1
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Asadollahi K, Scott DJ, Gooley PR. NMR applications to GPCR recognition by peptide ligands. Curr Opin Pharmacol 2023; 70:102366. [PMID: 37003111 DOI: 10.1016/j.coph.2023.102366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 04/03/2023]
Abstract
Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo significant conformational changes upon binding that is essential for receptor recognition and activation. Conformational selection and induced fit are the extreme mechanisms of coupled folding and binding that can be distinguished by analysis of binding pathways by methods that include NMR. However, the large size of GPCRs in membrane-mimetic environments limits NMR applications. In this review, we highlight advances in the field that can be adopted to address coupled folding and binding of peptide ligands to their cognate receptors.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
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2
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Overduin M, Trieber C, Prosser RS, Picard LP, Sheff JG. Structures and Dynamics of Native-State Transmembrane Protein Targets and Bound Lipids. MEMBRANES 2021; 11:451. [PMID: 34204456 PMCID: PMC8235241 DOI: 10.3390/membranes11060451] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Membrane proteins work within asymmetric bilayers of lipid molecules that are critical for their biological structures, dynamics and interactions. These properties are lost when detergents dislodge lipids, ligands and subunits, but are maintained in native nanodiscs formed using styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers. These amphipathic polymers allow extraction of multicomponent complexes of post-translationally modified membrane-bound proteins directly from organ homogenates or membranes from diverse types of cells and organelles. Here, we review the structures and mechanisms of transmembrane targets and their interactions with lipids including phosphoinositides (PIs), as resolved using nanodisc systems and methods including cryo-electron microscopy (cryo-EM) and X-ray diffraction (XRD). We focus on therapeutic targets including several G protein-coupled receptors (GPCRs), as well as ion channels and transporters that are driving the development of next-generation native nanodiscs. The design of new synthetic polymers and complementary biophysical tools bodes well for the future of drug discovery and structural biology of native membrane:protein assemblies (memteins).
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - Catharine Trieber
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Louis-Philippe Picard
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Joey G. Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada;
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3
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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4
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Lavington S, Watts A. Lipid nanoparticle technologies for the study of G protein-coupled receptors in lipid environments. Biophys Rev 2020; 12:10.1007/s12551-020-00775-5. [PMID: 33215301 PMCID: PMC7755959 DOI: 10.1007/s12551-020-00775-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family of integral membrane proteins which conduct a wide range of biological roles and represent significant drug targets. Most biophysical and structural studies of GPCRs have been conducted on detergent-solubilised receptors, and it is clear that detergents can have detrimental effects on GPCR function. Simultaneously, there is increasing appreciation of roles for specific lipids in modulation of GPCR function. Lipid nanoparticles such as nanodiscs and styrene maleic acid lipid particles (SMALPs) offer opportunities to study integral membrane proteins in lipid environments, in a form that is soluble and amenable to structural and biophysical experiments. Here, we review the application of lipid nanoparticle technologies to the study of GPCRs, assessing the relative merits and limitations of each system. We highlight how these technologies can provide superior platforms to detergents for structural and biophysical studies of GPCRs and inform on roles for protein-lipid interactions in GPCR function.
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Affiliation(s)
- Steven Lavington
- Biochemistry Department, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony Watts
- Biochemistry Department, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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5
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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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6
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Mizumura T, Kondo K, Kurita M, Kofuku Y, Natsume M, Imai S, Shiraishi Y, Ueda T, Shimada I. Activation of adenosine A 2A receptor by lipids from docosahexaenoic acid revealed by NMR. SCIENCE ADVANCES 2020; 6:eaay8544. [PMID: 32206717 PMCID: PMC7080496 DOI: 10.1126/sciadv.aay8544] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/18/2019] [Indexed: 05/05/2023]
Abstract
The lipid composition of the plasma membrane is a key parameter in controlling signal transduction through G protein-coupled receptors (GPCRs). Adenosine A2A receptor (A2AAR) is located in the lipid bilayers of cells, containing acyl chains derived from docosahexaenoic acid (DHA). For the NMR studies, we prepared A2AAR in lipid bilayers of nanodiscs, containing DHA chains and other acyl chains. The DHA chains in nanodiscs enhanced the activation of G proteins by A2AAR. Our NMR studies revealed that the DHA chains redistribute the multiple conformations of A2AAR toward those preferable for G protein binding. In these conformations, the rotational angle of transmembrane helix 6 is similar to that in the A2AAR-G protein complex, suggesting that the population shift of the equilibrium causes the enhanced activation of G protein by A2AAR. These findings provide insights into the control of neurotransmissions by A2AAR and the effects of lipids on various GPCR functions.
