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İnak E, De Rouck S, Koç-İnak N, Erdem E, Rüstemoğlu M, Dermauw W, Van Leeuwen T. Identification and CRISPR-Cas9 validation of a novel β-adrenergic-like octopamine receptor mutation associated with amitraz resistance in Varroa destructor. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 204:106080. [PMID: 39277393 DOI: 10.1016/j.pestbp.2024.106080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 08/07/2024] [Indexed: 09/17/2024]
Abstract
Varroa destructor is widely recognized as a significant contributor to colony collapse disorder. Chemical acaricides, such as amitraz, have been extensively used for Varroa control due to their selectivity within beehives. However, the increasing number of cases of amitraz resistance across global V. destructor populations poses a significant challenge. In this study, we conducted a comprehensive molecular screening of the β-adrenergic-like octopamine receptor (Octβ2R), the target-site of amitraz, across 66 Turkish and 63 Belgian V. destructor populations. Although previously reported amitraz resistance mutations were not detected, the screening revealed a novel Y337F mutation located within transmembrane 7 (TM7) of Octβ2R in Turkish Varroa populations. Notably, this mutation was identified in the last residue of the highly conserved NPxxY motif associated with the activation of G-protein coupled receptors (GPCR). Among the 66 Varroa samples from Türkiye, twenty harbored the Y337F mutation, with eight samples exhibiting fixation of the mutation. Subsequent bioassays revealed over 8-fold resistance to amitraz in populations that contain the Y337F mutation. Genotyping of mites after exposure to 10 mg a.i./l amitraz demonstrated that all surviving mites were homozygous for the Y337F mutation, whereas dead mites carried susceptible alleles, providing genetic linkage between mutation and phenotype. Further, we used CRISPR-Cas9 editing to introduce the Y337F mutation in the orthologous Octβ2R of the model organism Tetranychus urticae. Crispants exhibited over threefold resistance to amitraz. In conclusion, this study identified and validated a novel amitraz resistance mutation. Additional research is required to further evaluate the phenotypic strength of Y337F in the context of operational resistance with current treatment strategies.
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Affiliation(s)
- Emre İnak
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Department of Plant Protection, Faculty of Agriculture, Ankara University, Diskapi, 06110, Ankara, Türkiye.
| | - Sander De Rouck
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Nafiye Koç-İnak
- Department of Parasitology, Faculty of Veterinary Medicine, Ankara University, Altindag, 06070, Ankara, Türkiye.
| | - Esengül Erdem
- Plant Protection Department, Faculty of Agriculture, Şırnak University, Şırnak, Türkiye.
| | - Mustafa Rüstemoğlu
- Plant Protection Department, Faculty of Agriculture, Şırnak University, Şırnak, Türkiye
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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2
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Bertalan É, Rodrigues MJ, Schertler GFX, Bondar AN. Graph-based algorithms to dissect long-distance water-mediated H-bond networks for conformational couplings in GPCRs. Br J Pharmacol 2024. [PMID: 38636539 DOI: 10.1111/bph.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/03/2024] [Accepted: 03/02/2024] [Indexed: 04/20/2024] Open
Abstract
Changes in structure and dynamics elicited by agonist ligand binding at the extracellular side of G protein coupled receptors (GPCRs) must be relayed to the cytoplasmic G protein binding side of the receptors. To decipher the role of water-mediated hydrogen-bond networks in this relay mechanism, we have developed graph-based algorithms and analysis methodologies applicable to datasets of static structures of distinct GPCRs. For a reference dataset of static structures of bovine rhodopsin solved at the same resolution, we show that graph analyses capture the internal protein-water hydrogen-bond network. The extended analyses of static structures of rhodopsins and opioid receptors suggest a relay mechanism whereby inactive receptors have in place much of the internal core hydrogen-bond network required for long-distance relay of structural change, with extensive local H-bond clusters observed in structures solved at high resolution and with internal water molecules.
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Affiliation(s)
- Éva Bertalan
- Physikzentrum, RWTH-Aachen University, Aachen, Germany
| | | | | | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany
- Faculty of Physics, University of Bucharest, Măgurele, Romania
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3
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Rodgers J, Wright P, Ballister ER, Hughes RB, Storchi R, Wynne J, Martial FP, Lucas RJ. Modulating signalling lifetime to optimise a prototypical animal opsin for optogenetic applications. Pflugers Arch 2023; 475:1387-1407. [PMID: 38036775 PMCID: PMC10730688 DOI: 10.1007/s00424-023-02879-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Animal opsins are light activated G-protein-coupled receptors, capable of optogenetic control of G-protein signalling for research or therapeutic applications. Animal opsins offer excellent photosensitivity, but their temporal resolution can be limited by long photoresponse duration when expressed outside their native cellular environment. Here, we explore methods for addressing this limitation for a prototypical animal opsin (human rod opsin) in HEK293T cells. We find that the application of the canonical rhodopsin kinase (GRK1)/visual arrestin signal termination mechanism to this problem is complicated by a generalised suppressive effect of GRK1 expression. This attenuation can be overcome using phosphorylation-independent mutants of arrestin, especially when these are tethered to the opsin protein. We further show that point mutations targeting the Schiff base stability of the opsin can also reduce signalling lifetime. Finally, we apply one such mutation (E122Q) to improve the temporal fidelity of restored visual responses following ectopic opsin expression in the inner retina of a mouse model of retinal degeneration (rd1). Our results reveal that these two strategies (targeting either arrestin binding or Schiff-base hydrolysis) can produce more time-delimited opsin signalling under heterologous expression and establish the potential of this approach to improve optogenetic performance.
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Affiliation(s)
- Jessica Rodgers
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
| | - Phillip Wright
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Edward R Ballister
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons of Columbia University, New York, 10032, NY, USA
| | - Rebecca B Hughes
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Riccardo Storchi
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Jonathan Wynne
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Franck P Martial
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Robert J Lucas
- Centre for Biological Timing, Division of Neuroscience, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
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4
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Abstract
Rhodopsin is the photoreceptor in human rod cells responsible for dim-light vision. The visual receptors are part of the large superfamily of G protein-coupled receptors (GPCRs) that mediate signal transduction in response to diverse diffusible ligands. The high level of sequence conservation within the transmembrane helices of the visual receptors and the family A GPCRs has long been considered evidence for a common pathway for signal transduction. I review recent studies that reveal a comprehensive mechanism for how light absorption by the retinylidene chromophore drives rhodopsin activation and highlight those features of the mechanism that are conserved across the ligand-activated GPCRs.
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Affiliation(s)
- Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA;
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5
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Sano FK, Akasaka H, Shihoya W, Nureki O. Cryo-EM structure of the endothelin-1-ET B-G i complex. eLife 2023; 12:85821. [PMID: 37096326 PMCID: PMC10129325 DOI: 10.7554/elife.85821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/23/2023] [Indexed: 04/26/2023] Open
Abstract
The endothelin ETB receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ETB signaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle. Consequently, ETB agonists are expected to be drugs for neuroprotection and improved anti-tumor drug delivery. Here, we report the cryo-electron microscopy structure of the endothelin-1-ETB-Gi complex at 2.8 Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ETB receptor structures revealed how endothelin-1 activates the ETB receptor. The NPxxY motif, essential for G-protein activation, is not conserved in ETB, resulting in a unique structural change upon G-protein activation. Compared with other GPCR-G-protein complexes, ETB binds Gi in the shallowest position, further expanding the diversity of G-protein binding modes. This structural information will facilitate the elucidation of G-protein activation and the rational design of ETB agonists.
