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Wu FJ, Williams LM, Abdul-Ridha A, Gunatilaka A, Vaid TM, Kocan M, Whitehead AR, Griffin MDW, Bathgate RAD, Scott DJ, Gooley PR. Probing the correlation between ligand efficacy and conformational diversity at the α 1A-adrenoreceptor reveals allosteric coupling of its microswitches. J Biol Chem 2020; 295:7404-7417. [PMID: 32303636 PMCID: PMC7247315 DOI: 10.1074/jbc.ra120.012842] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
G protein-coupled receptors (GPCRs) use a series of conserved microswitches to transmit signals across the cell membrane via an allosteric network encompassing the ligand-binding site and the G protein-binding site. Crystal structures of GPCRs provide snapshots of their inactive and active states, but poorly describe the conformational dynamics of the allosteric network that underlies GPCR activation. Here, we analyzed the correlation between ligand binding and receptor conformation of the α1A-adrenoreceptor, a GPCR that stimulates smooth muscle contraction in response to binding noradrenaline. NMR of [13CϵH3]methionine-labeled α1A-adrenoreceptor variants, each exhibiting differing signaling capacities, revealed how different classes of ligands modulate the conformational equilibria of this receptor. [13CϵH3]Methionine residues near the microswitches exhibited distinct states that correlated with ligand efficacies, supporting a conformational selection mechanism. We propose that allosteric coupling among the microswitches controls the conformation of the α1A-adrenoreceptor and underlies the mechanism of ligand modulation of GPCR signaling in cells.
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Affiliation(s)
- Feng-Jie Wu
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Lisa M Williams
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Alaa Abdul-Ridha
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Avanka Gunatilaka
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Tasneem M Vaid
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Martina Kocan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Alice R Whitehead
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia.
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia.
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52
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Schuster M, Deluigi M, Pantić M, Vacca S, Baumann C, Scott DJ, Plückthun A, Zerbe O. Optimizing the α 1B-adrenergic receptor for solution NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183354. [PMID: 32413443 DOI: 10.1016/j.bbamem.2020.183354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/01/2020] [Accepted: 05/09/2020] [Indexed: 12/14/2022]
Abstract
Sample preparation for NMR studies of G protein-coupled receptors faces special requirements: Proteins need to be stable for prolonged measurements at elevated temperatures, they should ideally be uniformly labeled with the stable isotopes 13C, 15N, and all carbon-bound protons should be replaced by deuterons. In addition, certain NMR experiments require protonated methyl groups in the presence of a perdeuterated background. All these requirements are most easily satisfied when using Escherichia coli as the expression host. Here we describe a workflow, starting from a temperature-stabilized mutant of the α1B-adrenergic receptor, obtained using the CHESS methodology, into an even more stable species, in which flexible parts from termini were removed and the intracellular loop 3 (ICL3) was stabilized against proteolytic cleavage. The yield after purification corresponds to 1-2 mg/L of D2O culture. The final purification step is ligand-affinity chromatography to ensure that only well-folded ligand-binding protein is isolated. Proper selection of detergent has a remarkable influence on the quality of NMR spectra. All optimization steps of sequence and detergent are monitored on a small scale by monitoring the melting temperature and long-term thermal stability to allow for screening of many conditions. The stabilized mutant of the α1B-adrenergic receptor was additionally incorporated in nanodiscs, but displayed slightly inferior spectra compared to a sample in detergent micelles. Finally, both [15N,1H]- as well as [13C,1H]-HSQC spectra are shown highlighting the high quality of the final NMR sample. Importantly, the quality of [13C,1H]-HSQC spectra indicates that the so prepared receptor could be used for studying side-chain dynamics.