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Affiliation(s)
- Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masatoshi Kurita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Corresponding author.
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7
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Nasr ML. Large nanodiscs going viral. Curr Opin Struct Biol 2020; 60:150-156. [PMID: 32066086 PMCID: PMC10712563 DOI: 10.1016/j.sbi.2020.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
Covalently circularized and DNA-corralled nanodisc technologies have enabled engineering of large-sized bilayer nanodiscs up to 90nm. These large nanodiscs have the potential to extend the applicability of nanodisc technology from studying small and medium-sized membrane proteins to acting as surrogate membranes to investigate functional and structural aspects of viral entry. Here, we discuss the recent technical developments leading to construction of large circularized and DNA-corralled nanodiscs and examine their application in viral entry.
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Affiliation(s)
- Mahmoud L Nasr
- Division of Renal Medicine, Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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8
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Ayoubi-Joshaghani MH, Dianat-Moghadam H, Seidi K, Jahanban-Esfahalan A, Zare P, Jahanban-Esfahlan R. Cell-free protein synthesis: The transition from batch reactions to minimal cells and microfluidic devices. Biotechnol Bioeng 2020; 117:1204-1229. [PMID: 31840797 DOI: 10.1002/bit.27248] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/23/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Thanks to the synthetic biology, the laborious and restrictive procedure for producing a target protein in living microorganisms by biotechnological approaches can now experience a robust, pliant yet efficient alternative. The new system combined with lab-on-chip microfluidic devices and nanotechnology offers a tremendous potential envisioning novel cell-free formats such as DNA brushes, hydrogels, vesicular particles, droplets, as well as solid surfaces. Acting as robust microreactors/microcompartments/minimal cells, the new platforms can be tuned to perform various tasks in a parallel and integrated manner encompassing gene expression, protein synthesis, purification, detection, and finally enabling cell-cell signaling to bring a collective cell behavior, such as directing differentiation process, characteristics of higher order entities, and beyond. In this review, we issue an update on recent cell-free protein synthesis (CFPS) formats. Furthermore, the latest advances and applications of CFPS for synthetic biology and biotechnology are highlighted. In the end, contemporary challenges and future opportunities of CFPS systems are discussed.
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Affiliation(s)
| | | | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
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9
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NMR investigation of protein-ligand interactions for G-protein coupled receptors. Future Med Chem 2019; 11:1811-1825. [PMID: 31287732 DOI: 10.4155/fmc-2018-0312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this review, we report NMR studies of ligand-GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a major role for the generation of novel molecules both as new tools for the understanding of the GPCR function and as therapeutic compounds for a large diversity of pathologies.
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10
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Toyama Y, Shimada I. Frequency selective coherence transfer NMR spectroscopy to study the structural dynamics of high molecular weight proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 304:62-77. [PMID: 31129430 DOI: 10.1016/j.jmr.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/05/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Multidimensional nuclear magnetic resonance (NMR) spectroscopy has enabled detailed characterizations of protein structures and dynamics that are closely linked to functions. However, it leads to a large sensitivity loss in applications to high molecular weight proteins, which is caused by spin relaxation during the frequency discrimination period in the indirect dimension. Here, we describe a selective coherence transfer scheme, which enables us to selectively observe 1H nuclei bonded to 15N or 13C nuclei with specified resonance frequencies. By utilizing this scheme, we achieved a 2.5- to 6-fold increase in signal height per unit of time with this scheme by avoiding the relaxation loss in the indirect dimension, as compared to the conventional two-dimensional heteronuclear correlation spectroscopy. We also demonstrated the effectiveness of this approach with applications to the membrane protein KirBac1.1, and characterized the functionally relevant conformational exchange process in both detergent micelles and a reconstituted membrane environment, corresponding to the apparent molecular masses of 220 kDa and 300 kDa, respectively.
