olfr73 agonists beyond traditional odorants, of which 17 compounds, some with therapeutic potential, were validated in cell-based assays. Our modeling suggests a molecular basis for reduced interaction contacts between an odorant and its OR and thus the typical low potency of OR-activating compounds. These results provide a proof-of-principle for identifying novel therapeutic OR agonists.
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Affiliation(s)
- Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory of Biomodelling, Faculty of Chemistry & Biological and Chemical Research Centre, Uni-versity of Warsaw, 02-093 Warsaw, Poland
| | - Thamani Dahoun
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marc Brugarolas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Horst Pick
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodelling, Faculty of Chemistry & Biological and Chemical Research Centre, Uni-versity of Warsaw, 02-093 Warsaw, Poland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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42
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Song W, Yen HY, Robinson CV, Sansom MSP. State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes. Structure 2019; 27:392-403.e3. [PMID: 30581046 PMCID: PMC7031699 DOI: 10.1016/j.str.2018.10.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/02/2018] [Accepted: 10/25/2018] [Indexed: 01/01/2023]
Abstract
Membranes are known to have modulatory effects on G protein-coupled receptors (GPCRs) via specific lipid interactions. However, the mechanisms of such modulations in physiological conditions and how they influence GPCR functions remain unclear. Here we report coarse-grained molecular dynamics simulations on the Adenosine A2a receptor in different conformational states embedded in an in vivo-mimetic membrane model. Nine lipid interaction sites were revealed. The strength of lipid interactions with these sites showed a degree of dependence on the conformational states of the receptor, suggesting that these lipids may regulate the conformational dynamics of the receptor. In particular, we revealed a dual role of PIP2 on A2aR activation that involves both stabilization of the characteristic outward tilt of TM6 and enhancement of A2aR-mini-Gs association. Our results demonstrated that the bound lipids allosterically regulate the functional properties of GPCRs. These protein-lipid interactions provide a springboard for design of allosteric modulators of GPCRs.
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Affiliation(s)
- Wanling Song
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QY, UK
| | - Carol V Robinson
- Chemical Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QY, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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43
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Wang J, Miao Y. Recent advances in computational studies of GPCR-G protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 116:397-419. [PMID: 31036298 PMCID: PMC6986689 DOI: 10.1016/bs.apcsb.2018.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions are key in cellular signaling. G protein-coupled receptors (GPCRs), the largest superfamily of human membrane proteins, are able to transduce extracellular signals (e.g., hormones and neurotransmitters) to intracellular proteins, in particular the G proteins. Since GPCRs serve as primary targets of ~1/3 of currently marketed drugs, it is important to understand mechanisms of GPCR signaling in order to design selective and potent drug molecules. This chapter focuses on recent advances in computational studies of the GPCR-G protein interactions using bioinformatics, protein-protein docking and molecular dynamics simulation approaches.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States.
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44
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Heyder N, Kleinau G, Szczepek M, Kwiatkowski D, Speck D, Soletto L, Cerdá-Reverter JM, Krude H, Kühnen P, Biebermann H, Scheerer P. Signal Transduction and Pathogenic Modifications at the Melanocortin-4 Receptor: A Structural Perspective. Front Endocrinol (Lausanne) 2019; 10:515. [PMID: 31417496 PMCID: PMC6685040 DOI: 10.3389/fendo.2019.00515] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) can be endogenously activated by binding of melanocyte-stimulating hormones (MSH), which mediates anorexigenic effects. In contrast, the agouti-related peptide (AgRP) acts as an endogenous inverse agonist and suppresses ligand-independent basal signaling activity (orexigenic effects). Binding of ligands to MC4R leads to the activation of different G-protein subtypes or arrestin and concomitant signaling pathways. This receptor is a key protein in the hypothalamic regulation of food intake and energy expenditure and naturally-occurring inactivating MC4R variants are the most frequent cause of monogenic obesity. In general, obesity is a growing problem on a global scale and is of social, medical, and economic relevance. A significant goal is to develop optimized pharmacological tools targeting MC4R without adverse effects. To date, this has not been achieved because of inter alia non-selective ligands across the five functionally different MCR subtypes (MC1-5R). This motivates further investigation of (i) the three-dimensional MC4R structure, (ii) binding mechanisms of various ligands, and (iii) the molecular transfer process of signal transduction, with the aim of understanding how structural features are linked with functional-physiological aspects. Unfortunately, experimentally elucidated structural information is not yet available for the MC receptors, a group of class A G-protein coupled receptors (GPCRs). We, therefore, generated MC4R homology models and complexes with interacting partners to describe approximate structural properties associated with signaling mechanisms. In addition, molecular insights from pathogenic mutations were incorporated to discriminate more precisely their individual malfunction of the signal transfer mechanism.
