51
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Abstract
Sigma1 (also known as this sigma-1 receptor) is an unusual and enigmatic transmembrane protein implicated in a diverse array of biological processes ranging from neurodegenerative disease to cancer. Despite decades of research, the molecular architecture of Sigma1 is only beginning to become clear. Recent work has established that Sigma1 is an oligomer, and crystallographic studies have now offered the first high-resolution views of its molecular structure. For the first time, these results provide a detailed framework to understand mutagenesis data and the molecular pharmacology of Sigma1 ligands. Structural data also raise new questions surrounding the mechanisms of ligand activity and the molecular basis for interactions between Sigma1 and other proteins. As Sigma1 research enters the structural era, the field is poised for new discoveries and reevaluation of old data and old models.
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Affiliation(s)
- Andrew Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Seeley G. Mudd Building, 250 Longwood Ave., Boston, MA, 02115, USA.
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52
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Eddy MT, Didenko T, Stevens RC, Wüthrich K. β 2-Adrenergic Receptor Conformational Response to Fusion Protein in the Third Intracellular Loop. Structure 2016; 24:2190-2197. [PMID: 27839952 DOI: 10.1016/j.str.2016.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/16/2016] [Accepted: 10/07/2016] [Indexed: 12/11/2022]
Abstract
Fluorine-19 nuclear magnetic resonance (NMR) was used to study conformational equilibria at the intracellular tips of helices VI and VII in a variant β2-adrenergic receptor (β2AR) containing T4-lysozyme fused into the third intracellular loop (β2AR-T4L), a G protein-coupled receptor (GPCR) modification widely used in crystal structure determination. G-protein signaling at helix VI showed nearly complete population of an active-like state for all ligand efficacies in the absence of an intracellular protein. For arrestin signaling at helix VII, a native-like equilibrium was observed, except for complexes with ligands devoid of a hydrophobic moiety at the ethanolamine end. These data confirm that response of G-protein and arrestin signaling to ligand efficacy is not coupled, and presents evidence for long-range effects between fusion protein and orthosteric binding cavity, which are suppressed by voluminous bound ligands. Solution NMR thus provides complementary information, which should be considered in functional interpretations of GPCR crystal structures obtained with ICL3 fusions.
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Affiliation(s)
- Matthew T Eddy
- Departments of Biological Sciences and Chemistry, Bridge Institute, The University of Southern California, South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Tatiana Didenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, The University of Southern California, South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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53
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Casiraghi M, Damian M, Lescop E, Point E, Moncoq K, Morellet N, Levy D, Marie J, Guittet E, Banères JL, Catoire LJ. Functional Modulation of a G Protein-Coupled Receptor Conformational Landscape in a Lipid Bilayer. J Am Chem Soc 2016; 138:11170-5. [DOI: 10.1021/jacs.6b04432] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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, F-75005 Paris, France
| | - Marjorie Damian
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, Faculté de Pharmacie, 15 Avenue
C. Flahault, F-34093 Montpellier, France
| | - Ewen Lescop
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Elodie Point
- 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, F-75005 Paris, France
| | - Karine Moncoq
- 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, F-75005 Paris, France
| | - Nelly Morellet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Daniel Levy
- Institut Curie, Centre de Recherche, 75231 Paris, France
- UMR
168, CNRS, 75231 Paris, France
- Université Pierre et Marie Curie, F-75248 Paris, France
| | - Jacky Marie
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, Faculté de Pharmacie, 15 Avenue
C. Flahault, F-34093 Montpellier, France
| | - Eric Guittet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Jean-Louis Banères
- Institut
des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, Faculté de Pharmacie, 15 Avenue
C. Flahault, F-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, F-75005 Paris, France
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54
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Gee CT, Arntson KE, Urick AK, Mishra NK, Hawk LML, Wisniewski AJ, Pomerantz WCK. Protein-observed (19)F-NMR for fragment screening, affinity quantification and druggability assessment. Nat Protoc 2016; 11:1414-27. [PMID: 27414758 DOI: 10.1038/nprot.2016.079] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy can be used to quantify the binding affinity between proteins and low-complexity molecules, termed 'fragments'; this versatile screening approach allows researchers to assess the druggability of new protein targets. Protein-observed (19)F-NMR (PrOF NMR) using (19)F-labeled amino acids generates relatively simple spectra that are able to provide dynamic structural information toward understanding protein folding and function. Changes in these spectra upon the addition of fragment molecules can be observed and quantified. This protocol describes the sequence-selective labeling of three proteins (the first bromodomains of Brd4 and BrdT, and the KIX domain of the CREB-binding protein) using commercially available fluorinated aromatic amino acids and fluorinated precursors as example applications of the method developed by our research group. Fragment-screening approaches are discussed, as well as Kd determination, ligand-efficiency calculations and druggability assessment, i.e., the ability to target these proteins using small-molecule ligands. Experiment times on the order of a few minutes and the simplicity of the NMR spectra obtained make this approach well-suited to the investigation of small- to medium-sized proteins, as well as the screening of multiple proteins in the same experiment.