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Affiliation(s)
- Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mattia Deluigi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Milica Pantić
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Santiago Vacca
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel J Scott
- Florey Institute of Neuroscience and Mental Health, Department of Biochemistry and Molecular Biology, The University of Melbourne, 30 Royal Parade Parkville, 3052, Victoria, Australia
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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53
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Grahl A, Abiko LA, Isogai S, Sharpe T, Grzesiek S. A high-resolution description of β 1-adrenergic receptor functional dynamics and allosteric coupling from backbone NMR. Nat Commun 2020; 11:2216. [PMID: 32371991 PMCID: PMC7200737 DOI: 10.1038/s41467-020-15864-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by extra- and intracellular ligands occurs via modulation of complex conformational equilibria, but their exact kinetic details and underlying atomic mechanisms are unknown. Here we quantified these dynamic equilibria in the β1-adrenergic receptor in its apo form and seven ligand complexes using 1H/15N NMR spectroscopy. We observe three major exchanging conformations: an inactive conformation (Ci), a preactive conformation (Cp) and an active conformation (Ca), which becomes fully populated in a ternary complex with a G protein mimicking nanobody. The Ci ↔ Cp exchange occurs on the microsecond scale, the Cp ↔ Ca exchange is slower than ~5 ms and only occurs in the presence of two highly conserved tyrosines (Y5.58, Y7.53), which stabilize the active conformation of TM6. The Cp→Ca chemical shift changes indicate a pivoting motion of the entire TM6 that couples the effector site to the orthosteric ligand pocket. Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by ligands occurs via modulation of complex conformational equilibria. Here authors quantify these equilibria and their dynamics in the β1-adrenergic receptor in its apo form and seven ligand complexes using NMR.
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Affiliation(s)
- Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Shin Isogai
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Core Facility, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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54
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Beyond structure: emerging approaches to study GPCR dynamics. Curr Opin Struct Biol 2020; 63:18-25. [PMID: 32305785 DOI: 10.1016/j.sbi.2020.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/22/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest superfamily of membrane proteins that are involved in regulation of sensory and physiological processes and implicated in many diseases. The last decade revolutionized the GPCR field by unraveling multiple high-resolution structures of many different receptors in complexes with various ligands and signaling partners. A complete understanding of the complex nature of GPCR function is, however, impossible to attain without combining static structural snapshots with information about GPCR dynamics obtained by complementary spectroscopic techniques. As illustrated in this review, structure and dynamics studies are now paving the way for understanding important questions of GPCR biology such as partial and biased agonism, allostery, oligomerization, and other fundamental aspects of GPCR signaling.
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55
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Park SH, Lee JH. Dynamic G Protein-Coupled Receptor Signaling Probed by Solution NMR Spectroscopy. Biochemistry 2020; 59:1065-1080. [PMID: 32092261 DOI: 10.1021/acs.biochem.0c00032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating various dynamic features of G protein-coupled receptor (GPCR) signaling. In this Perspective, we focus on NMR techniques to characterize ligand-dependent conformational dynamics of GPCRs as well as the interaction of GPCRs with their environment and ligands. We also describe circumstances under which each technique should be applied, their advantages and disadvantages, and how they can be combined with other strategies to deepen the understanding of GPCR signaling at the molecular level.
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Affiliation(s)
- Sho Hee Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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56
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Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
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57
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Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β 1-adrenergic receptor. Nat Commun 2020; 11:669. [PMID: 32015348 PMCID: PMC6997182 DOI: 10.1038/s41467-020-14526-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are allosteric signaling proteins that transmit an extracellular stimulus across the cell membrane. Using 19F NMR and site-specific labelling, we investigate the response of the cytoplasmic region of transmembrane helices 6 and 7 of the β1-adrenergic receptor to agonist stimulation and coupling to a Gs-protein-mimetic nanobody. Agonist binding shows the receptor in equilibrium between two inactive states and a pre-active form, increasingly populated with higher ligand efficacy. Nanobody coupling leads to a fully active ternary receptor complex present in amounts correlating directly with agonist efficacy, consistent with partial agonism. While for different agonists the helix 6 environment in the active-state ternary complexes resides in a well-defined conformation, showing little conformational mobility, the environment of the highly conserved NPxxY motif on helix 7 remains dynamic adopting diverse, agonist-specific conformations, implying a further role of this region in receptor function. An inactive nanobody-coupled ternary receptor form is also observed.