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Affiliation(s)
- Nicolas Heyder
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- *Correspondence: Gunnar Kleinau
| | - Michal Szczepek
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dennis Kwiatkowski
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Speck
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucia Soletto
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - José Miguel Cerdá-Reverter
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Kühnen
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Patrick Scheerer
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45
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Randáková A, Dolejší E, Rudajev V, Zimčík P, Doležal V, El-Fakahany EE, Jakubík J. Role of membrane cholesterol in differential sensitivity of muscarinic receptor subtypes to persistently bound xanomeline. Neuropharmacology 2018; 133:129-144. [PMID: 29407765 DOI: 10.1016/j.neuropharm.2018.01.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 01/03/2018] [Accepted: 01/21/2018] [Indexed: 01/24/2023]
Abstract
Xanomeline (3-(Hexyloxy)-4-(1-methyl-1,2,5,6-tetrahydropyridin-3-yl)-1,2,5-thiadiazole) is a muscarinic agonist that is considered to be functionally selective for the M1/M4 receptor subtypes. Part of xanomeline binding is resistant to washing. Wash-resistant xanomeline activates muscarinic receptors persistently, except for the M5 subtype. Mutation of leucine 6.46 to isoleucine at M1 or M4 receptors abolished persistent activation by wash-resistant xanomeline. Reciprocal mutation of isoleucine 6.46 to leucine at the M5 receptor made it sensitive to activation by wash-resistant xanomeline. Lowering of membrane cholesterol made M1 and M4 mutants and M5 wild type receptors sensitive to activation by wash-resistant xanomeline. Molecular docking revealed a cholesterol binding site in the groove between transmembrane helices 6 and 7. Molecular dynamics showed that interaction of cholesterol with this binding site attenuates receptor activation. We hypothesize that differences in cholesterol binding to this site between muscarinic receptor subtypes may constitute the basis for xanomeline apparent functional selectivity and may have notable therapeutic implications. Differences in receptor-membrane interactions, rather than in agonist-receptor interactions, represent a novel possibility to achieve pharmacological selectivity. Our findings may be applicable to other G protein coupled receptors.
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Affiliation(s)
- Alena Randáková
- Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Eva Dolejší
- Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Vladimír Rudajev
- Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Pavel Zimčík
- Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Vladimír Doležal
- Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Esam E El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN 55455, USA
| | - Jan Jakubík
- Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic.
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46
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Glukhova A, Draper-Joyce CJ, Sunahara RK, Christopoulos A, Wootten D, Sexton PM. Rules of Engagement: GPCRs and G Proteins. ACS Pharmacol Transl Sci 2018; 1:73-83. [PMID: 32219204 PMCID: PMC7089011 DOI: 10.1021/acsptsci.8b00026] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 11/29/2022]
Abstract
G protein-coupled receptors (GPCRs) are a key drug target class. They account for over one-third of current pharmaceuticals, and both drugs that inhibit and promote receptor function are important therapeutically; in some cases, the same GPCR can be targeted with agonists and inhibitors, depending upon disease context. There have been major breakthroughs in understanding GPCR structure and drug binding through advances in X-ray crystallography, and membrane protein stabilization. Nonetheless, these structures have predominately been of inactive receptors bound to inhibitors. Efforts to capture structures of fully active GPCRs, in particular those in complex with the canonical, physiological transducer G protein, have been limited via this approach. Very recently, advances in cryo-electron microscopy have provided access to agonist:GPCR:G protein complex structures. These promise to revolutionize our understanding of GPCR:G protein engagement and provide insight into mechanisms of efficacy and coupling selectivity and how these might be controlled by biased agonists. Here we review what we have currently learned from the new GPCR:Gs and GPCR:Gi/o complex structures.