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Affiliation(s)
- Clifford T Gee
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Keith E Arntson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Neeraj K Mishra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura M L Hawk
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrea J Wisniewski
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
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55
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Abstract
Structural characterization of integral membrane proteins (MPs) demands that the samples be pure, monodisperse, and stable. Detergents are required to extract MPs from the lipid bilayer in which they reside and to stabilize them for downstream biophysical analyses. Some of the best MP-stabilizing detergents pose problems for cryo-EM studies, but in this issue of Structure, Hauer et al. (2015) now offer a solution called GraDeR.
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Affiliation(s)
- Satinder K Singh
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
| | - Fred J Sigworth
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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56
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Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA. Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure 2015; 24:300-9. [PMID: 26749445 DOI: 10.1016/j.str.2015.11.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 01/18/2023]
Abstract
A major challenge in membrane biophysics is to define the mechanistic linkages between a protein's conformational transitions and its function. We describe a novel approach to stabilize transient functional states of membrane proteins in native-like lipid environments allowing for their structural and biochemical characterization. This is accomplished by combining the power of antibody Fab-based phage display selection with the benefits of embedding membrane protein targets in lipid-filled nanodiscs. In addition to providing a stabilizing lipid environment, nanodiscs afford significant technical advantages over detergent-based formats. This enables the production of a rich pool of high-performance Fab binders that can be used as crystallization chaperones, as fiducial markers for single-particle cryoelectron microscopy, and as probes of different conformational states. Moreover, nanodisc-generated Fabs can be used to identify detergents that best mimic native membrane environments for use in biophysical studies.
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Affiliation(s)
- Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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57
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Logez C, Damian M, Legros C, Dupré C, Guéry M, Mary S, Wagner R, M’Kadmi C, Nosjean O, Fould B, Marie J, Fehrentz JA, Martinez J, Ferry G, Boutin JA, Banères JL. Detergent-free Isolation of Functional G Protein-Coupled Receptors into Nanometric Lipid Particles. Biochemistry 2015; 55:38-48. [DOI: 10.1021/acs.biochem.5b01040] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christel Logez
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Marjorie Damian
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Céline Legros
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Clémence Dupré
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Mélody Guéry
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Sophie Mary
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Renaud Wagner
- CNRS
UMR7242, Institut de Recherche de l’ESBS, Biotechnologie et
Signalisation Cellulaire, Université de Strasbourg, 300 Boulevard
Sébastien Brant, 67412 Ilkirch cedex, France
| | - Céline M’Kadmi
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Olivier Nosjean
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jacky Marie
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Jean-Alain Fehrentz
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Jean Martinez
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Gilles Ferry
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jean A. Boutin
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jean-Louis Banères
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
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58
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Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I. Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ-Opioid Receptor. Angew Chem Int Ed Engl 2015; 54:15771-6. [PMID: 26568421 PMCID: PMC4722849 DOI: 10.1002/anie.201508794] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/19/2015] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptor (GPCR) ligands impart differing degrees of signaling in the G-protein and arrestin pathways, in phenomena called "biased signaling". However, the mechanism underlying the biased signaling of GPCRs is still unclear, although crystal structures of GPCRs bound to the G protein or arrestin are available. In this study, we observed the NMR signals from methionine residues of the μ-opioid receptor (μOR) in the balanced- and biased-ligand-bound states. We found that the intracellular cavity of μOR exists in an equilibrium between closed and multiple open conformations with coupled conformational changes on the transmembrane helices 3, 5, 6, and 7, and that the population of each open conformation determines the G-protein- and arrestin-mediated signaling levels in each ligand-bound state. These findings provide insight into the biased signaling of GPCRs and will be helpful for development of analgesics that stimulate μOR with reduced tolerance and dependence.
