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Fouillen A, Bous J, Granier S, Mouillac B, Sounier R. Bringing GPCR Structural Biology to Medical Applications: Insights from Both V2 Vasopressin and Mu-Opioid Receptors. Membranes (Basel) 2023; 13:606. [PMID: 37367810 DOI: 10.3390/membranes13060606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
G-protein coupled receptors (GPCRs) are versatile signaling proteins that regulate key physiological processes in response to a wide variety of extracellular stimuli. The last decade has seen a revolution in the structural biology of clinically important GPCRs. Indeed, the improvement in molecular and biochemical methods to study GPCRs and their transducer complexes, together with advances in cryo-electron microscopy, NMR development, and progress in molecular dynamic simulations, have led to a better understanding of their regulation by ligands of different efficacy and bias. This has also renewed a great interest in GPCR drug discovery, such as finding biased ligands that can either promote or not promote specific regulations. In this review, we focus on two therapeutically relevant GPCR targets, the V2 vasopressin receptor (V2R) and the mu-opioid receptor (µOR), to shed light on the recent structural biology studies and show the impact of this integrative approach on the determination of new potential clinical effective compounds.
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Affiliation(s)
- Aurélien Fouillen
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
- Centre de Biochimie Structurale (CBS), Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Julien Bous
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
| | - Remy Sounier
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
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Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier JP, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nat Commun 2019; 10:2697. [PMID: 31217444 PMCID: PMC6584647 DOI: 10.1038/s41467-019-10490-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available. NMR structure determination is challenging for proteins with a molecular weight above 30 kDa and atomic-resolution structure determination from cryo-EM data is currently not the rule. Here the authors describe an integrated structure determination approach that simultaneously uses NMR and EM data and allows them to determine the structure of the 468 kDa dodecameric aminopeptidase TET2 complex.
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Affiliation(s)
- Diego F Gauto
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Leandro F Estrozi
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.
| | - Charles D Schwieters
- Laboratory of Imaging Sciences, Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA
| | - Gregory Effantin
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Pavel Macek
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,NMR-Bio, 5 Place Robert Schuman, F-38025, Grenoble, France
| | - Remy Sounier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,Institut de Génomique Fonctionnelle, CNRS UMR-5203, INSERM U1191, University of Montpellier, F-34000, Montpellier, France
| | - Astrid C Sivertsen
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Elena Schmidt
- Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Rime Kerfah
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,NMR-Bio, 5 Place Robert Schuman, F-38025, Grenoble, France
| | - Guillaume Mas
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.,Biozentrum University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Jacques-Philippe Colletier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.,Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.,Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Adrien Favier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Paul Schanda
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France.
| | - Jerome Boisbouvier
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, F-38044, Grenoble, France
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Sounier R, Yang Y, Hagelberger J, Granier S, Déméné H. 1H, 13C and 15N backbone chemical shift assignments of camelid single-domain antibodies against active state µ-opioid receptor. Biomol NMR Assign 2017; 11:117-121. [PMID: 28239762 PMCID: PMC5406611 DOI: 10.1007/s12104-017-9733-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Nanobodies are single chain antibodies that have become a highly valuable and versatile tool for biomolecular and therapeutic research. One application field is the stabilization of active states of flexible proteins, among which G-protein coupled receptors represent a very important class of membrane proteins. Here we present the backbone and side-chain assignment of the 1H, 13C and 15N resonances of Nb33 and Nb39, two nanobodies that recognize and stabilize the µ-opioid receptor to opioids in its active agonist-bound conformation. In addition, we present a comparison of their secondary structures as derived from NMR chemical shifts.
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Affiliation(s)
- Remy Sounier
- Institut de Genomique Fonctionnelle (IGF), CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France.
| | - Yinshan Yang
- Centre de Biochimie Structurale, CNRS UMR 5048-INSERM 1054, University of Montpellier, 29 rue de Navacelles, 34090, Montpellier Cedex, France
| | - Joanna Hagelberger
- Institut de Genomique Fonctionnelle (IGF), CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Sébastien Granier
- Institut de Genomique Fonctionnelle (IGF), CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Hélène Déméné
- Centre de Biochimie Structurale, CNRS UMR 5048-INSERM 1054, University of Montpellier, 29 rue de Navacelles, 34090, Montpellier Cedex, France.
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Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy has come a long way in characterizing the structure and function of biological molecules since the first one-dimensional spectrum of protein was recorded about 30 years ago. To date (September 1, 2012), there are 9,521 solution NMR structures in the Protein Data Bank, compared to 74,009 determined by crystallographic methods. Unlike X-ray and electron microscopy (EM) methods, which are based on the concepts of Fourier optics and image reconstruction, structure determination by NMR involves measuring structural restraints and finding structural solutions that satisfy the restraints. Although the NMR approach is much less direct in a physical sense, it has proven itself over the years to be capable of de novo structure determination at high precision. Moreover, the method is highly versatile and can be used in a variety of ways for addressing mechanistic questions. NMR measurements of protein internal dynamics and protein-protein or protein-ligand interaction are directly relevant to function in vivo because the molecules are often in physiological buffer conditions. The method can also be applied to investigate protein-folding intermediates, conformational changes, as well as intrinsically unfolded proteins. Recently, along with X-ray and EM, solution NMR has entered a state of rapid growth for structural studies of membrane proteins, already demonstrating its feasibility in de novo structure determination of membrane-embedded ion channels and receptors. As the hardware advances rapidly, especially in cryogenic probes that have much higher sensitivity, the sample concentration required for solution NMR investigation is decreasing, hopefully soon to a concentration level at which nonspecific protein aggregation is no longer an issue. After three decades of improvement in spectrometer technology, NMR pulse experiments, isotope labeling schemes, and structure determination software, we believe that solution NMR will truly enter the production phase in the next decade to answer biological questions of high impact, and to become more versatile than ever in complementing X-ray and EM in investigating protein structure and function.
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Affiliation(s)
- James J Chou
- Jack and Eileen Connors Structural Biology Laboratory, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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