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Affiliation(s)
- Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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11
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Conole D, Myers SH, Mota F, Hobbs AJ, Selwood DL. Biophysical screening methods for extracellular domain peptide receptors, application to natriuretic peptide receptor C ligands. Chem Biol Drug Des 2019; 93:1011-1020. [PMID: 30218492 PMCID: PMC6879014 DOI: 10.1111/cbdd.13395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/15/2018] [Accepted: 09/04/2018] [Indexed: 12/20/2022]
Abstract
Endothelium-derived C-type natriuretic peptide possesses cytoprotective and anti-atherogenic functions that regulate vascular homeostasis. The vasoprotective effects of C-type natriuretic peptide are somewhat mediated by the natriuretic peptide receptor C, suggesting that this receptor represents a novel therapeutic target for the treatment of cardiovascular diseases. In order to facilitate our drug discovery efforts, we have optimized an array of biophysical methods including surface plasmon resonance, fluorescence polarization and thermal shift assays to aid in the design, assessment and characterization of small molecule agonist interactions with natriuretic peptide receptors. Assay conditions are investigated to explore the feasibility and dynamic range of each method, and peptide-based agonists and antagonists are used as controls to validate these conditions. Once established, each technique was compared and contrasted with respect to their drug discovery utility. We foresee that such techniques will facilitate the discovery and development of potential therapeutic agents for NPR-C and other large extracellular domain membrane receptors.
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Affiliation(s)
- Daniel Conole
- Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | - Samuel H. Myers
- Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | - Filipa Mota
- Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
| | - Adrian J. Hobbs
- William Harvey Research InstituteHeart Centre, Barts & The London School of MedicineQueen Mary University of LondonLondonUK
| | - David L. Selwood
- Wolfson Institute for Biomedical ResearchUniversity College LondonLondonUK
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12
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Yokogawa M, Fukuda M, Osawa M. Nanodiscs for Structural Biology in a Membranous Environment. Chem Pharm Bull (Tokyo) 2019; 67:321-326. [PMID: 30930435 DOI: 10.1248/cpb.c18-00941] [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] [Indexed: 11/22/2022]
Abstract
The structures of many membrane proteins have been analyzed in detergent micelles. However, the environment of detergent micelles differs somewhat from that of the lipid bilayer, where membrane proteins exhibit physiological functions. Therefore, a more membrane-like environment has been awaited for structural analysis of membrane proteins. Nanodiscs are "hockey-puck"-shaped lipid bilayer particles that distribute in a monodispersed manner in aqueous solution. We review how nanodiscs or protein-reconstituted nanodiscs are prepared and how they are utilized to analyze protein structure, dynamics, and interactions with lipid molecules using solution NMR and cryo-electron microscopy.
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Affiliation(s)
- Mariko Yokogawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy
| | - Masahiro Fukuda
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy
| | - Masanori Osawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy
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13
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Kano H, Toyama Y, Imai S, Iwahashi Y, Mase Y, Yokogawa M, Osawa M, Shimada I. Structural mechanism underlying G protein family-specific regulation of G protein-gated inwardly rectifying potassium channel. Nat Commun 2019; 10:2008. [PMID: 31043612 PMCID: PMC6494913 DOI: 10.1038/s41467-019-10038-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 01/26/2023] Open
Abstract
G protein-gated inwardly rectifying potassium channel (GIRK) plays a key role in regulating neurotransmission. GIRK is opened by the direct binding of the G protein βγ subunit (Gβγ), which is released from the heterotrimeric G protein (Gαβγ) upon the activation of G protein-coupled receptors (GPCRs). GIRK contributes to precise cellular responses by specifically and efficiently responding to the Gi/o-coupled GPCRs. However, the detailed mechanisms underlying this family-specific and efficient activation are largely unknown. Here, we investigate the structural mechanism underlying the Gi/o family-specific activation of GIRK, by combining cell-based BRET experiments and NMR analyses in a reconstituted membrane environment. We show that the interaction formed by the αA helix of Gαi/o mediates the formation of the Gαi/oβγ-GIRK complex, which is responsible for the family-specific activation of GIRK. We also present a model structure of the Gαi/oβγ-GIRK complex, which provides the molecular basis underlying the specific and efficient regulation of GIRK.