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Affiliation(s)
- Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Akasaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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6
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Inukai S, Katayama K, Koyanagi M, Terakita A, Kandori H. Counterion at an atypical position: Investigating the mechanism of photoisomerization in jellyfish rhodopsin. J Biol Chem 2023; 299:104726. [PMID: 37094700 DOI: 10.1016/j.jbc.2023.104726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 04/26/2023] Open
Abstract
The position of the counterion in animal rhodopsins plays a crucial role in maintaining visible light sensitivity and facilitating the photoisomerization of their retinal chromophore. The counterion displacement is thought to be closely related to the evolution of rhodopsins, with different positions found in invertebrates and vertebrates. Interestingly, box jellyfish rhodopsin (JelRh) acquired the counterion in transmembrane 2 (TM2) independently. This is a unique feature, as in most animal rhodopsins, the counterion is found in a different location. In this study, we used Fourier Transform Infrared spectroscopy to examine the structural changes that occur in the early photointermediate state of JelRh. We aimed to determine whether the photochemistry of JelRh is similar to that of other animal rhodopsins by comparing its spectra to those of vertebrate bovine rhodopsin (BovRh) and invertebrate squid rhodopsin (SquRh). We observed that the N-D stretching band of the retinal Schiff base was similar to that of BovRh, indicating the interaction between the Schiff base and the counterion is similar in both rhodopsins, despite their different counterion positions. Furthermore, we found that the chemical structure of the retinal in JelRh is similar to that in BovRh, including the changes in the hydrogen-out-of-plane band that indicates a retinal distortion. Overall, the protein conformational changes induced by the photoisomerization of JelRh yielded spectra that resemble an intermediate between BovRh and SquRh, suggesting a unique spectral property of JelRh, and making it the only animal rhodopsin with a counterion in TM2 and an ability to activate Gs protein.
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Affiliation(s)
- Shino Inukai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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7
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Abiko LA, Dias Teixeira R, Engilberge S, Grahl A, Mühlethaler T, Sharpe T, Grzesiek S. Filling of a water-free void explains the allosteric regulation of the β 1-adrenergic receptor by cholesterol. Nat Chem 2022; 14:1133-1141. [PMID: 35953642 DOI: 10.1038/s41557-022-01009-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
Recent high-pressure NMR results indicate that the preactive conformation of the β1-adrenergic receptor (β1AR) harbours completely empty cavities of ~100 Å3 volume, which disappear in the active conformation of the receptor. Here we have localized these cavities using X-ray crystallography of xenon-derivatized β1AR crystals. One of the cavities is in direct contact with the cholesterol-binding pocket. Solution NMR shows that addition of the cholesterol analogue cholesteryl hemisuccinate impedes the formation of the active conformation of detergent-solubilized β1AR by blocking conserved G protein-coupled receptor microswitches, concomitant with an affinity reduction of both isoprenaline and G protein-mimicking nanobody Nb80 for β1AR detected by isothermal titration calorimetry. This wedge-like action explains the function of cholesterol as a negative allosteric modulator of β1AR. A detailed understanding of G protein-coupled receptor regulation by cholesterol by filling of a dry void and the easy scouting for such voids by xenon may provide new routes for the development of allosteric drugs.
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Affiliation(s)
| | | | - Sylvain Engilberge
- Paul Scherrer Institut, Villigen, Switzerland.,European Synchrotron Radiation Facility, Grenoble, France
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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8
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Yen YC, Schafer CT, Gustavsson M, Eberle SA, Dominik PK, Deneka D, Zhang P, Schall TJ, Kossiakoff AA, Tesmer JJG, Handel TM. Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. SCIENCE ADVANCES 2022; 8:eabn8063. [PMID: 35857509 PMCID: PMC9278869 DOI: 10.1126/sciadv.abn8063] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/26/2022] [Indexed: 05/12/2023]
Abstract
Both CXC chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3) are activated by the chemokine CXCL12 yet evoke distinct cellular responses. CXCR4 is a canonical G protein-coupled receptor (GPCR), whereas ACKR3 is intrinsically biased for arrestin. The molecular basis for this difference is not understood. Here, we describe cryo-EM structures of ACKR3 in complex with CXCL12, a more potent CXCL12 variant, and a small-molecule agonist. The bound chemokines adopt an unexpected pose relative to those established for CXCR4 and observed in other receptor-chemokine complexes. Along with functional studies, these structures provide insight into the ligand-binding promiscuity of ACKR3, why it fails to couple to G proteins, and its bias toward β-arrestin. The results lay the groundwork for understanding the physiological interplay of ACKR3 with other GPCRs.
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Affiliation(s)
- Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Christopher T. Schafer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stefanie A. Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Pawel K. Dominik
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Dawid Deneka
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Department of Biophysics, Jagiellonian University, Krakow, Poland
| | - Penglie Zhang
- ChemoCentryx Inc., 835 Industrial Rd., Suite 600, San Carlos, CA 94070, USA
| | - Thomas J. Schall
- ChemoCentryx Inc., 835 Industrial Rd., Suite 600, San Carlos, CA 94070, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - John J. G. Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Molecular Pharmacology and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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9
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Huang SK, Prosser RS. Dynamics and Mechanistic Underpinnings to Pharmacology of Class A GPCRs - An NMR Perspective. Am J Physiol Cell Physiol 2022; 322:C739-C753. [PMID: 35235425 DOI: 10.1152/ajpcell.00044.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
One-third of current pharmaceuticals target G protein-coupled receptors (GPCRs), the largest receptor superfamily in humans and mediators of diverse physiological processes. This review summarizes the recent progress in GPCR structural dynamics, focusing on class A receptors and insights derived from nuclear magnetic resonance (NMR) and other spectroscopic techniques. We describe the structural aspects of GPCR activation and the various pharmacological models that capture aspects of receptor signaling behaviour. Spectroscopic studies revealed that receptors and their signaling complexes are dynamic allosteric systems that sample multiple functional states under basal conditions. The distribution of states within the conformational ensemble and the kinetics of transitions between states are regulated through the binding of ligands, allosteric modulators, and the membrane environment. This ensemble view of GPCRs provides a mechanistic framework for understanding many of the pharmacological phenomena associated with receptor signaling, such as basal activity, efficacy, and functional bias.
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Affiliation(s)
- Shuya Kate Huang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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10
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Chandler B, Todd L, Smith SO. Magic angle spinning NMR of G protein-coupled receptors. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:25-43. [PMID: 35282868 PMCID: PMC10718405 DOI: 10.1016/j.pnmrs.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) have a simple seven transmembrane helix architecture which has evolved to recognize a diverse number of chemical signals. The more than 800 GPCRs encoded in the human genome function as receptors for vision, smell and taste, and mediate key physiological processes. Consequently, these receptors are a major target for pharmaceuticals. Protein crystallography and electron cryo-microscopy have provided high resolution structures of many GPCRs in both active and inactive conformations. However, these structures have not sparked a surge in rational drug design, in part because GPCRs are inherently dynamic and the structural changes induced by ligand or drug binding to stabilize inactive or active conformations are often subtle rearrangements in packing or hydrogen-bonding interactions. NMR spectroscopy provides a sensitive probe of local structure and dynamics at specific sites within these receptors as well as global changes in receptor structure and dynamics. These methods can also capture intermediate states and conformations with low populations that provide insights into the activation pathways. We review the use of solid-state magic angle spinning NMR to address the structure and activation mechanisms of GPCRs. The focus is on the large and diverse class A family of receptors. We highlight three specific class A GPCRs in order to illustrate how solid-state, as well as solution-state, NMR spectroscopy can answer questions in the field involving how different GPCR classes and subfamilies are activated by their associated ligands, and how small molecule drugs can modulate GPCR activation.
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Affiliation(s)
- Bianca Chandler
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Lauren Todd
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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11
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Smith SO. Deconstructing the transmembrane core of class A G protein-coupled receptors. Trends Biochem Sci 2021; 46:1017-1029. [PMID: 34538727 PMCID: PMC8595765 DOI: 10.1016/j.tibs.2021.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023]
Abstract
Class A G protein-coupled receptors have evolved to recognize ligands ranging from small-molecule odorants to proteins. Although they are among the most diverse membrane receptors in eukaryotic organisms, they possess a highly conserved core within their seven-transmembrane helix framework. The conservation of the transmembrane core has led to the idea of a common mechanism by which ligand binding is coupled to the outward rotation of helix H6, the hallmark of an active receptor. Nevertheless, there is still no consensus on the mechanism of coupling or on the roles of specific residues within the core. Recent insights from crystallography and NMR spectroscopy provide a way to decompose the core into its essential structural and functional elements that shed new light on this important region.