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58
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Yang Y, Padilla A, de Guillen K, Mammri L, Gracy J, Declerck N, Déméné H. Structural Insights into of the Allosteric Activation of the LicT Antiterminator by PTS-Mediated Phosphorylation. Structure 2020; 28:244-251.e3. [DOI: 10.1016/j.str.2019.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/05/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
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59
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Schütz S, Sprangers R. Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:56-84. [PMID: 32130959 DOI: 10.1016/j.pnmrs.2019.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/25/2019] [Indexed: 05/21/2023]
Abstract
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
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Affiliation(s)
- Stefan Schütz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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60
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Kooijman L, Ansorge P, Schuster M, Baumann C, Löhr F, Jurt S, Güntert P, Zerbe O. Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs. JOURNAL OF BIOMOLECULAR NMR 2020; 74:45-60. [PMID: 31754899 PMCID: PMC7015963 DOI: 10.1007/s10858-019-00289-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/11/2019] [Indexed: 05/21/2023]
Abstract
Resonance assignments are challenging for membrane proteins due to the size of the lipid/detergent-protein complex and the presence of line-broadening from conformational exchange. As a consequence, many correlations are missing in the triple-resonance NMR experiments typically used for assignments. Herein, we present an approach in which correlations from these solution-state NMR experiments are supplemented by data from 13C unlabeling, single-amino acid type labeling, 4D NOESY data and proximity of moieties to lipids or water in combination with a structure of the protein. These additional data are used to edit the expected peaklists for the automated assignment protocol FLYA, a module of the program package CYANA. We demonstrate application of the protocol to the 262-residue proton pump from archaeal bacteriorhodopsin (bR) in lipid nanodiscs. The lipid-protein assembly is characterized by an overall correlation time of 44 ns. The protocol yielded assignments for 62% of all backbone (H, N, Cα, Cβ, C') resonances of bR, corresponding to 74% of all observed backbone spin systems, and 60% of the Ala, Met, Ile (δ1), Leu and Val methyl groups, thus enabling to assign a large fraction of the protein without mutagenesis data. Most missing resonances stem from the extracellular half, likely due intermediate exchange line-broadening. Further analysis revealed that missing information of the amino acid type of the preceding residue is the largest problem, and that 4D NOESY experiments are particularly helpful to compensate for that information loss.
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Affiliation(s)
- Laurens Kooijman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Philipp Ansorge
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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61
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Molecular Basis of Opioid Action: From Structures to New Leads. Biol Psychiatry 2020; 87:6-14. [PMID: 31653480 PMCID: PMC6898784 DOI: 10.1016/j.biopsych.2019.08.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 02/06/2023]
Abstract
Since the isolation of morphine from the opium poppy over 200 years ago, the molecular basis of opioid action has remained the subject of intense inquiry. The identification of specific receptors responsible for opioid function and the discovery of many chemically diverse molecules with unique opioid-like efficacies have provided glimpses into the molecular logic of opioid action. Recent revolutions in the structural biology of transmembrane proteins have, for the first time, yielded high-resolution views into the 3-dimensional shapes of all 4 opioid receptors. These studies have begun to decode the chemical logic that enables opioids to specifically bind and activate their receptor targets. A combination of spectroscopic experiments and computational simulations has provided a view into the molecular movements of the opioid receptors, which itself gives rise to the complex opioid pharmacology observed at the cellular and behavioral levels. Further diversity in opioid receptor structure is driven by both genetic variation and receptor oligomerization. These insights have enabled computational drug discovery efforts, with some evidence of success in the design of completely novel opioids with unique efficacies. The combined progress over the past few years provides hope for new, efficacious opioids devoid of the side effects that have made them the scourge of humanity for millennia.
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62
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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63
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Abstract
Ligand-receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded efficacy receptor conformations predicted by receptor theory has been limited but is critical to fully validate theoretical models. We applied quantitative structure-function approaches to characterize the effects of structurally similar and structurally diverse agonists on the conformational ensemble of nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ). For all ligands, agonist functional efficacy is correlated to a shift in the conformational ensemble equilibrium from a ground state toward an active state, which is detected by NMR spectroscopy but not observed in crystal structures. For the structurally similar ligands, ligand potency and affinity are also correlated to efficacy and conformation, indicating ligand residence times among related analogs may influence receptor conformation and function. Our results derived from quantitative graded activity-conformation correlations provide experimental evidence and a platform with which to extend and test theoretical models of receptor pharmacology to more accurately describe and predict ligand-dependent receptor activity.