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Affiliation(s)
- Alisa Glukhova
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Christopher J. Draper-Joyce
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Roger K. Sunahara
- Department
of Pharmacology, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Arthur Christopoulos
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Denise Wootten
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School
of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Patrick M. Sexton
- Drug
Discovery Biology and Department of Pharmacology, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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47
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Maeda S, Koehl A, Matile H, Hu H, Hilger D, Schertler GFX, Manglik A, Skiniotis G, Dawson RJP, Kobilka BK. Development of an antibody fragment that stabilizes GPCR/G-protein complexes. Nat Commun 2018; 9:3712. [PMID: 30213947 PMCID: PMC6137068 DOI: 10.1038/s41467-018-06002-w] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/25/2018] [Indexed: 11/10/2022] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM) has recently enabled high-resolution structure determination of numerous biological macromolecular complexes. Despite this progress, the application of high-resolution cryo-EM to G protein coupled receptors (GPCRs) in complex with heterotrimeric G proteins remains challenging, owning to both the relative small size and the limited stability of these assemblies. Here we describe the development of antibody fragments that bind and stabilize GPCR-G protein complexes for the application of high-resolution cryo-EM. One antibody in particular, mAb16, stabilizes GPCR/G-protein complexes by recognizing an interface between Gα and Gβγ subunits in the heterotrimer, and confers resistance to GTPγS-triggered dissociation. The unique recognition mode of this antibody makes it possible to transfer its binding and stabilizing effect to other G-protein subtypes through minimal protein engineering. This antibody fragment is thus a broadly applicable tool for structural studies of GPCR/G-protein complexes. The determination of high resolution structures of G protein coupled receptors (GPCRs) in complex with heterotrimeric G proteins is challenging. Here authors develop an antibody fragment, mAB16, which stabilizes GPCR/G-protein complexes and facilitates the application of high resolution cryo-EM.
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Affiliation(s)
- Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Antoine Koehl
- Department of Structural Biology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Hugues Matile
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Hongli Hu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94143, USA.,Department of Anesthesia and Perioperative Care, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94143, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Roger J P Dawson
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA.
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48
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Tsai CJ, Pamula F, Nehmé R, Mühle J, Weinert T, Flock T, Nogly P, Edwards PC, Carpenter B, Gruhl T, Ma P, Deupi X, Standfuss J, Tate CG, Schertler GFX. Crystal structure of rhodopsin in complex with a mini-G o sheds light on the principles of G protein selectivity. SCIENCE ADVANCES 2018; 4:eaat7052. [PMID: 30255144 PMCID: PMC6154990 DOI: 10.1126/sciadv.aat7052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/10/2018] [Indexed: 05/20/2023]
Abstract
Selective coupling of G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-Go protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a "structural switch," allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR-G protein interface suggests that the precise position of the carboxyl-terminal "hook-like" element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.
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Affiliation(s)
- Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Corresponding author. (C.-J.T.); (G.F.X.S.)
| | - Filip Pamula
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Rony Nehmé
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Tilman Flock
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
- Fitzwilliam College, University of Cambridge, Cambridge, UK
| | - Przemyslaw Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Patricia C. Edwards
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Byron Carpenter
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Thomas Gruhl
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
| | - Pikyee Ma
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Condensed Matter Theory Group, PSI, 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher G. Tate
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland
- Corresponding author. (C.-J.T.); (G.F.X.S.)
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49
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Chan HCS, Wang J, Palczewski K, Filipek S, Vogel H, Liu ZJ, Yuan S. Exploring a new ligand binding site of G protein-coupled receptors. Chem Sci 2018; 9:6480-6489. [PMID: 30310578 PMCID: PMC6115637 DOI: 10.1039/c8sc01680a] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023] Open
Abstract
Identifying a target ligand binding site is an important step for structure-based rational drug design as shown here for G protein-coupled receptors (GPCRs), which are among the most popular drug targets. We applied long-time scale molecular dynamics simulations, coupled with mutagenesis studies, to two prototypical GPCRs, the M3 and M4 muscarinic acetylcholine receptors. Our results indicate that unlike synthetic antagonists, which bind to the classic orthosteric site, the endogenous agonist acetylcholine is able to diffuse into a much deeper binding pocket. We also discovered that the most recently resolved crystal structure of the LTB4 receptor comprised a bound inverse agonist, which extended its benzamidine moiety to the same binding pocket discovered in this work. Analysis on all resolved GPCR crystal structures indicated that this new pocket could exist in most receptors. Our findings provide new opportunities for GPCR drug discovery.
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Affiliation(s)
| | - Jingjing Wang
- iHuman Institute , ShanghaiTech University , China .
| | | | - Slawomir Filipek
- Faculty of Chemistry , Biological and Chemical Research Centre , University of Warsaw , Poland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Switzerland . ;
| | - Zhi-Jie Liu
- iHuman Institute , ShanghaiTech University , China .
| | - Shuguang Yuan
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Switzerland . ;
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50
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Structure of the adenosine-bound human adenosine A1 receptor–Gi complex. Nature 2018; 558:559-563. [DOI: 10.1038/s41586-018-0236-6] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/16/2018] [Indexed: 12/19/2022]
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