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Affiliation(s)
- Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0075 (Japan)
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Motohiko Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Naoyuki Nobuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Kento Onishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Masahiro Maeda
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561-0825 (Japan)
| | - Hideki Tsujishita
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561-0825 (Japan)
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan).
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59
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Sušac L, O'Connor C, Stevens RC, Wüthrich K. In-Membrane Chemical Modification (IMCM) for Site-Specific Chromophore Labeling of GPCRs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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60
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Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I. Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ‐Opioid Receptor. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Chiyoda‐ku, Tokyo 102‐0075 (Japan)
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Motohiko Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Naoyuki Nobuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Kento Onishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Masahiro Maeda
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561‐0825 (Japan)
| | - Hideki Tsujishita
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561‐0825 (Japan)
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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61
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Sušac L, O'Connor C, Stevens RC, Wüthrich K. In-Membrane Chemical Modification (IMCM) for Site-Specific Chromophore Labeling of GPCRs. Angew Chem Int Ed Engl 2015; 54:15246-9. [PMID: 26545333 DOI: 10.1002/anie.201508506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 11/08/2022]
Abstract
We present in-membrane chemical modification (IMCM) for obtaining selective chromophore labeling of intracellular surface cysteines in G-protein-coupled receptors (GPCRs) with minimal mutagenesis. This method takes advantage of the natural protection of most cysteines by the membrane environment. Practical use of IMCM is illustrated with the site-specific introduction of chromophores for NMR and fluorescence spectroscopy in the human κ-opioid receptor (KOR) and the human A2A adenosine receptor (A2A AR). IMCM is applicable to a wide range of in vitro studies of GPCRs, including single-molecule spectroscopy, and is a promising platform for in-cell spectroscopy experiments.
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Affiliation(s)
- Lukas Sušac
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Casey O'Connor
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA).,Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, Los Angeles, CA 90089 (USA)
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, 3430 South Vermont Avenue, Los Angeles, CA 90089 (USA)
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA). .,Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA). .,Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich (Switzerland).
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62
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Amin A, Hariharan P, Chae PS, Guan L. Effect of Detergents on Galactoside Binding by Melibiose Permeases. Biochemistry 2015; 54:5849-55. [PMID: 26352464 DOI: 10.1021/acs.biochem.5b00660] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of various detergents on the stability and function of the melibiose permeases of Escherichia coli (MelBEc) and Salmonella typhimurium (MelBSt) was studied. In n-dodecyl-β-d-maltoside (DDM) or n-undecyl-β-d-maltoside (UDM), WT MelBSt binds melibiose with an affinity similar to that in the membrane. However, with WT MelBEc or MelBSt mutants (Arg141 → Cys, Arg295 → Cys, or Arg363 → Cys), galactoside binding is not detected in these detergents, but binding to the phosphotransferase protein IIA(Glc) is maintained. In the amphiphiles lauryl maltose neopentyl glycol (MNG-3) or glyco-diosgenin (GDN), galactoside binding with all of the MelB proteins is observed, with slightly reduced affinities. MelBSt is more thermostable than MelBEc, and the thermostability of either MelB is largely increased in MNG-3 or GDN. Therefore, the functional defect with DDM or UDM likely results from the relative instability of the sensitive MelB proteins, and stability, as well as galactoside binding, is retained in MNG-3 or GDN. Furthermore, isothermal titration calorimetry of melibiose binding with MelBSt shows that the favorable entropic contribution to the binding free energy is decreased in MNG-3, indicating that the conformational dynamics of MelB is restricted in this detergent.