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64
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Abiko LA, Grahl A, Grzesiek S. High Pressure Shifts the β 1-Adrenergic Receptor to the Active Conformation in the Absence of G Protein. J Am Chem Soc 2019; 141:16663-16670. [PMID: 31564099 DOI: 10.1021/jacs.9b06042] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
G protein-coupled receptors (GPCRs) are versatile chemical sensors, which transmit the signal of an extracellular binding event across the plasma membrane to the intracellular side. This function is achieved via the modulation of highly dynamical equilibria of various conformational receptor states. Here we have probed the effect of pressure on the conformational equilibria of a functional thermostabilized β1-adrenergic GPCR (β1AR) by solution NMR. High pressure induces a large shift in the conformational equilibrium (midpoint ∼600 bar) from the preactive conformation of agonist-bound β1AR to the fully active conformation, which under normal pressure is only populated when a G protein or a G protein-mimicking nanobody (Nb) binds to the intracellular side of the β1AR·agonist complex. No such large effects are observed for an antagonist-bound β1AR or the ternary β1AR·agonist·Nb80 complex. The detected structural changes of agonist-bound β1AR around the orthosteric ligand binding pocket indicate that the fully active receptor occupies an ∼100 Å3 smaller volume than that of its preactive form. Most likely, this volume reduction is caused by the compression of empty (nonhydrated) cavities in the ligand binding pocket and the center of the receptor, which increases the ligand receptor interactions and explains the ∼100-fold affinity increase of agonists in the presence of G protein. The finding that isotropic pressure induces a directed motion from the preactive to the fully active GPCR conformation provides evidence of the high mechanical robustness of this important functional switch.
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Affiliation(s)
- Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
| | - Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
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65
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Liu RR, Song LT, Meng YJ, Zhu M, Zhai HL. Study on Biocompatibility of AuNPs and Theoretical Design of a Multi-CDR-Functional Nanobody. J Phys Chem B 2019; 123:7570-7577. [DOI: 10.1021/acs.jpcb.9b05147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rui Rui Liu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Li Ting Song
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Ya Jie Meng
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Min Zhu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
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66
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NMR investigation of protein-ligand interactions for G-protein coupled receptors. Future Med Chem 2019; 11:1811-1825. [PMID: 31287732 DOI: 10.4155/fmc-2018-0312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this review, we report NMR studies of ligand-GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a major role for the generation of novel molecules both as new tools for the understanding of the GPCR function and as therapeutic compounds for a large diversity of pathologies.
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67
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Xu J, Hu Y, Kaindl J, Risel P, Hübner H, Maeda S, Niu X, Li H, Gmeiner P, Jin C, Kobilka BK. Conformational Complexity and Dynamics in a Muscarinic Receptor Revealed by NMR Spectroscopy. Mol Cell 2019; 75:53-65.e7. [PMID: 31103421 DOI: 10.1016/j.molcel.2019.04.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/25/2019] [Accepted: 04/19/2019] [Indexed: 11/28/2022]
Abstract
The M2 muscarinic acetylcholine receptor (M2R) is a prototypical GPCR that plays important roles in regulating heart rate and CNS functions. Crystal structures provide snapshots of the M2R in inactive and active states, but the allosteric link between the ligand binding pocket and cytoplasmic surface remains poorly understood. Here we used solution NMR to examine the structure and dynamics of the M2R labeled with 13CH3-ε-methionine upon binding to various orthosteric and allosteric ligands having a range of efficacy for both G protein activation and arrestin recruitment. We observed ligand-specific changes in the NMR spectra of 13CH3-ε-methionine probes in the M2R extracellular domain, transmembrane core, and cytoplasmic surface, allowing us to correlate ligand structure with changes in receptor structure and dynamics. We show that the M2R has a complex energy landscape in which ligands with different efficacy profiles stabilize distinct receptor conformations.