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Affiliation(s)
- Hanaho Kano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuki Toyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shunsuke Imai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuta Iwahashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoko Mase
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmacy, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Pharmacy, Keio University, Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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14
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Kobayashi Y, Konno Y, Kanda A, Yamada Y, Yasuba H, Sakata Y, Fukuchi M, Tomoda K, Iwai H, Ueki S. Critical role of CCL4 in eosinophil recruitment into the airway. Clin Exp Allergy 2019; 49:853-860. [PMID: 30854716 DOI: 10.1111/cea.13382] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Excessive eosinophil airway infiltration is a clinically critical condition in some cases. Eosinophilic pneumonia (EP) is a pulmonary condition involving eosinophil infiltration of the lungs. Although several chemokines, including eotaxin-1 (CCL11), RANTES (CCL5) and macrophage inflammatory protein 1β (MIP-1β or CCL4), have been detected in bronchoalveolar lavage fluid (BALF) from patients with EP, the pathophysiological mechanisms underlying EP, including potential relationships between eosinophils and CCL4, have not been fully elucidated. OBJECTIVE To examine the involvement of CCL4 in eosinophilic airway inflammation. METHODS We analysed supernatants of activated eosinophils and BALF from 16 patients with eosinophilic pneumonia (EP). Further, we examined the effects of CCL4 on eosinophil functions in vitro and those of anti-CCL4 neutralizing antibody in an in vivo model. RESULTS We found that purified human eosinophils stimulated with IL-5 predominantly secreted CCL4 and that patients with EP had elevated CCL11 and CCL4 levels in BALF compared with samples from individuals without EP. Because CCL4 levels were more strongly correlated with eosinophil count and expression of eosinophil granule proteins than CCL11, in vitro experiments using purified eosinophils concentrated on the former chemokine. Interestingly, CCL4 acted as a chemoattractant for eosinophils. In a mouse model, administration of a CCL4-neutralizing antibody attenuated eosinophilic airway infiltration and airway hyperresponsiveness. CONCLUSIONS AND CLINICAL RELEVANCE Overall, these findings highlight an important role of CCL4 in the mechanisms underlying eosinophil recruitment into the airway and may provide a novel insight into this potential therapeutic target.
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Affiliation(s)
- Yoshiki Kobayashi
- Airway Disease Section, Department of Otolaryngology, Kansai Medical University, Osaka, Japan.,Allergy Center, Kansai Medical University Hospital, Osaka, Japan
| | - Yasunori Konno
- Department of General Medical Practice and Laboratory Diagnostic Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Akira Kanda
- Airway Disease Section, Department of Otolaryngology, Kansai Medical University, Osaka, Japan.,Allergy Center, Kansai Medical University Hospital, Osaka, Japan
| | - Yoshiyuki Yamada
- Department of Allergy and Immunology, Gunma Children's Medical Center, Gunma, Japan
| | - Hirotaka Yasuba
- Department of Airway Medicine, Mitsubishi Kyoto Hospital, Kyoto, Japan
| | - Yoshiko Sakata
- Central Research of Laboratory, Kansai Medical University, Osaka, Japan
| | - Mineyo Fukuchi
- Department of General Medical Practice and Laboratory Diagnostic Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Koichi Tomoda
- Airway Disease Section, Department of Otolaryngology, Kansai Medical University, Osaka, Japan
| | - Hiroshi Iwai
- Airway Disease Section, Department of Otolaryngology, Kansai Medical University, Osaka, Japan
| | - Shigeharu Ueki
- Department of General Medical Practice and Laboratory Diagnostic Medicine, Akita University Graduate School of Medicine, Akita, Japan