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Affiliation(s)
- Anowarul Amin
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center , Lubbock, Texas 79430, United States
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center , Lubbock, Texas 79430, United States
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University , Ansan 426-791, Korea
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center , Lubbock, Texas 79430, United States
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63
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Manglik A, Kim T, Masureel M, Altenbach C, Yang Z, Hilger D, Lerch M, Kobilka T, Thian F, Hubbell W, Prosser R, Kobilka B. Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling. Cell 2015. [DOI: 10.1016/j.cell.2015.08.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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64
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GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM. Structure 2015; 23:1769-1775. [DOI: 10.1016/j.str.2015.06.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/02/2015] [Accepted: 06/04/2015] [Indexed: 12/21/2022]
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65
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Jaremko Ł, Jaremko M, Nowakowski M, Ejchart A. The Quest for Simplicity: Remarks on the Free-Approach Models. J Phys Chem B 2015; 119:11978-87. [PMID: 26301699 DOI: 10.1021/acs.jpcb.5b07181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear magnetic relaxation provides a powerful method giving insight into molecular motions at atomic resolution on a broad time scale. Dynamics of biological macromolecules has been widely exploited by measuring (15)N and (13)C relaxation data. Interpretation of these data relies almost exclusively on the use of the model-free approach (MFA) and its extended version (EMFA) which requires no particular physical model of motion and a small number of parameters. It is shown that EMFA is often unable to cope with three different time scales and fails to describe slow internal motions properly. In contrast to EMFA, genuine MFA with two time scales can reproduce internal motions slower than the overall tumbling. It is also shown that MFA and simplified EMFA are equivalent with respect to the values of the N-H bond length and chemical shift anisotropy. Therefore, the vast majority of (15)N relaxation data for proteins can be satisfactorily interpreted solely with MFA.
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Affiliation(s)
- Łukasz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Am Fassberg 11, 37077 Göttingen, Germany
| | - Mariusz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Michał Nowakowski
- Centre of New Technologies, University of Warsaw , Banacha 2C, 02-097 Warsaw, Poland
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawinskiego 5A, 02-106 Warsaw, Poland
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66
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Thomas L, Kahr J, Schmidt P, Krug U, Scheidt HA, Huster D. The dynamics of the G protein-coupled neuropeptide Y2 receptor in monounsaturated membranes investigated by solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2015; 61:347-59. [PMID: 25556885 DOI: 10.1007/s10858-014-9892-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/20/2014] [Indexed: 05/14/2023]
Abstract
In contrast to the static snapshots provided by protein crystallography, G protein-coupled receptors constitute a group of proteins with highly dynamic properties, which are required in the receptors' function as signaling molecule. Here, the human neuropeptide Y2 receptor was reconstituted into a model membrane composed of monounsaturated phospholipids and solid-state NMR was used to characterize its dynamics. Qualitative static (15)N NMR spectra and quantitative determination of (1)H-(13)C order parameters through measurement of the (1)H-(13)C dipolar couplings of the CH, CH2 and CH3 groups revealed axially symmetric motions of the whole molecule in the membrane and molecular fluctuations of varying amplitude from all molecular segments. The molecular order parameters (S(backbone) = 0.59-0.67, S(CH2) = 0.41-0.51 and S(CH3) = 0.22) obtained in directly polarized (13)C NMR experiments demonstrate that the Y2 receptor is highly mobile in the native-like membrane. Interestingly, according to these results the receptor was found to be slightly more rigid in the membranes formed by the monounsaturated phospholipids than by saturated phospholipids as investigated previously. This could be caused by an increased chain length of the monounsaturated lipids, which may result in a higher helical content of the receptor. Furthermore, the incorporation of cholesterol, phosphatidylethanolamine, or negatively charged phosphatidylserine into the membrane did not have a significant influence on the molecular mobility of the Y2 receptor.
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Affiliation(s)
- Lars Thomas
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, 04107, Leipzig, Germany
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67
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Li S, Lee SY, Chung KY. Conformational analysis of g protein-coupled receptor signaling by hydrogen/deuterium exchange mass spectrometry. Methods Enzymol 2015; 557:261-78. [PMID: 25950969 DOI: 10.1016/bs.mie.2014.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Conformational change and protein-protein interactions are two major mechanisms of membrane protein signal transduction, including G protein-coupled receptors (GPCRs). Upon agonist binding, GPCRs change conformation, resulting in interaction with downstream signaling molecules such as G proteins. To understand the precise signaling mechanism, studies have investigated the structural mechanism of GPCR signaling using X-ray crystallography, nuclear magnetic resonance (NMR), or electron paramagnetic resonance. In addition to these techniques, hydrogen/deuterium exchange mass spectrometry (HDX-MS) has recently been used in GPCR studies. HDX-MS measures the rate at which peptide amide hydrogens exchange with deuterium in the solvent. Exposed or flexible regions have higher exchange rates and excluded or ordered regions have lower exchange rates. Therefore, HDX-MS is a useful tool for studying protein-protein interfaces and conformational changes after protein activation or protein-protein interactions. Although HDX-MS does not give high-resolution structures, it analyzes protein conformations that are difficult to study with X-ray crystallography or NMR. Furthermore, conformational information from HDX-MS can help in the crystallization of X-ray crystallography by suggesting highly flexible regions. Interactions between GPCRs and downstream signaling molecules are not easily analyzed by X-ray crystallography or NMR because of the large size of the GPCR-signaling molecule complexes, hydrophobicity, and flexibility of GPCRs. HDX-MS could be useful for analyzing the conformational mechanism of GPCR signaling. In this chapter, we discuss details of HDX-MS for analyzing GPCRs using the β2AR-G protein complex as a model system.