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Affiliation(s)
- Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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12
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Hilger D. The role of structural dynamics in GPCR‐mediated signaling. FEBS J 2021; 288:2461-2489. [DOI: 10.1111/febs.15841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel Hilger
- Department of Pharmaceutical Chemistry Philipps‐University Marburg Germany
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13
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Schafer CT, Shumate A, Farrens DL. Novel fluorescent GPCR biosensor detects retinal equilibrium binding to opsin and active G protein and arrestin signaling conformations. J Biol Chem 2020; 295:17486-17496. [PMID: 33453993 DOI: 10.1074/jbc.ra120.014631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/25/2020] [Indexed: 01/14/2023] Open
Abstract
Rhodopsin is a canonical class A photosensitive G protein-coupled receptor (GPCR), yet relatively few pharmaceutical agents targeting this visual receptor have been identified, in part due to the unique characteristics of its light-sensitive, covalently bound retinal ligands. Rhodopsin becomes activated when light isomerizes 11-cis-retinal into an agonist, all-trans-retinal (ATR), which enables the receptor to activate its G protein. We have previously demonstrated that, despite being covalently bound, ATR can display properties of equilibrium binding, yet how this is accomplished is unknown. Here, we describe a new approach for both identifying compounds that can activate and attenuate rhodopsin and testing the hypothesis that opsin binds retinal in equilibrium. Our method uses opsin-based fluorescent sensors, which directly report the formation of active receptor conformations by detecting the binding of G protein or arrestin fragments that have been fused onto the receptor's C terminus. We show that these biosensors can be used to monitor equilibrium binding of the agonist, ATR, as well as the noncovalent binding of β-ionone, an antagonist for G protein activation. Finally, we use these novel biosensors to observe ATR release from an activated, unlabeled receptor and its subsequent transfer to the sensor in real time. Taken together, these data support the retinal equilibrium binding hypothesis. The approach we describe should prove directly translatable to other GPCRs, providing a new tool for ligand discovery and mutant characterization.
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Affiliation(s)
- Christopher T Schafer
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA.
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14
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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15
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Pope AL, Sanchez-Reyes OB, South K, Zaitseva E, Ziliox M, Vogel R, Reeves PJ, Smith SO. A Conserved Proline Hinge Mediates Helix Dynamics and Activation of Rhodopsin. Structure 2020; 28:1004-1013.e4. [PMID: 32470317 DOI: 10.1016/j.str.2020.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 01/05/2023]
Abstract
Despite high-resolution crystal structures of both inactive and active G protein-coupled receptors (GPCRs), it is still not known how ligands trigger the large structural change on the intracellular side of the receptor since the conformational changes that occur within the extracellular ligand-binding region upon activation are subtle. Here, we use solid-state NMR and Fourier transform infrared spectroscopy on rhodopsin to show that Trp2656.48 within the CWxP motif on transmembrane helix H6 constrains a proline hinge in the inactive state, suggesting that activation results in unraveling of the H6 backbone within this motif, a local change in dynamics that allows helix H6 to swing outward. Notably, Tyr3017.48 within activation switch 2 appears to mimic the negative allosteric sodium ion found in other family A GPCRs, a finding that is broadly relevant to the mechanism of receptor activation.
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Affiliation(s)
- Andreyah L Pope
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Omar B Sanchez-Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Kieron South
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Ekaterina Zaitseva
- Biophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Hermann Herder Strasse, 79104 Freiburg, Germany
| | - Martine Ziliox
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Reiner Vogel
- Biophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Hermann Herder Strasse, 79104 Freiburg, Germany
| | - Philip J Reeves
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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16
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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: 35] [Impact Index Per Article: 8.8] [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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17
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Jung O, Beauvais DM, Adams KM, Rapraeger AC. VLA-4 phosphorylation during tumor and immune cell migration relies on its coupling to VEGFR2 and CXCR4 by syndecan-1. J Cell Sci 2019; 132:jcs.232645. [PMID: 31562188 DOI: 10.1242/jcs.232645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
When targeted by the tumor-promoting enzyme heparanase, cleaved and shed syndecan-1 (Sdc1) then couples VEGFR2 (also known as KDR) to VLA-4, activating VEGFR2 and the directed migration of myeloma cells. But how VEGFR2 activates VLA-4-mediated motility has remained unknown. We now report that VEGFR2 causes PKA-mediated phosphorylation of VLA-4 on S988, an event known to stimulate tumor metastasis while suppressing cytotoxic immune cells. A key partner in this mechanism is the chemokine receptor CXCR4, a well-known mediator of cell motility in response to gradients of the chemokine SDF-1 (also known as CXCL12). The entire machinery necessary to phosphorylate VLA-4, consisting of CXCR4, AC7 (also known as ADCY7) and PKA, is constitutively associated with VEGFR2 and is localized to the integrin by Sdc1. VEGFR2 carries out the novel phosphorylation of Y135 within the DRY microswitch of CXCR4, sequentially activating Gαiβγ, AC7 and PKA, which phosphorylates S988 on the integrin. This mechanism is blocked by a syndecan-mimetic peptide (SSTNVEGFR2), which, by preventing VEGFR2 linkage to VLA-4, arrests tumor cell migration that depends on VLA-4 phosphorylation and stimulates the LFA-1-mediated migration of cytotoxic leukocytes.
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Affiliation(s)
- Oisun Jung
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA.,Graduate Program in Molecular and Cellular Pharmacology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - DeannaLee M Beauvais
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Kristin M Adams
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
| | - Alan C Rapraeger
- Department of Human Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA .,Graduate Program in Molecular and Cellular Pharmacology, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705, USA
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18
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Varma N, Mutt E, Mühle J, Panneels V, Terakita A, Deupi X, Nogly P, Schertler GFX, Lesca E. Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR. Proc Natl Acad Sci U S A 2019; 116:14547-14556. [PMID: 31249143 PMCID: PMC6642406 DOI: 10.1073/pnas.1902192116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Light-sensitive G protein-coupled receptors (GPCRs)-rhodopsins-absorb photons to isomerize their covalently bound retinal, triggering conformational changes that result in downstream signaling cascades. Monostable rhodopsins release retinal upon isomerization as opposed to the retinal in bistable rhodopsins that "reisomerize" upon absorption of a second photon. Understanding the mechanistic differences between these light-sensitive GPCRs has been hindered by the scarcity of recombinant models of the latter. Here, we reveal the high-resolution crystal structure of a recombinant bistable rhodopsin, jumping spider rhodopsin-1, bound to the inverse agonist 9-cis retinal. We observe a water-mediated network around the ligand hinting toward the basis of their bistable nature. In contrast to bovine rhodopsin (monostable), the transmembrane bundle of jumping spider rhodopsin-1 as well that of the bistable squid rhodopsin adopts a more "activation-ready" conformation often observed in other nonphotosensitive class A GPCRs. These similarities suggest the role of jumping spider rhodopsin-1 as a potential model system in the study of the structure-function relationship of both photosensitive and nonphotosensitive class A GPCRs.