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Affiliation(s)
- Jun Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100084, China
| | - Jonas Kaindl
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Philipp Risel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100084, China
| | - Hongwei Li
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100084, China
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100084, China.
| | - Brian K Kobilka
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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68
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Bostock MJ, Solt AS, Nietlispach D. The role of NMR spectroscopy in mapping the conformational landscape of GPCRs. Curr Opin Struct Biol 2019; 57:145-156. [PMID: 31075520 DOI: 10.1016/j.sbi.2019.03.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/19/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
Abstract
Over recent years, nuclear magnetic resonance (NMR) spectroscopy has developed into a powerful mechanistic tool for the investigation of G protein-coupled receptors (GPCRs). NMR provides insights which underpin the dynamic nature of these important receptors and reveals experimental evidence for a complex conformational energy landscape that is explored during receptor activation resulting in signalling. NMR studies have highlighted both the dynamic properties of different receptor states as well as the exchange pathways and intermediates formed during activation, extending the static view of GPCRs obtained from other techniques. NMR studies can be undertaken in realistic membrane-like phospholipid environments and an ever-increasing choice of labelling strategies provides comprehensive, receptor-wide information. Combined with other structural methods, NMR is contributing to our understanding of allosteric signal propagation and the interaction of GPCRs with intracellular binding partners (IBP), crucial to explaining cellular signalling.
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Affiliation(s)
- Mark J Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Andras S Solt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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69
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Casiraghi M, Point E, Pozza A, Moncoq K, Banères JL, Catoire LJ. NMR analysis of GPCR conformational landscapes and dynamics. Mol Cell Endocrinol 2019; 484:69-77. [PMID: 30690069 DOI: 10.1016/j.mce.2018.12.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/13/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022]
Abstract
Understanding the signal transduction mechanism mediated by the G Protein-Coupled Receptors (GPCRs) in eukaryote cells represents one of the main issues in modern biology. At the molecular level, various biophysical approaches have provided important insights on the functional plasticity of these complex allosteric machines. In this context, X-ray crystal structures published during the last decade represent a major breakthrough in GPCR structural biology, delivering important information on the activation process of these receptors through the description of the three-dimensional organization of their active and inactive states. In complement to crystals and cryo-electronic microscopy structures, information on the probability of existence of different GPCR conformations and the dynamic barriers separating those structural sub-states is required to better understand GPCR function. Among the panel of techniques available, nuclear magnetic resonance (NMR) spectroscopy represents a powerful tool to characterize both conformational landscapes and dynamics. Here, we will outline the potential of NMR to address such biological questions, and we will illustrate the functional insights that NMR has brought in the field of GPCRs in the recent years.
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Affiliation(s)
- Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Elodie Point
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Alexandre Pozza
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Jean-Louis Banères
- Institut des Biomoléćules Max Mousseron (IBMM), UMR 5247 CNRS, Université; Montpellier, ENSCM, 15 av. Charles Flahault, 34093, Montpellier, France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR7099, CNRS/Université; Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France.
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70
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Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations. Cell 2019; 176:468-478.e11. [PMID: 30639099 DOI: 10.1016/j.cell.2018.12.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/13/2018] [Accepted: 12/04/2018] [Indexed: 01/14/2023]
Abstract
"Biased" G protein-coupled receptor (GPCR) agonists preferentially activate pathways mediated by G proteins or β-arrestins. Here, we use double electron-electron resonance spectroscopy to probe the changes that ligands induce in the conformational distribution of the angiotensin II type I receptor. Monitoring distances between 10 pairs of nitroxide labels distributed across the intracellular regions enabled mapping of four underlying sets of conformations. Ligands from different functional classes have distinct, characteristic effects on the conformational heterogeneity of the receptor. Compared to angiotensin II, the endogenous agonist, agonists with enhanced Gq coupling more strongly stabilize an "open" conformation with an accessible transducer-binding site. β-arrestin-biased agonists deficient in Gq coupling do not stabilize this open conformation but instead favor two more occluded conformations. These data suggest a structural mechanism for biased ligand action at the angiotensin receptor that can be exploited to rationally design GPCR-targeting drugs with greater specificity of action.
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71
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Bumbak F, Bathgate RAD, Scott DJ, Gooley PR. Expression and Purification of a Functional E. coli 13CH 3-Methionine-Labeled Thermostable Neurotensin Receptor 1 Variant for Solution NMR Studies. Methods Mol Biol 2019; 1947:31-55. [PMID: 30969410 DOI: 10.1007/978-1-4939-9121-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Escherichia coli (E. coli) is the most widely used expression host for recombinant proteins due to high expression yields and straightforward molecular cloning. Directed evolution of G protein-coupled receptors (GPCRs) has made several of these difficult to express membrane proteins amenable to prokaryotic expression. Here, we describe a protocol for near complete 13CH3-methionine labeling of a thermostable neurotensin receptor 1 (enNTS1) variant in E. coli for solution NMR-based dynamics studies. Our expression strategy utilizes methionine biosynthesis pathway inhibition forcing E. coli to incorporate exogenous methionine with 96% efficiency at expression levels of 2.6 mg enNTS1 per liter of expression culture containing 50 mg of 13CH3-methionine. We also provide a 3-step purification protocol that produces final yields of 0.6 mg of functional Apo-state enNTS1.