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15
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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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16
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G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System. Life (Basel) 2018; 8:life8040054. [PMID: 30400226 PMCID: PMC6316570 DOI: 10.3390/life8040054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins are important drug targets which play a pivotal role in various cellular activities. However, unlike cytosolic proteins, most of them are difficult-to-express proteins. In this study, to synthesize and produce sufficient quantities of membrane proteins for functional and structural analysis, we used a bottom-up approach in a reconstituted cell-free synthesis system, the PURE system, supplemented with artificial lipid mimetics or micelles. Membrane proteins were synthesized by the cell-free system and integrated into lipid bilayers co-translationally. Membrane proteins such as the G-protein coupled receptors were expressed in the PURE system and a productivity ranging from 0.04 to 0.1 mg per mL of reaction was achieved with a correct secondary structure as predicted by circular dichroism spectrum. In addition, a ligand binding constant of 27.8 nM in lipid nanodisc and 39.4 nM in micelle was obtained by surface plasmon resonance and the membrane protein localization was confirmed by confocal microscopy in giant unilamellar vesicles. We found that our method is a promising approach to study the different classes of membrane proteins in their native-like artificial lipid bilayer environment for functional and structural studies.
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17
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Shenkarev ZO, Karlova MG, Kulbatskii DS, Kirpichnikov MP, Lyukmanova EN, Sokolova OS. Recombinant Production, Reconstruction in Lipid-Protein Nanodiscs, and Electron Microscopy of Full-Length α-Subunit of Human Potassium Channel Kv7.1. BIOCHEMISTRY (MOSCOW) 2018; 83:562-573. [PMID: 29738690 DOI: 10.1134/s0006297918050097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Voltage-gated potassium channel Kv7.1 plays an important role in the excitability of cardiac muscle. The α-subunit of Kv7.1 (KCNQ1) is the main structural element of this channel. Tetramerization of KCNQ1 in the membrane results in formation of an ion channel, which comprises a pore and four voltage-sensing domains. Mutations in the human KCNQ1 gene are one of the major causes of inherited arrhythmias, long QT syndrome in particular. The construct encoding full-length human KCNQ1 protein was synthesized in this work, and an expression system in the Pichia pastoris yeast cells was developed. The membrane fraction of the yeast cells containing the recombinant protein (rKCNQ1) was solubilized with CHAPS detergent. To better mimic the lipid environment of the channel, lipid-protein nanodiscs were formed using solubilized membrane fraction and MSP2N2 protein. The rKCNQ1/nanodisc and rKCNQ1/CHAPS samples were purified using the Rho1D4 tag introduced at the C-terminus of the protein. Protein samples were examined using transmission electron microscopy with negative staining. In both cases, homogeneous rKCNQ1 samples were observed based on image analysis. Statistical analysis of the images of individual protein particles solubilized in the detergent revealed the presence of a tetrameric structure confirming intact subunit assembly. A three-dimensional channel structure reconstructed at 2.5-nm resolution represents a compact density with diameter of the membrane part of ~9 nm and height ~11 nm. Analysis of the images of rKCNQ1 in nanodiscs revealed additional electron density corresponding to the lipid bilayer fragment and the MSP2N2 protein. These results indicate that the nanodiscs facilitate protein isolation, purification, and stabilization in solution and can be used for further structural studies of human Kv7.1.