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Affiliation(s)
- Niranjan Varma
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Eshita Mutt
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Jonas Mühle
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Valérie Panneels
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Akihisa Terakita
- Department of Biology and Geosciences, Osaka City University, 558-8585 Osaka, Japan
| | - Xavier Deupi
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Gebhard F X Schertler
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland;
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Elena Lesca
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland;
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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19
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Van Nynatten A, Janzen FH, Brochu K, Maldonado-Ocampo JA, Crampton WGR, Chang BSW, Lovejoy NR. To see or not to see: molecular evolution of the rhodopsin visual pigment in neotropical electric fishes. Proc Biol Sci 2019; 286:20191182. [PMID: 31288710 DOI: 10.1098/rspb.2019.1182] [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: 12/12/2022] Open
Abstract
Functional variation in rhodopsin, the dim-light-specialized visual pigment, frequently occurs in species inhabiting light-limited environments. Variation in visual function can arise through two processes: relaxation of selection or adaptive evolution improving photon detection in a given environment. Here, we investigate the molecular evolution of rhodopsin in Gymnotiformes, an order of mostly nocturnal South American fishes that evolved sophisticated electrosensory capabilities. Our initial sequencing revealed a mutation associated with visual disease in humans. As these fishes are thought to have poor vision, this would be consistent with a possible sensory trade-off between the visual system and a novel electrosensory system. To investigate this, we surveyed rhodopsin from 147 gymnotiform species, spanning the order, and analysed patterns of molecular evolution. In contrast with our expectation, we detected strong selective constraint in gymnotiform rhodopsin, with rates of non-synonymous to synonymous substitutions lower in gymnotiforms than in other vertebrate lineages. In addition, we found evidence for positive selection on the branch leading to gymnotiforms and on a branch leading to a clade of deep-channel specialized gymnotiform species. We also found evidence that deleterious effects of a human disease-associated substitution are likely to be masked by epistatic substitutions at nearby sites. Our results suggest that rhodopsin remains an important component of the gymnotiform sensory system alongside electrolocation, and that photosensitivity of rhodopsin is well adapted for vision in dim-light environments.
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Affiliation(s)
- Alexander Van Nynatten
- 1 Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario , Canada M5S 3G5.,2 Department of Biological Sciences, University of Toronto Scarborough , Toronto, Ontario , Canada M1C 1A4
| | - Francesco H Janzen
- 3 Department of Biology, University of Ottawa , Ottawa, Ontario , Canada K1N 6N5.,4 Canadian Museum of Nature , Ottawa, Ontario , Canada K1P 6P4
| | - Kristen Brochu
- 5 Department of Entomology, Penn State University , University Park, Pennsylvania 16802 USA
| | - Javier A Maldonado-Ocampo
- 6 Laboratorio de Ictiología, Unidad de Ecología y Sistemática-UNESIS, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - William G R Crampton
- 7 Department of Biology, University of Central Florida , Orlando, FL 32816 , USA
| | - Belinda S W Chang
- 1 Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario , Canada M5S 3G5.,8 Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario , Canada M5S 3B2.,9 Centre for the Analysis of Genome Evolution and Function, University of Toronto , Toronto, Ontario , Canada M5S 3B2
| | - Nathan R Lovejoy
- 1 Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario , Canada M5S 3G5.,2 Department of Biological Sciences, University of Toronto Scarborough , Toronto, Ontario , Canada M1C 1A4.,8 Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario , Canada M5S 3B2
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20
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An X, Bai Q, Bing Z, Zhou S, Shi D, Liu H, Yao X. How Does Agonist and Antagonist Binding Lead to Different Conformational Ensemble Equilibria of the κ-Opioid Receptor: Insight from Long-Time Gaussian Accelerated Molecular Dynamics Simulation. ACS Chem Neurosci 2019; 10:1575-1584. [PMID: 30372027 DOI: 10.1021/acschemneuro.8b00535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The opioid receptors belong to the class A seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). The κ-opioid receptor (KOR) is a subfamily of four opioid receptors. The endogenous peptide and a variety of selective agonists and antagonists of KOR have been developed. The structurally similar ligands at the same site cause completely opposite biological functions and induce different conformational changes. To shed light on the conformation ensembles and conformational dynamics in activation and deactivation processes of KOR, we performed all-atom, long-time Gaussian accelerated molecular dynamics simulation (GaMD) on KOR binding with agonist epoxymorphinan MP1104 and antagonist JDTic, respectively. Our results revealed different conformation ensembles of KOR binding with agonist and with antagonist. Agonist binding stabilizes the active state of key motifs including DYYNM motif and CWxP motif, and biases the conformation equilibria toward the active state. Antagonist binding will not destroy inactive conformation equilibria, by keeping the stable inactive state of these crucial motifs. We found that the inactive apo form of KOR is the most stable state, while the active apo form relaxes readily to inactive state. Our results also revealed a stable intermediate (I), which is attributed to the hydrophobic interactions between Tyr2465.58 and TM6, as well as the steric hindrance of them. Our results not only show the conformation equilibria bias of KOR by binding with agonist and antagonist, but also provide the structural information for the design and discovery of potential ligands with different functions.
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Affiliation(s)
- Xiaoli An
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Qifeng Bai
- School of Basic Medical Science, Lanzhou University, Lanzhou 730000, China
| | - Zhitong Bing
- School of Basic Medical Science, Lanzhou University, Lanzhou 730000, China
- Institute of Modern Physics of Chinese Academy of Sciences, Gansu Province, Lanzhou 730000, China
| | - Shuangyan Zhou
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- School of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau China
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21
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Singh KD, Unal H, Desnoyer R, Karnik SS. Mechanism of Hormone Peptide Activation of a GPCR: Angiotensin II Activated State of AT 1R Initiated by van der Waals Attraction. J Chem Inf Model 2019; 59:373-385. [PMID: 30608150 DOI: 10.1021/acs.jcim.8b00583] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We present a succession of structural changes involved in hormone peptide activation of a prototypical GPCR. Microsecond molecular dynamics simulation generated conformational ensembles reveal propagation of structural changes through key "microswitches" within human AT1R bound to native hormone. The endocrine octa-peptide angiotensin II (AngII) activates AT1R signaling in our bodies which maintains physiological blood pressure, electrolyte balance, and cardiovascular homeostasis. Excessive AT1R activation is associated with pathogenesis of hypertension and cardiovascular diseases which are treated by sartan drugs. The mechanism of AT1R inhibition by sartans has been elucidated by 2.8 Å X-ray structures, mutagenesis, and computational analyses. Yet, the mechanism of AT1R activation by AngII is unclear. The current study delineates an activation scheme initiated by AngII binding. A van der Waals "grasp" interaction between Phe8AngII with Ile2887.39 in AT1R induced mechanical strain pulling Tyr2927.43 and breakage of critical interhelical H-bonds, first between Tyr2927.43 and Val1083.32 and second between Asn1113.35 and Asn2957.46. Subsequently changes are observed in conserved microswitches DRYTM3, Yx7K(R)TM5, CWxPTM6, and NPxxYTM7 in AT1R. Activating the microswitches in the intracellular region of AT1R may trigger formation of the G-protein binding pocket as well as exposure of helix-8 to cytoplasm. Thus, the active-like conformation of AT1R is initiated by the van der Waals interaction of Phe8AngII with Ile2887.39, followed by systematic reorganization of critical interhelical H-bonds and activation of microswitches.
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Affiliation(s)
- Khuraijam Dhanachandra Singh
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
| | - Hamiyet Unal
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
| | - Russell Desnoyer
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
| | - Sadashiva S Karnik
- Department of Molecular Cardiology, Lerner Research Institute , Cleveland Clinic Foundation , Cleveland , Ohio 44195 , United States
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22
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Rodgers J, Peirson SN, Hughes S, Hankins MW. Functional characterisation of naturally occurring mutations in human melanopsin. Cell Mol Life Sci 2018; 75:3609-3624. [PMID: 29700553 PMCID: PMC6133154 DOI: 10.1007/s00018-018-2813-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/06/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
Abstract
Melanopsin is a blue light-sensitive opsin photopigment involved in a range of non-image forming behaviours, including circadian photoentrainment and the pupil light response. Many naturally occurring genetic variants exist within the human melanopsin gene (OPN4), yet it remains unclear how these variants affect melanopsin protein function and downstream physiological responses to light. Here, we have used bioinformatic analysis and in vitro expression systems to determine the functional phenotypes of missense human OPN4 variants. From 1242 human OPN4 variants collated in the NCBI Short Genetic Variation database (dbSNP), we identified 96 that lead to non-synonymous amino acid substitutions. These 96 missense mutations were screened using sequence alignment and comparative approaches to select 16 potentially deleterious variants for functional characterisation using calcium imaging of melanopsin-driven light responses in HEK293T cells. We identify several previously uncharacterised OPN4 mutations with altered functional properties, including attenuated or abolished light responses, as well as variants demonstrating abnormal response kinetics. These data provide valuable insight into the structure-function relationships of human melanopsin, including several key functional residues of the melanopsin protein. The identification of melanopsin variants with significantly altered function may serve to detect individuals with disrupted melanopsin-based light perception, and potentially highlight those at increased risk of sleep disturbance, circadian dysfunction, and visual abnormalities.