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Affiliation(s)
- Fabian Bumbak
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia. .,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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72
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Isotopic Labeling of Eukaryotic Membrane Proteins for NMR Studies of Interactions and Dynamics. Methods Enzymol 2018; 614:37-65. [PMID: 30611431 DOI: 10.1016/bs.mie.2018.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Membrane proteins, and especially G-protein coupled receptors (GPCRs), are increasingly important targets of structural biology studies due to their involvement in many biomedically critical pathways in humans. These proteins are often highly dynamic and thus benefit from studies by NMR spectroscopy in parallel with complementary crystallographic and cryo-EM analyses. However, such studies are often complicated by a range of practical concerns, including challenges in preparing suitably isotopically labeled membrane protein samples, large sizes of protein/detergent or protein/lipid complexes, and limitations on sample concentrations and stabilities. Here we describe our approach to addressing these challenges via the use of simple eukaryotic expression systems and modified NMR experiments, using the human adenosine A2A receptor as an example. Protocols are provided for the preparation of U-2H (13C,1H-Ile δ1)-labeled membrane proteins from overexpression in the methylotrophic yeast Pichia pastoris, as well as techniques for studying the fast ns-ps sidechain dynamics of the methyl groups of such samples. We believe that, with the proper optimization, these protocols should be generalizable to other GPCRs and human membrane proteins.
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73
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Abstract
The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.
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Affiliation(s)
- Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
| | - Hans Koss
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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74
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Kleist AB, Peterson F, Tyler RC, Gustavsson M, Handel TM, Volkman BF. Solution NMR spectroscopy of GPCRs: Residue-specific labeling strategies with a focus on 13C-methyl methionine labeling of the atypical chemokine receptor ACKR3. Methods Cell Biol 2018; 149:259-288. [PMID: 30616824 DOI: 10.1016/bs.mcb.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The past decade has witnessed remarkable progress in the determination of G protein-coupled receptor (GPCR) structures, profoundly expanding our understanding of how GPCRs recognize ligands, become activated, and interact with intracellular signaling components. In recent years, numerous studies have used solution nuclear magnetic resonance (NMR) spectroscopy to investigate GPCRs, providing fundamental insights into GPCR conformational changes, allostery, dynamics, and other facets of GPCR function are challenging to study using other structural techniques. Despite these advantages, NMR-based studies of GPCRs are few relative to the number of published structures, due in part to the challenges and limitations of NMR for the characterization of large membrane proteins. Several studies have circumvented these challenges using a variety of isotopic labeling strategies, including side chain derivatization and metabolic incorporation of NMR-active nuclei. In this chapter, we provide an overview of different isotopic labeling strategies and describe an in-depth protocol for the expression, purification, and NMR studies of the chemokine GPCR atypical chemokine receptor 3 (ACKR3) via 13CH3-methionine incorporation. The goal of this chapter is to provide a resource to the GPCR community for those interested in pursuing NMR studies of GPCRs.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Francis Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Robert C Tyler
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States.
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75
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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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76
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Clark L, Dikiy I, Rosenbaum DM, Gardner KH. On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies. JOURNAL OF BIOMOLECULAR NMR 2018; 71:203-211. [PMID: 30121871 PMCID: PMC7282444 DOI: 10.1007/s10858-018-0204-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 05/21/2023]
Abstract
NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. We review the different expression systems for production of isotopically labeled membrane proteins and highlight the use of the yeast Pichia pastoris to achieve perdeuteration and 13C methyl probe incorporation within isoleucine sidechains. We further illustrate the use of this method for labeling of several biomedically significant GPCRs.
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Affiliation(s)
- Lindsay Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA.
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY, 10016, USA.