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Affiliation(s)
- Z O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - M G Karlova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - D S Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - M P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - E N Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - O S Sokolova
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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18
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Yong KJ, Vaid TM, Shilling PJ, Wu FJ, Williams LM, Deluigi M, Plückthun A, Bathgate RAD, Gooley PR, Scott DJ. Determinants of Ligand Subtype-Selectivity at α 1A-Adrenoceptor Revealed Using Saturation Transfer Difference (STD) NMR. ACS Chem Biol 2018. [PMID: 29537256 DOI: 10.1021/acschembio.8b00191] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
α1A- and α1B-adrenoceptors (α1A-AR and α1B-AR) are closely related G protein-coupled receptors (GPCRs) that modulate the cardiovascular and nervous systems in response to binding epinephrine and norepinephrine. The GPCR gene superfamily is made up of numerous subfamilies that, like α1A-AR and α1B-AR, are activated by the same endogenous agonists but may modulate different physiological processes. A major challenge in GPCR research and drug discovery is determining how compounds interact with receptors at the molecular level, especially to assist in the optimization of drug leads. Nuclear magnetic resonance spectroscopy (NMR) can provide great insight into ligand-binding epitopes, modes, and kinetics. Ideally, ligand-based NMR methods require purified, well-behaved protein samples. The instability of GPCRs upon purification in detergents, however, makes the application of NMR to study ligand binding challenging. Here, stabilized α1A-AR and α1B-AR variants were engineered using Cellular High-throughput Encapsulation, Solubilization, and Screening (CHESS), allowing the analysis of ligand binding with Saturation Transfer Difference NMR (STD NMR). STD NMR was used to map the binding epitopes of epinephrine and A-61603 to both receptors, revealing the molecular determinants for the selectivity of A-61603 for α1A-AR over α1B-AR. The use of stabilized GPCRs for ligand-observed NMR experiments will lead to a deeper understanding of binding processes and assist structure-based drug design.
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Affiliation(s)
- Kelvin J. Yong
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tasneem M. Vaid
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Patrick J. Shilling
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Feng-Jie Wu
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lisa M. Williams
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
| | - Mattia Deluigi
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Ross A. D. Bathgate
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul R. Gooley
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Daniel J. Scott
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
- The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
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19
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Phosphorylation-induced conformation of β 2-adrenoceptor related to arrestin recruitment revealed by NMR. Nat Commun 2018; 9:194. [PMID: 29335412 PMCID: PMC5768704 DOI: 10.1038/s41467-017-02632-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023] Open
Abstract
The C-terminal region of G-protein-coupled receptors (GPCRs), stimulated by agonist binding, is phosphorylated by GPCR kinases, and the phosphorylated GPCRs bind to arrestin, leading to the cellular responses. To understand the mechanism underlying the formation of the phosphorylated GPCR-arrestin complex, we performed NMR analyses of the phosphorylated β2-adrenoceptor (β2AR) and the phosphorylated β2AR–β-arrestin 1 complex, in the lipid bilayers of nanodisc. Here we show that the phosphorylated C-terminal region adheres to either the intracellular side of the transmembrane region or lipids, and that the phosphorylation of the C-terminal region allosterically alters the conformation around M2155.54 and M2796.41, located on transemembrane helices 5 and 6, respectively. In addition, we found that the conformation induced by the phosphorylation is similar to that corresponding to the β-arrestin-bound state. The phosphorylation-induced structures revealed in this study propose a conserved structural motif of GPCRs that enables β-arrestin to recognize dozens of GPCRs. Upon stimulation by agonist binding, the C-terminal regions of G-protein-coupled receptors (GPCRs) become phosphorylated by GPCR kinases, and phosphorylated GPCRs bind arrestin. Here the authors give structural insights into the phosphorylation induced conformational changes in GPCRs by performing NMR studies with the β2-adrenoceptor.
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20
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Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y. Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2018; 57:2072-2076. [PMID: 29266648 DOI: 10.1002/anie.201710147] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/06/2017] [Indexed: 12/21/2022]
Abstract
Building upon DNA origami technology, we introduce a method to reconstitute a single membrane protein into a self-assembled DNA nanobarrel that scaffolds a nanodisc-like lipid environment. Compared with the membrane-scaffolding-protein nanodisc technique, our approach gives rise to defined stoichiometry, controlled sizes, as well as enhanced stability and homogeneity in membrane protein reconstitution. We further demonstrate potential applications of the DNA nanobarrels in the structural analysis of membrane proteins.