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Affiliation(s)
- Jessica Rodgers
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK
| | - Stuart N Peirson
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK
| | - Steven Hughes
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK.
| | - Mark W Hankins
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK.
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23
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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: 30] [Impact Index Per Article: 5.0] [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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24
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Jiménez-Rosés M, Matsoukas MT, Caltabiano G, Cordomí A. Ligand-Triggered Structural Changes in the M 2 Muscarinic Acetylcholine Receptor. J Chem Inf Model 2018; 58:1074-1082. [PMID: 29671585 DOI: 10.1021/acs.jcim.8b00108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The muscarinic M2 acetylcholine receptor, one of the few G-protein coupled receptors that has not only been crystallized in both active and inactive conformations but also in the presence of a positive allosteric modulator, is an interesting system to study the molecular mechanisms of GPCR activation and ligand allosterism. Here, we have employed molecular dynamics (MD) simulations (adding to 14 μs in total) to study conformational changes triggered by the inverse agonist R-(-)-3-quinuclidinyl-benzilate (QNB) in the structure of the active M2 receptor (PBD ID 4MQS ) after replacement of the agonist iperoxo by the inverse agonist QNB. This permitted us to identify the sequence of events in the deactivation mechanism of the M2 acetylcholine receptor, which results first in the rearrangement of the transmission switch, the subsequent opening of the extracellular portion of the receptor and finally, the closure of the intracellular part. We also evaluate the effect of the positive allosteric modulator LY2119620 when bound simultaneously with the orthosteric agonist iperoxo and find that it restricts the conformation of Trp4227.35 in a position that modulates the orientation of the Tyr4267.39 at the orthosteric-binding pocket.
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Affiliation(s)
- Mireia Jiménez-Rosés
- Laboratori de Medicina Computacional, Unitat de Bioestadística , Facultat de Medicina, Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | | | - Gianluigi Caltabiano
- Laboratori de Medicina Computacional, Unitat de Bioestadística , Facultat de Medicina, Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística , Facultat de Medicina, Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
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25
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Abstract
G protein-coupled receptors (GPCRs), which mediate processes as diverse as olfaction and maintenance of metabolic homeostasis, have become the single most effective class of therapeutic drug targets. As a result, understanding the molecular basis for their activity is of paramount importance. Recent technological advances have made GPCR structural biology increasingly tractable, offering views of these receptors in unprecedented atomic detail. Structural and biophysical data have shown that GPCRs function as complex allosteric machines, communicating ligand-binding events through conformational change. Changes in receptor conformation lead to activation of effector proteins, such as G proteins and arrestins, which are themselves conformational switches. Here, we review how structural biology has illuminated the agonist-induced cascade of conformational changes that culminate in a cellular response to GPCR activation.
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Affiliation(s)
- Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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26
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Elgeti M, Kazmin R, Rose AS, Szczepek M, Hildebrand PW, Bartl FJ, Scheerer P, Hofmann KP. The arrestin-1 finger loop interacts with two distinct conformations of active rhodopsin. J Biol Chem 2018; 293:4403-4410. [PMID: 29363577 DOI: 10.1074/jbc.m117.817890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/17/2018] [Indexed: 11/06/2022] Open
Abstract
Signaling of the prototypical G protein-coupled receptor (GPCR) rhodopsin through its cognate G protein transducin (Gt) is quenched when arrestin binds to the activated receptor. Although the overall architecture of the rhodopsin/arrestin complex is known, many questions regarding its specificity remain unresolved. Here, using FTIR difference spectroscopy and a dual pH/peptide titration assay, we show that rhodopsin maintains certain flexibility upon binding the "finger loop" of visual arrestin (prepared as synthetic peptide ArrFL-1). We found that two distinct complexes can be stabilized depending on the protonation state of E3.49 in the conserved (D)ERY motif. Both complexes exhibit different interaction modes and affinities of ArrFL-1 binding. The plasticity of the receptor within the rhodopsin/ArrFL-1 complex stands in contrast to the complex with the C terminus of the Gt α-subunit (GαCT), which stabilizes only one specific substate out of the conformational ensemble. However, Gt α-subunit binding and both ArrFL-1-binding modes involve a direct interaction to conserved R3.50, as determined by site-directed mutagenesis. Our findings highlight the importance of receptor conformational flexibility and cytoplasmic proton uptake for modulation of rhodopsin signaling and thereby extend the picture provided by crystal structures of the rhodopsin/arrestin and rhodopsin/ArrFL-1 complexes. Furthermore, the two binding modes of ArrFL-1 identified here involve motifs of conserved amino acids, which indicates that our results may have elucidated a common modulation mechanism of class A GPCR-G protein/-arrestin signaling.
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Affiliation(s)
- Matthias Elgeti
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany,
| | - Roman Kazmin
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Alexander S Rose
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Group ProteInformatics
| | - Michal Szczepek
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction
| | - Peter W Hildebrand
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Franz J Bartl
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Patrick Scheerer
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.,Group Protein X-ray Crystallography and Signal Transduction
| | - Klaus Peter Hofmann
- From the Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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27
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Abstract
G protein-coupled receptors (GPCRs) are critical regulators of human physiology and make up the largest single class of therapeutic drug targets. Although GPCRs regulate highly diverse physiology, they share a common signaling mechanism whereby extracellular stimuli induce conformational changes in the receptor that enable activation of heterotrimeric G proteins and other intracellular effectors. Advances in GPCR structural biology have made it possible to examine ligand-induced GPCR activation at an unprecedented level of detail. Here, we review the structural basis for family A GPCR activation, with a focus on GPCRs for which structures are available in both active or active-like states and inactive states. Crystallographic and other biophysical data show how chemically diverse ligands stabilize highly conserved conformational changes on the intracellular side of the receptors, allowing many different extracellular stimuli to utilize shared downstream signaling molecules. Finally, we discuss the remaining challenges in understanding GPCR activation and signaling and highlight new technologies that may allow unanswered questions to be resolved.
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Affiliation(s)
- Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
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28
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Banyikwa A, Goos A, Kiemle DJ, Foulkes MAC, Braiman MS. Experimental and Computational Modeling of H-Bonded Arginine-Tyrosine Groupings in Aprotic Environments. ACS OMEGA 2017; 2:5641-5659. [PMID: 31457828 PMCID: PMC6644469 DOI: 10.1021/acsomega.7b00282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/28/2017] [Indexed: 06/08/2023]
Abstract
H-bonds between neutral tyrosine and arginine in nonpolar environments are modeled by small-molecule phenol/guanidine complexes. From the temperature and concentration dependence of UV spectra, a value of ΔH° = -74 ± 4 kJ mol-1 is deduced for the formation of H-bonded p-cresol/dodecylguanidine in hexane. ΔE = -71 kJ mol-1 is computed with density functional theory (in vacuo). In dimethyl sulfoxide or crystals, (p-phenolyl)alkylguanidines form head-to-tail homodimers with two strong H-bonding interactions, as evidenced by UV, IR, and NMR spectral shifts, strong IR continuum absorbance bands, and short O···N distances in X-ray crystal structures. Phenol/alkylguanidine H-bonded complexes consist of polarizable rapidly interconverting tautomers, with the proton shift from phenol to guanidine increasing with increase in the polarity of the aprotic solvent. As measured by NMR, both groups in these strongly H-bonded neutral complexes can simultaneously appear to be predominantly protonated. These systems serve as models for the hypothetical hydrogen-Bonded Uncharged (aRginine + tYrosine), or "BU(RY)", motifs in membrane proteins.