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77
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Franke B, Opitz C, Isogai S, Grahl A, Delgado L, Gossert AD, Grzesiek S. Production of isotope-labeled proteins in insect cells for NMR. JOURNAL OF BIOMOLECULAR NMR 2018; 71:173-184. [PMID: 29687312 DOI: 10.1007/s10858-018-0172-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Baculovirus-infected insect cells have become a powerful tool to express recombinant proteins for structural and functional studies by NMR spectroscopy. This article provides an introduction into the insect cell/baculovirus expression system and its use for the production of recombinant isotope-labeled proteins. We discuss recent advances in inexpensive isotope-labeling methods using labeled algal or yeast extracts as the amino acid source and give examples of advanced NMR applications for proteins, which have become accessible by this eukaryotic expression host.
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Affiliation(s)
- Bastian Franke
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Christian Opitz
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Shin Isogai
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Leonildo Delgado
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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78
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Yong KJ, Vaid TM, Shilling PJ, Wu FJ, Williams LM, Deluigi M, Plückthun A, Bathgate RAD, Gooley PR, Scott DJ. Determinants of Ligand Subtype-Selectivity at α 1A-Adrenoceptor Revealed Using Saturation Transfer Difference (STD) NMR. ACS Chem Biol 2018. [PMID: 29537256 DOI: 10.1021/acschembio.8b00191] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
α1A- and α1B-adrenoceptors (α1A-AR and α1B-AR) are closely related G protein-coupled receptors (GPCRs) that modulate the cardiovascular and nervous systems in response to binding epinephrine and norepinephrine. The GPCR gene superfamily is made up of numerous subfamilies that, like α1A-AR and α1B-AR, are activated by the same endogenous agonists but may modulate different physiological processes. A major challenge in GPCR research and drug discovery is determining how compounds interact with receptors at the molecular level, especially to assist in the optimization of drug leads. Nuclear magnetic resonance spectroscopy (NMR) can provide great insight into ligand-binding epitopes, modes, and kinetics. Ideally, ligand-based NMR methods require purified, well-behaved protein samples. The instability of GPCRs upon purification in detergents, however, makes the application of NMR to study ligand binding challenging. Here, stabilized α1A-AR and α1B-AR variants were engineered using Cellular High-throughput Encapsulation, Solubilization, and Screening (CHESS), allowing the analysis of ligand binding with Saturation Transfer Difference NMR (STD NMR). STD NMR was used to map the binding epitopes of epinephrine and A-61603 to both receptors, revealing the molecular determinants for the selectivity of A-61603 for α1A-AR over α1B-AR. The use of stabilized GPCRs for ligand-observed NMR experiments will lead to a deeper understanding of binding processes and assist structure-based drug design.
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Affiliation(s)
- Kelvin J. Yong
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tasneem M. Vaid
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Patrick J. Shilling
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Feng-Jie Wu
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lisa M. Williams
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
| | - Mattia Deluigi
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Ross A. D. Bathgate
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul R. Gooley
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Daniel J. Scott
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
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79
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Casiraghi M, Damian M, Lescop E, Banères JL, Catoire LJ. Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry 2018; 57:2297-2307. [PMID: 29607648 DOI: 10.1021/acs.biochem.8b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Conformational dynamics of GPCRs are central to their function but are difficult to explore at the atomic scale. Solution-state NMR has provided the major contribution in that area of study during the past decade, despite nonoptimized labeling schemes due to the use of insect cells and, to a lesser extent, yeast as the main expression hosts. Indeed, the most efficient isotope-labeling scheme ever to address energy landscape issues for large proteins or protein complexes relies on the use of 13CH3 probes immersed in a perdeuterated dipolar environment, which is essentially out of reach of eukaryotic expression systems. In contrast, although its contribution has been underestimated because of technical issues, Escherichia coli is by far the best-adapted host for such labeling. As it is now tightly controlled, we show in this review that bacterial expression can provide an NMR spectral resolution never achieved in the GPCR field.
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Affiliation(s)
- Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay , 1 av. de la Terrasse , 91198 Gif-sur-Yvette , France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Université Montpellier, ENSCM , 15 av. Charles Flahault , 34093 Montpellier , France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires , UMR 7099, CNRS/Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique (FRC 550) , 13 rue Pierre et Marie Curie , 75005 Paris , France
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