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Affiliation(s)
- Sheng Li
- Department of Medicine, University of California at San Diego, San Diego, California, USA
| | - Su Youn Lee
- 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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68
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Abstract
Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies.
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Affiliation(s)
- Rieko Ishima
- Address correspondence to Rieko Ishima: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Tel: 412-648-9056; Fax: 412-648-9008;
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69
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Prosser RS, Kim TH. Nuts and Bolts of CF3 and CH 3 NMR Toward the Understanding of Conformational Exchange of GPCRs. Methods Mol Biol 2015; 1335:39-51. [PMID: 26260593 DOI: 10.1007/978-1-4939-2914-6_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
With the advent of efficient protein expression and functional purification protocols, it is now possible to reconstitute many G protein-coupled receptors (GPCRs) in detergent micelles at concentrations of 25 μM or more. Such concentrations are sufficient for studies of conformational states and dynamics relating to function and the mechanism of activation of GPCRs, using solution state NMR. In particular, methyl spectroscopy, in the form of one-dimensional (19)F NMR or two-dimensional ((1)H,(13)C) NMR, provides high fidelity spectra which reveal detailed features associated with conformational states and their lifetimes, as a function of ligand. While X-ray crystallography provides exquisitely detailed structures of lowest energy states associated with ligands, G proteins, and other proteins, NMR is able to validate such states, while providing insight into higher energy states that form part of the conformational landscape and are involved in activation. Through relaxation experiments spanning microseconds to seconds, lifetimes of these functional states can often be measured. By determining the effect of ligands on both equilibrium populations and rates of interconversion between states, it becomes possible to understand activation in terms of an ensemble description and in turn relate the ensemble to pharmaceutical phenomena.
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Affiliation(s)
- R Scott Prosser
- Department of Chemistry, University of Toronto (UTM), 3359 Mississauga Road North, Mississauga, ON, Canada, L5L 1C6,
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70
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Stubborn contaminants: influence of detergents on the purity of the multidrug ABC transporter BmrA. PLoS One 2014; 9:e114864. [PMID: 25517996 PMCID: PMC4269414 DOI: 10.1371/journal.pone.0114864] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022] Open
Abstract
Despite the growing interest in membrane proteins, their crystallization remains a major challenge. In the course of a crystallographic study on the multidrug ATP-binding cassette transporter BmrA, mass spectral analyses on samples purified with six selected detergents revealed unexpected protein contamination visible for the most part on overloaded SDS-PAGE. A major contamination from the outer membrane protein OmpF was detected in purifications with Foscholine 12 (FC12) but not with Lauryldimethylamine-N-oxide (LDAO) or any of the maltose-based detergents. Consequently, in the FC12 purified BmrA, OmpF easily crystallized over BmrA in a new space group, and whose structure is reported here. We therefore devised an optimized protocol to eliminate OmpF during the FC12 purification of BmrA. On the other hand, an additional band visible at ∼110 kDa was detected in all samples purified with the maltose-based detergents. It contained AcrB that crystallized over BmrA despite its trace amounts. Highly pure BmrA preparations could be obtained using either a ΔacrAB E. coli strain and n-dodecyl-β-D-maltopyranoside, or a classical E. coli strain and lauryl maltose neopentyl glycol for the overexpression and purification, respectively. Overall our results urge to incorporate a proteomics-based purity analysis into quality control checks prior to commencing crystallization assays of membrane proteins that are notoriously arduous to crystallize. Moreover, the strategies developed here to selectively eliminate obstinate contaminants should be applicable to the purification of other membrane proteins overexpressed in E. coli.