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Affiliation(s)
- Andrew
Toyi Banyikwa
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
| | - Alan Goos
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
| | - David J. Kiemle
- Analytical
and Technical Services, SUNY College of
Environmental Science and Forestry, 123 Jahn Laboratory, Syracuse, New York 13210, United
States
| | - Michael A. C. Foulkes
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
| | - Mark S. Braiman
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
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29
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Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Molecules 2017; 22:molecules22081347. [PMID: 28809779 PMCID: PMC6152068 DOI: 10.3390/molecules22081347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/05/2023] Open
Abstract
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.
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Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37204, USA.
| | - Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Seu-Na Lee
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Min-Duk Seo
- Department of Molecular Science and Technology & College of Pharmacy, Ajou University, Suwon 16499, Korea.
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Korea.
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea.
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30
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Sanchez-Reyes OB, Cooke ALG, Tranter DB, Rashid D, Eilers M, Reeves PJ, Smith SO. G Protein-Coupled Receptors Contain Two Conserved Packing Clusters. Biophys J 2017; 112:2315-2326. [PMID: 28591604 DOI: 10.1016/j.bpj.2017.04.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/24/2017] [Accepted: 04/28/2017] [Indexed: 01/01/2023] Open
Abstract
G protein-coupled receptors (GPCRs) have evolved a seven-transmembrane helix framework that is responsive to a wide range of extracellular signals. An analysis of the interior packing of family A GPCR crystal structures reveals two clusters of highly packed residues that facilitate tight transmembrane helix association. These clusters are centered on amino acid positions 2.47 and 4.53, which are highly conserved as alanine and serine, respectively. Ala2.47 mediates the interaction between helices H1 and H2, while Ser4.53 mediates the interaction between helices H3 and H4. The helical interfaces outside of these clusters are lined with residues that are more loosely packed, a structural feature that facilitates motion of helices H5, H6, and H7, which is required for receptor activation. Mutation of the conserved small side chain at position 4.53 within packing cluster 2 is shown to disrupt the structure of the visual receptor rhodopsin, whereas sites in packing cluster 1 (e.g., positions 1.46 and 2.47) are more tolerant to mutation but affect the overall stability of the protein. These findings reveal a common structural scaffold of GPCRs that is important for receptor folding and activation.
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Affiliation(s)
- Omar B Sanchez-Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Aidan L G Cooke
- School of Biological Sciences, University of Essex, Essex, United Kingdom
| | - Dale B Tranter
- School of Biological Sciences, University of Essex, Essex, United Kingdom
| | - Dawood Rashid
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Markus Eilers
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Essex, United Kingdom.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York.
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31
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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32
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Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys 2017; 46:175-198. [PMID: 28532213 PMCID: PMC5764094 DOI: 10.1146/annurev-biophys-051013-022942] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemokines and their cell surface G protein-coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novel epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
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33
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Shigeta A, Ito S, Inoue K, Okitsu T, Wada A, Kandori H, Kawamura I. Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin. Biochemistry 2017; 56:543-550. [PMID: 28040890 DOI: 10.1021/acs.biochem.6b00999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. 15N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the 15N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na+-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
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34
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Flanagan CA, Manilall A. Gonadotropin-Releasing Hormone (GnRH) Receptor Structure and GnRH Binding. Front Endocrinol (Lausanne) 2017; 8:274. [PMID: 29123501 PMCID: PMC5662886 DOI: 10.3389/fendo.2017.00274] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
Gonadotropin-releasing hormone (GnRH) regulates reproduction. The human GnRH receptor lacks a cytoplasmic carboxy-terminal tail but has amino acid sequence motifs characteristic of rhodopsin-like, class A, G protein-coupled receptors (GPCRs). This review will consider how recent descriptions of X-ray crystallographic structures of GPCRs in inactive and active conformations may contribute to understanding GnRH receptor structure, mechanism of activation and ligand binding. The structures confirmed that ligands bind to variable extracellular surfaces, whereas the seven membrane-spanning α-helices convey the activation signal to the cytoplasmic receptor surface, which binds and activates heterotrimeric G proteins. Forty non-covalent interactions that bridge topologically equivalent residues in different transmembrane (TM) helices are conserved in class A GPCR structures, regardless of activation state. Conformation-independent interhelical contacts account for a conserved receptor protein structure and their importance in the GnRH receptor structure is supported by decreased expression of receptors with mutations of residues in the network. Many of the GnRH receptor mutations associated with congenital hypogonadotropic hypogonadism, including the Glu2.53(90) Lys mutation, involve amino acids that constitute the conserved network. Half of the ~250 intramolecular interactions in GPCRs differ between inactive and active structures. Conformation-specific interhelical contacts depend on amino acids changing partners during activation. Conserved inactive conformation-specific contacts prevent receptor activation by stabilizing proximity of TM helices 3 and 6 and a closed G protein-binding site. Mutations of GnRH receptor residues involved in these interactions, such as Arg3.50(139) of the DRY/S motif or Tyr7.53(323) of the N/DPxxY motif, increase or decrease receptor expression and efficiency of receptor coupling to G protein signaling, consistent with the native residues stabilizing the inactive GnRH receptor structure. Active conformation-specific interhelical contacts stabilize an open G protein-binding site. Progress in defining the GnRH-binding site has recently slowed, with evidence that Tyr6.58(290) contacts Tyr5 of GnRH, whereas other residues affect recognition of Trp3 and Gly10NH2. The surprisingly consistent observations that GnRH receptor mutations that disrupt GnRH binding have less effect on "conformationally constrained" GnRH peptides may now be explained by crystal structures of agonist-bound peptide receptors. Analysis of GPCR structures provides insight into GnRH receptor function.
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Affiliation(s)
- Colleen A. Flanagan
- Faculty of Health Sciences, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Colleen A. Flanagan,
| | - Ashmeetha Manilall
- Faculty of Health Sciences, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
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35
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Decay of an active GPCR: Conformational dynamics govern agonist rebinding and persistence of an active, yet empty, receptor state. Proc Natl Acad Sci U S A 2016; 113:11961-11966. [PMID: 27702898 DOI: 10.1073/pnas.1606347113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Here, we describe two insights into the role of receptor conformational dynamics during agonist release (all-trans retinal, ATR) from the visual G protein-coupled receptor (GPCR) rhodopsin. First, we show that, after light activation, ATR can continually release and rebind to any receptor remaining in an active-like conformation. As with other GPCRs, we observe that this equilibrium can be shifted by either promoting the active-like population or increasing the agonist concentration. Second, we find that during decay of the signaling state an active-like, yet empty, receptor conformation can transiently persist after retinal release, before the receptor ultimately collapses into an inactive conformation. The latter conclusion is based on time-resolved, site-directed fluorescence labeling experiments that show a small, but reproducible, lag between the retinal leaving the protein and return of transmembrane helix 6 (TM6) to the inactive conformation, as determined from tryptophan-induced quenching studies. Accelerating Schiff base hydrolysis and subsequent ATR dissociation, either by addition of hydroxylamine or introduction of mutations, further increased the time lag between ATR release and TM6 movement. These observations show that rhodopsin can bind its agonist in equilibrium like a traditional GPCR, provide evidence that an active GPCR conformation can persist even after agonist release, and raise the possibility of targeting this key photoreceptor protein by traditional pharmaceutical-based treatments.