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71
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Zhang X, Miller KW. Dodecyl maltopyranoside enabled purification of active human GABA type A receptors for deep and direct proteomic sequencing. Mol Cell Proteomics 2014; 14:724-38. [PMID: 25473089 DOI: 10.1074/mcp.m114.042556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The challenge in high-quality membrane proteomics is all about sample preparation prior to HPLC, and the cell-to-protein step poses a long-standing bottleneck. Traditional protein extraction methods apply ionic or poly-disperse detergents, harsh denaturation, and repeated protein/peptide precipitation/resolubilization afterward, but suffer low yield, low reproducibility, and low sequence coverage. Contrary to attempts to subdue, we resolved this challenge by providing proteins nature-and-activity-promoting conditions throughout preparation. Using 285-kDa hetero-pentameric human GABA type A receptor overexpressed in HEK293 as a model, we describe a n-dodecyl-β-d-maltopyranoside/cholesteryl hemisuccinate (DDM/CHS)-based affinity purification method, that produced active receptors, supported protease activity, and allowed high performance with both in-gel and direct gel-free proteomic analyses-without detergent removal. Unlike conventional belief that detergents must be removed before HPLC MS, the high-purity low-dose nonionic detergent DDM did not interfere with peptides, and obviated removal or desalting. Sonication or dropwise addition of detergent robustly solubilized over 90% of membrane pellets. The purification conditions were comparable to those applied in successful crystallizations of most membrane proteins. These results enabled streamlined proteomics of human synaptic membrane proteins, and more importantly, allowed directly coupling proteomics with crystallography to characterize both static and dynamic structures of membrane proteins in crystallization pipelines.
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Affiliation(s)
- Xi Zhang
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, §Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Keith W Miller
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, §Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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72
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Loll PJ. Membrane proteins, detergents and crystals: what is the state of the art? ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1576-83. [PMID: 25484203 DOI: 10.1107/s2053230x14025035] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022]
Abstract
At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures published since 2012 reveals that the direct crystallization of protein-detergent complexes remains the dominant methodology; in addition, lipidic mesophases have proven immensely useful, particularly in specific niches, and bicelles, while perhaps undervalued, have provided important contributions as well. Evolving trends include the addition of lipids to protein-detergent complexes and the gradual incorporation of new detergents into the standard repertoire. Stability has emerged as a critical parameter controlling how a membrane protein behaves in the presence of detergent, and efforts to enhance stability are discussed. Finally, although discovery-based screening approaches continue to dwarf mechanistic efforts to unravel crystallization, recent technical advances offer hope that future experiments might incorporate the rational manipulation of crystallization behaviors.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
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73
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LeVine MV, Weinstein H. NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS Comput Biol 2014; 10:e1003603. [PMID: 24785005 PMCID: PMC4006702 DOI: 10.1371/journal.pcbi.1003603] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/24/2014] [Indexed: 11/23/2022] Open
Abstract
Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems. We developed the new information theory-based analysis framework presented here, NbIT analysis, for the study of allosteric mechanisms in biomolecular systems from Molecular Dynamics trajectories. The illustrative application of NbIT to the analysis of the occluded state in the bacterial transporter LeuT, produced a quantitative representation of the allosteric behavior, and identified intramolecular channels that enable the long-distance information transmission. Our findings, identifying the roles of specific residues in the communication of the allosteric information, were validated by the recognition of residues that have been previously shown to play functional roles in this very well studied system. In addition, we show that application of NbIT analysis leads to the discrimination of functional roles by differentiating between residues that are essential to the dynamics within functional sites (e.g., the substrate binding sites), and residues whose role is to communicate between such functional sites. These results demonstrate that the information theoretical analysis presented here is a powerful tool for quantifying complex allosteric behavior in biomolecular systems and for identifying the crucial components underlying those behaviors.
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Affiliation(s)
- Michael V. LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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74
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Lee S, Bhattacharya S, Grisshammer R, Tate C, Vaidehi N. Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor. J Phys Chem B 2014; 118:3355-65. [PMID: 24579769 PMCID: PMC3983344 DOI: 10.1021/jp411618h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
The adenosine A2A receptor
(A2AR) belongs
to the superfamily of membrane proteins called the G-protein-coupled
receptors (GPCRs) that form one of the largest superfamilies of drug
targets. Deriving thermostable mutants has been one of the strategies
used for crystallization of A2AR in both the agonist and
antagonist bound conformational states. The crystal structures do
not reveal differences in the activation mechanism of the mutant receptors
compared to the wild type receptor, that have been observed experimentally.
These differences stem from the dynamic behavior of the mutant receptors.
Furthermore, it is not understood how the mutations confer thermostability.
Since these details are difficult to obtain from experiments, we have
used atomic level simulations to elucidate the dynamic behavior of
the agonist and antagonist bound mutants as well the wild type A2AR. We found that significant enthalpic contribution leads
to stabilization of both the inactive state (StaR2) and active-like
state (GL31) thermostable mutants of A2AR. Stabilization
resulting from mutations of bulky residues to alanine is due to the
formation of interhelical hydrogen bonds and van der Waals packing
that improves the transmembrane domain packing. The thermostable mutant
GL31 shows less movement of the transmembrane helix TM6 with respect
to TM3 than the wild type receptor. While restricted dynamics of GL31
is advantageous in its purification and crystallization, it could
also be the reason why these mutants are not efficient in activating
the G proteins. We observed that the calculated stress on each residue
is higher in the wild type receptor compared to the thermostable mutants,
and this stress is required for activation to occur. Thus, reduced
dynamic behavior of the thermostable mutants leading to lowered activation
of these receptors originates from reduced stress on each residue.
Finally, accurate calculation of the change in free energy for single
mutations shows good correlation with the change in the measured thermostability.
These results provide insights into the effect of mutations that can
be incorporated in deriving thermostable mutants for other GPCRs.
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Affiliation(s)
- Sangbae Lee
- Division of Immunology, Beckman Research Institute of the City of Hope , 1500 East Duarte Road, Duarte, California 91010, United States
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75
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Sridharan R, Zuber J, Connelly SM, Mathew E, Dumont ME. Fluorescent approaches for understanding interactions of ligands with G protein coupled receptors. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:15-33. [PMID: 24055822 PMCID: PMC3926105 DOI: 10.1016/j.bbamem.2013.09.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 09/03/2013] [Accepted: 09/08/2013] [Indexed: 11/18/2022]
Abstract
G protein coupled receptors are responsible for a wide variety of signaling responses in diverse cell types. Despite major advances in the determination of structures of this class of receptors, the underlying mechanisms by which binding of different types of ligands specifically elicits particular signaling responses remain unclear. The use of fluorescence spectroscopy can provide important information about the process of ligand binding and ligand dependent conformational changes in receptors, especially kinetic aspects of these processes that can be difficult to extract from X-ray structures. We present an overview of the extensive array of fluorescent ligands that have been used in studies of G protein coupled receptors and describe spectroscopic approaches for assaying binding and probing the environment of receptor-bound ligands with particular attention to examples involving yeast pheromone receptors. In addition, we discuss the use of fluorescence spectroscopy for detecting and characterizing conformational changes in receptors induced by the binding of ligands. Such studies have provided strong evidence for diversity of receptor conformations elicited by different ligands, consistent with the idea that GPCRs are not simple on and off switches. This diversity of states constitutes an underlying mechanistic basis for biased agonism, the observation that different stimuli can produce different responses from a single receptor. It is likely that continued technical advances will allow fluorescence spectroscopy to play an important role in continued probing of structural transitions in G protein coupled receptors. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Rajashri Sridharan
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Jeffrey Zuber
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Sara M. Connelly
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Elizabeth Mathew
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Mark E. Dumont
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
- Department of Pediatrics, P.O. Box 777, University of Rochester Medical Center, Rochester, NY 14642
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76
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Horst R, Liu JJ, Stevens RC, Wüthrich K. β₂-adrenergic receptor activation by agonists studied with ¹⁹F NMR spectroscopy. Angew Chem Int Ed Engl 2013; 52:10762-5. [PMID: 23956158 DOI: 10.1002/anie.201305286] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Reto Horst
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA); Present address: Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340 (USA)
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77
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β2-Adrenergic Receptor Activation by Agonists Studied with19F NMR Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305286] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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78
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Fluorine-19 NMR of integral membrane proteins illustrated with studies of GPCRs. Curr Opin Struct Biol 2013; 23:740-747. [PMID: 23932201 DOI: 10.1016/j.sbi.2013.07.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 07/02/2013] [Indexed: 01/26/2023]
Abstract
Fluorine-19 is a spin-½ NMR isotope with high sensitivity and large chemical shift dispersion, which makes it attractive for high resolution NMR spectroscopy in solution. For studies of membrane proteins it is further of interest that (19)F is rarely found in biological materials, which enables observation of extrinsic (19)F labels with minimal interference from background signals. Today, after a period with rather limited use of (19)F NMR in structural biology, we witness renewed interest in this technology for studies of complex supramolecular systems. Here we report on recent (19)F NMR studies with the G protein-coupled receptor family of membrane proteins.