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36
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Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation. Nat Commun 2016; 7:12683. [PMID: 27585742 PMCID: PMC5025775 DOI: 10.1038/ncomms12683] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/22/2016] [Indexed: 01/28/2023] Open
Abstract
The 11-cis retinal chromophore is tightly packed within the interior of the visual receptor rhodopsin and isomerizes to the all-trans configuration following absorption of light. The mechanism by which this isomerization event drives the outward rotation of transmembrane helix H6, a hallmark of activated G protein-coupled receptors, is not well established. To address this question, we use solid-state NMR and FTIR spectroscopy to define the orientation and interactions of the retinal chromophore in the active metarhodopsin II intermediate. Here we show that isomerization of the 11-cis retinal chromophore generates strong steric interactions between its β-ionone ring and transmembrane helices H5 and H6, while deprotonation of its protonated Schiff's base triggers the rearrangement of the hydrogen-bonding network involving residues on H6 and within the second extracellular loop. We integrate these observations with previous structural and functional studies to propose a two-stage mechanism for rhodopsin activation.
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37
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Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A 2016; 113:9928-33. [PMID: 27543332 DOI: 10.1073/pnas.1601278113] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The atomic-level mechanisms by which G protein-coupled receptors (GPCRs) transmit extracellular ligand binding events through their transmembrane helices to activate intracellular G proteins remain unclear. Using a comprehensive library of mutations covering all 352 residues of the GPCR CXC chemokine receptor 4 (CXCR4), we identified 41 amino acids that are required for signaling induced by the chemokine ligand CXCL12 (stromal cell-derived factor 1). CXCR4 variants with each of these mutations do not signal properly but remain folded, based on receptor surface trafficking, reactivity to conformationally sensitive monoclonal antibodies, and ligand binding. When visualized on the structure of CXCR4, the majority of these residues form a continuous intramolecular signaling chain through the transmembrane helices; this chain connects chemokine binding residues on the extracellular side of CXCR4 to G protein-coupling residues on its intracellular side. Integrated into a cohesive model of signal transmission, these CXCR4 residues cluster into five functional groups that mediate (i) chemokine engagement, (ii) signal initiation, (iii) signal propagation, (iv) microswitch activation, and (v) G protein coupling. Propagation of the signal passes through a "hydrophobic bridge" on helix VI that coordinates with nearly every known GPCR signaling motif. Our results agree with known conserved mechanisms of GPCR activation and significantly expand on understanding the structural principles of CXCR4 signaling.
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38
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Kimata N, Pope A, Sanchez-Reyes OB, Eilers M, Opefi CA, Ziliox M, Reeves PJ, Smith SO. Free backbone carbonyls mediate rhodopsin activation. Nat Struct Mol Biol 2016; 23:738-43. [PMID: 27376589 PMCID: PMC4972713 DOI: 10.1038/nsmb.3257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022]
Abstract
Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins.
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Affiliation(s)
- Naoki Kimata
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Andreyah Pope
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Omar B Sanchez-Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Markus Eilers
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | | | - Martine Ziliox
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Essex, UK
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
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39
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Kimura T, Jennings W, Epand RM. Roles of specific lipid species in the cell and their molecular mechanism. Prog Lipid Res 2016; 62:75-92. [PMID: 26875545 DOI: 10.1016/j.plipres.2016.02.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/04/2016] [Accepted: 02/10/2016] [Indexed: 12/19/2022]
Abstract
Thousands of different molecular species of lipids are present within a single cell, being involved in modulating the basic processes of life. The vast number of different lipid species can be organized into a number of different lipid classes, which may be defined as a group of lipids with a common chemical structure, such as the headgroup, apart from the nature of the hydrocarbon chains. Each lipid class has unique biological roles. In some cases, a relatively small change in the headgroup chemical structure can result in a drastic change in function. Such phenomena are well documented, and largely understood in terms of specific interactions with proteins. In contrast, there are observations that the entire structural specificity of a lipid molecule, including the hydrocarbon chains, is required for biological activity through specific interactions with membrane proteins. Understanding of these phenomena represents a fundamental change in our thinking of the functions of lipids in biology. There are an increasing number of diverse examples of roles for specific lipids in cellular processes including: Signal transduction; trafficking; morphological changes; cell division. We are gaining knowledge and understanding of the underlying molecular mechanisms. They are of growing importance in both basic and applied sciences.
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Affiliation(s)
- Tomohiro Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
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40
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Isogai S, Deupi X, Opitz C, Heydenreich FM, Tsai CJ, Brueckner F, Schertler GFX, Veprintsev DB, Grzesiek S. Backbone NMR reveals allosteric signal transduction networks in the β1-adrenergic receptor. Nature 2016; 530:237-41. [DOI: 10.1038/nature16577] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/04/2015] [Indexed: 01/20/2023]
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41
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Structural dynamics and energetics underlying allosteric inactivation of the cannabinoid receptor CB1. Proc Natl Acad Sci U S A 2015; 112:8469-74. [PMID: 26100912 DOI: 10.1073/pnas.1500895112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are surprisingly flexible molecules that can do much more than simply turn on G proteins. Some even exhibit biased signaling, wherein the same receptor preferentially activates different G-protein or arrestin signaling pathways depending on the type of ligand bound. Why this behavior occurs is still unclear, but it can happen with both traditional ligands and ligands that bind allosterically outside the orthosteric receptor binding pocket. Here, we looked for structural mechanisms underlying these phenomena in the marijuana receptor CB1. Our work focused on the allosteric ligand Org 27569, which has an unusual effect on CB1-it simultaneously increases agonist binding, decreases G--protein activation, and induces biased signaling. Using classical pharmacological binding studies, we find that Org 27569 binds to a unique allosteric site on CB1 and show that it can act alone (without need for agonist cobinding). Through mutagenesis studies, we find that the ability of Org 27569 to bind is related to how much receptor is in an active conformation that can couple with G protein. Using these data, we estimated the energy differences between the inactive and active states. Finally, site-directed fluorescence labeling studies show the CB1 structure stabilized by Org 27569 is different and unique from that stabilized by antagonist or agonist. Specifically, transmembrane helix 6 (TM6) movements associated with G-protein activation are blocked, but at the same time, helix 8/TM7 movements are enhanced, suggesting a possible mechanism for the ability of Org 27569 to induce biased signaling.
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42
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Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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43
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Heydenreich FM, Vuckovic Z, Matkovic M, Veprintsev DB. Stabilization of G protein-coupled receptors by point mutations. Front Pharmacol 2015; 6:82. [PMID: 25941489 PMCID: PMC4403299 DOI: 10.3389/fphar.2015.00082] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/31/2015] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are flexible integral membrane proteins involved in transmembrane signaling. Their involvement in many physiological processes makes them interesting targets for drug development. Determination of the structure of these receptors will help to design more specific drugs, however, their structural characterization has so far been hampered by the low expression and their inherent instability in detergents which made protein engineering indispensable for structural and biophysical characterization. Several approaches to stabilize the receptors in a particular conformation have led to breakthroughs in GPCR structure determination. These include truncations of the flexible regions, stabilization by antibodies and nanobodies, fusion partners, high affinity and covalently bound ligands as well as conformational stabilization by mutagenesis. In this review we focus on stabilization of GPCRs by insertion of point mutations, which lead to increased conformational and thermal stability as well as improved expression levels. We summarize existing mutagenesis strategies with different coverage of GPCR sequence space and depth of information, design and transferability of mutations and the molecular basis for stabilization. We also discuss whether mutations alter the structure and pharmacological properties of GPCRs.