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79
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Williams JK, Tietze D, Wang J, Wu Y, DeGrado WF, Hong M. Drug-induced conformational and dynamical changes of the S31N mutant of the influenza M2 proton channel investigated by solid-state NMR. J Am Chem Soc 2013; 135:9885-97. [PMID: 23758317 DOI: 10.1021/ja4041412] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The M2 protein of influenza A viruses forms a tetrameric proton channel that is targeted by the amantadine class of antiviral drugs. A S31N mutation in the transmembrane (TM) domain of the protein has caused widespread amantadine resistance in most of the currently circulating flu viruses. Recently, a new family of compounds based on amantadine- and aryl-substituted isoxazole were discovered to inhibit the S31N channel activity and reduce replication of S31N-harboring viruses. We now use solid-state NMR spectroscopy to investigate the effects of one of these isoxazole compounds, WJ352, on the conformation of the S31N TM segment and the dynamics of the proton-selective residue, His37. Chemical shift perturbations show that WJ352 changes the conformational equilibrium of multiple TM residues, with the maximal perturbation occurring at the crucial Asn31. (13)C-(2)H distance measurements and (1)H-(1)H NOE cross peaks indicate that the adamantane moiety of the drug is bound in the spacious pore between Asn31 and Gly34 while the phenyl tail is located near Val27. Thus, the polar amine points to the channel exterior rather than to His37, in contrast to amantadine and rimantadine in the wild-type channel, suggesting that the drug is significantly stabilized by hydrophobic interactions between the adamantane and the TM peptide. (15)N and (13)C chemical shifts indicate that at low pH, His37 undergoes fast exchange among the τ tautomer, the π tautomer, and the cationic state due to proton transfer with water. The exchange rate is higher than the wild-type channel, consistent with the larger single-channel conductance of the mutant. Drug binding at acidic pH largely suppresses this exchange, reverting the histidines to a similar charge distribution as that of the high-pH closed state.
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80
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Kim TH, Chung KY, Manglik A, Hansen AL, Dror RO, Mildorf TJ, Shaw DE, Kobilka BK, Prosser RS. The role of ligands on the equilibria between functional states of a G protein-coupled receptor. J Am Chem Soc 2013; 135:9465-74. [PMID: 23721409 DOI: 10.1021/ja404305k] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G protein-coupled receptors exhibit a wide variety of signaling behaviors in response to different ligands. When a small label was incorporated on the cytosolic interface of transmembrane helix 6 (Cys-265), (19)F NMR spectra of the β2 adrenergic receptor (β2AR) reconstituted in maltose/neopentyl glycol detergent micelles revealed two distinct inactive states, an activation intermediate state en route to activation, and, in the presence of a G protein mimic, a predominant active state. Analysis of the spectra as a function of temperature revealed that for all ligands, the activation intermediate is entropically favored and enthalpically disfavored. β2AR enthalpy changes toward activation are notably lower than those observed with rhodopsin, a likely consequence of basal activity and the fact that the ionic lock and other interactions stabilizing the inactive state of β2AR are weaker. Positive entropy changes toward activation likely reflect greater mobility (configurational entropy) in the cytoplasmic domain, as confirmed through an order parameter analysis. Ligands greatly influence the overall changes in enthalpy and entropy of the system and the corresponding changes in population and amplitude of motion of given states, suggesting a complex landscape of states and substates.
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Affiliation(s)
- Tae Hun Kim
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6
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Yan N. Structural advances for the major facilitator superfamily (MFS) transporters. Trends Biochem Sci 2013; 38:151-9. [PMID: 23403214 DOI: 10.1016/j.tibs.2013.01.003] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 01/18/2023]
Abstract
The major facilitator superfamily (MFS) is one of the largest groups of secondary active transporters conserved from bacteria to humans. MFS proteins selectively transport a wide spectrum of substrates across biomembranes and play a pivotal role in multiple physiological processes. Despite intense investigation, only seven MFS proteins from six subfamilies have been structurally elucidated. These structures were captured in distinct states during a transport cycle involving alternating access to binding sites from either side of the membrane. This review discusses recent progress in MFS structure analysis and focuses on the molecular basis for substrate binding, co-transport coupling, and alternating access.
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Affiliation(s)
- Nieng Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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