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Affiliation(s)
- Franziska M Heydenreich
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Milos Matkovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
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44
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Wolf S, Grünewald S. Sequence, structure and ligand binding evolution of rhodopsin-like G protein-coupled receptors: a crystal structure-based phylogenetic analysis. PLoS One 2015; 10:e0123533. [PMID: 25881057 PMCID: PMC4399913 DOI: 10.1371/journal.pone.0123533] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 02/20/2015] [Indexed: 01/04/2023] Open
Abstract
G protein-coupled receptors (GPCRs) form the largest family of membrane receptors in the human genome. Advances in membrane protein crystallization so far resulted in the determination of 24 receptors available as high-resolution atomic structures. We performed the first phylogenetic analysis of GPCRs based on the available set of GPCR structures. We present a new phylogenetic tree of known human rhodopsin-like GPCR sequences based on this structure set. We can distinguish the three separate classes of small-ligand binding GPCRs, peptide binding GPCRs, and olfactory receptors. Analyzing different structural subdomains, we found that small molecule binding receptors most likely have evolved from peptide receptor precursors, with a rhodopsin/S1PR1 ancestor, most likely an ancestral opsin, forming the link between both classes. A light-activated receptor therefore seems to be the origin of the small molecule hormone receptors of the central nervous system. We find hints for a common evolutionary path of both ligand binding site and central sodium/water binding site. Surprisingly, opioid receptors exhibit both a binding cavity and a central sodium/water binding site similar to the one of biogenic amine receptors instead of peptide receptors, making them seemingly prone to bind small molecule ligands, e.g. opiates. Our results give new insights into the relationship and the pharmacological properties of rhodopsin-like GPCRs.
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Affiliation(s)
- Steffen Wolf
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
- * E-mail:
| | - Stefan Grünewald
- CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
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45
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Opefi CA, Tranter D, Smith SO, Reeves PJ. Construction of stable mammalian cell lines for inducible expression of G protein-coupled receptors. Methods Enzymol 2015; 556:283-305. [PMID: 25857787 DOI: 10.1016/bs.mie.2014.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The large-scale expression of many membrane proteins, including the members of the G protein-coupled receptor superfamily, in a correctly folded and fully functional form remains a formidable challenge. In this chapter, we focus on the construction of stable mammalian cell lines to overcome this hurdle. First, we will outline the steps for establishing a tightly regulated gene expression system in human HEK293S cells. This system utilizes separate plasmids containing components of well-defined genetic control elements from the Escherichia coli tetracycline operon to control the powerful cytomegalovirus immediate early enhancer/promoter. Next, we describe the assembly of this expression system into HEK293S cells and a derivative cell line devoid of complex N-glycosylation. Finally, we describe methods for the growth of these cells lines in scalable suspension culture for the preparation of milligram amounts of recombinant protein.
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Affiliation(s)
- Chikwado A Opefi
- Department of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom
| | - Dale Tranter
- Department of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Philip J Reeves
- Department of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom.
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46
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Oxysterols act as promiscuous ligands of class-A GPCRs: In silico molecular modeling and in vitro validation. Cell Signal 2014; 26:2614-20. [DOI: 10.1016/j.cellsig.2014.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/15/2014] [Indexed: 01/12/2023]
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47
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Wang S, Ladizhansky V. Recent advances in magic angle spinning solid state NMR of membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 82:1-26. [PMID: 25444696 DOI: 10.1016/j.pnmrs.2014.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/16/2014] [Accepted: 07/20/2014] [Indexed: 05/14/2023]
Abstract
Membrane proteins mediate many critical functions in cells. Determining their three-dimensional structures in the native lipid environment has been one of the main objectives in structural biology. There are two major NMR methodologies that allow this objective to be accomplished. Oriented sample NMR, which can be applied to membrane proteins that are uniformly aligned in the magnetic field, has been successful in determining the backbone structures of a handful of membrane proteins. Owing to methodological and technological developments, Magic Angle Spinning (MAS) solid-state NMR (ssNMR) spectroscopy has emerged as another major technique for the complete characterization of the structure and dynamics of membrane proteins. First developed on peptides and small microcrystalline proteins, MAS ssNMR has recently been successfully applied to large membrane proteins. In this review we describe recent progress in MAS ssNMR methodologies, which are now available for studies of membrane protein structure determination, and outline a few examples, which highlight the broad capability of ssNMR spectroscopy.
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Affiliation(s)
- Shenlin Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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48
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Dynamics of bovine opsin bound to G-protein fragments. J Struct Biol 2014; 188:79-86. [DOI: 10.1016/j.jsb.2014.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/31/2014] [Accepted: 08/07/2014] [Indexed: 11/20/2022]
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49
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Kling RC, Tschammer N, Lanig H, Clark T, Gmeiner P. Active-state model of a dopamine D2 receptor-Gαi complex stabilized by aripiprazole-type partial agonists. PLoS One 2014; 9:e100069. [PMID: 24932547 PMCID: PMC4059746 DOI: 10.1371/journal.pone.0100069] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022] Open
Abstract
Partial agonists exhibit a submaximal capacity to enhance the coupling of one receptor to an intracellular binding partner. Although a multitude of studies have reported different ligand-specific conformations for a given receptor, little is known about the mechanism by which different receptor conformations are connected to the capacity to activate the coupling to G-proteins. We have now performed molecular-dynamics simulations employing our recently described active-state homology model of the dopamine D2 receptor-Gαi protein-complex coupled to the partial agonists aripiprazole and FAUC350, in order to understand the structural determinants of partial agonism better. We have compared our findings with our model of the D2R-Gαi-complex in the presence of the full agonist dopamine. The two partial agonists are capable of inducing different conformations of important structural motifs, including the extracellular loop regions, the binding pocket and, in particular, intracellular G-protein-binding domains. As G-protein-coupling to certain intracellular epitopes of the receptor is considered the key step of allosterically triggered nucleotide-exchange, it is tempting to assume that impaired coupling between the receptor and the G-protein caused by distinct ligand-specific conformations is a major determinant of partial agonist efficacy.
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Affiliation(s)
- Ralf C. Kling
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Erlangen, Germany
- Department of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich Alexander University, Erlangen, Germany
| | - Nuska Tschammer
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Erlangen, Germany
| | - Harald Lanig
- Department of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich Alexander University, Erlangen, Germany
- Central Institute for Scientific Computing, Friedrich Alexander University, Erlangen, Germany
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich Alexander University, Erlangen, Germany
- Centre for Molecular Design, University of Portsmouth, King Henry Building, Portsmouth, United Kingdom
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Erlangen, Germany
- * E-mail:
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50
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Schmidt P, Thomas L, Müller P, Scheidt HA, Huster D. The G-protein-coupled neuropeptide Y receptor type 2 is highly dynamic in lipid membranes as revealed by solid-state NMR spectroscopy. Chemistry 2014; 20:4986-92. [PMID: 24623336 DOI: 10.1002/chem.201304928] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/20/2014] [Indexed: 12/22/2022]
Abstract
In spite of the recent success in crystallizing several G-protein-coupled receptors (GPCRs), a comprehensive biophysical characterization of these molecules under physiological conditions also requires the study of the molecular dynamics of these proteins. The molecular mobility of the human neuropeptide Y receptor type 2 reconstituted into dimyristoylphosphatidylcholine (DMPC) membranes was investigated by means of solid-state NMR spectroscopy. Static (15) N NMR spectra show that the receptor performs axially symmetric motions in the membrane, and several residues undergo large amplitude fluctuations. This was confirmed by quantitative measurements of the motional (1) H,(13) C order parameter of the CH, CH2 , and CH3 groups. In directly polarized (13) C NMR experiments, these order parameters showed astonishingly low values of SCH =0.55, S CH 2=0.33, and S CH 3=0.17, which corresponds to segmental amplitudes of approximately 50° in the backbone and approximately 50-60° in the side chain. At physiological temperature, (2) H NMR spectra of the deuterated receptor showed a narrow component that is indicative of molecular order parameters of S≤0.3 superimposed with a very broad spectrum that could stem from the transmembrane α-helices. These results suggest that the crystal structures of GPCRs only represent a static snapshot of these highly mobile molecules, which undergo significant structural fluctuations with relatively large amplitudes in a liquid-crystalline membrane at physiological temperature.
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Affiliation(s)
- Peter Schmidt
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig (Germany)
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