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Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shuobing Chen
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, and Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, and Center for Quantitative Biology, Peking University, Beijing, 100871, China
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21
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Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y. Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
| | - Shuobing Chen
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Youdong Mao
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
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22
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Dynamic domain arrangement of CheA-CheY complex regulates bacterial thermotaxis, as revealed by NMR. Sci Rep 2017; 7:16462. [PMID: 29184123 PMCID: PMC5705603 DOI: 10.1038/s41598-017-16755-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
Bacteria utilize thermotaxis signal transduction proteins, including CheA, and CheY, to switch the direction of the cell movement. However, the thermally responsive machinery enabling warm-seeking behavior has not been identified. Here we examined the effects of temperature on the structure and dynamics of the full-length CheA and CheY complex, by NMR. Our studies revealed that the CheA-CheY complex exists in equilibrium between multiple states, including one state that is preferable for the autophosphorylation of CheA, and another state that is preferable for the phosphotransfer from CheA to CheY. With increasing temperature, the equilibrium shifts toward the latter state. The temperature-dependent population shift of the dynamic domain arrangement of the CheA-CheY complex induced changes in the concentrations of phosphorylated CheY that are comparable to those induced by chemical attractants or repellents. Therefore, the dynamic domain arrangement of the CheA-CheY complex functions as the primary thermally responsive machinery in warm-seeking behavior.
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23
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Nuclear Magnetic Resonance Approaches for Characterizing Protein-Protein Interactions. Methods Mol Biol 2017. [PMID: 29058188 DOI: 10.1007/978-1-4939-7362-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The gating of potassium ion (K+) channels is regulated by various kinds of protein-protein interactions (PPIs). Structural investigations of these PPIs provide useful information not only for understanding the gating mechanisms of K+ channels, but also for developing the pharmaceutical compounds targeting K+ channels. Here, we describe a nuclear magnetic resonance spectroscopic method, termed the cross saturation (CS) method, to accurately determine the binding surfaces of protein complexes, and its application to the investigation of the interaction between a G protein-coupled inwardly rectifying K+ channel and a G protein α subunit.
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24
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Rouck J, Krapf J, Roy J, Huff H, Das A. Recent advances in nanodisc technology for membrane protein studies (2012-2017). FEBS Lett 2017; 591:2057-2088. [PMID: 28581067 PMCID: PMC5751705 DOI: 10.1002/1873-3468.12706] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 01/01/2023]
Abstract
Historically, the main barrier to membrane protein investigations has been the tendency of membrane proteins to aggregate (due to their hydrophobic nature), in aqueous solution as well as on surfaces. The introduction of biomembrane mimetics has since stimulated momentum in the field. One such mimetic, the nanodisc (ND) system, has proved to be an exceptional system for solubilizing membrane proteins. Herein, we critically evaluate the advantages and imperfections of employing nanodiscs in biophysical and biochemical studies. Specifically, we examine the techniques that have been modified to study membrane proteins in nanodiscs. Techniques discussed here include fluorescence microscopy, solution-state/solid-state nuclear magnetic resonance, electron microscopy, small-angle X-ray scattering, and several mass spectroscopy methods. Newer techniques such as SPR, charge-sensitive optical detection, and scintillation proximity assays are also reviewed. Lastly, we cover how nanodiscs are advancing nanotechnology through nanoplasmonic biosensing, lipoprotein-nanoplatelets, and sortase-mediated labeling of nanodiscs.
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Affiliation(s)
- John Rouck
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - John Krapf
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Jahnabi Roy
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Hannah Huff
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Aditi Das
- Department of Comparative Biosciences, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Beckman Institute for Advanced Science, Division of Nutritional Sciences, Neuroscience Program and Department of Bioengineering, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
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25
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Expression, Purification, and Monitoring of Conformational Changes of hCB2 TMH67H8 in Different Membrane-Mimetic Lipid Mixtures Using Circular Dichroism and NMR Techniques. MEMBRANES 2017; 7:membranes7010010. [PMID: 28218648 PMCID: PMC5371971 DOI: 10.3390/membranes7010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 12/13/2022]
Abstract
This work was intended to develop self-assembly lipids for incorporating G-protein coupled receptors (GPCRs) in order to improve the success rate for nuclear magnetic resonance spectroscopy (NMR) structural elucidation. We hereby report the expression and purification of uniformly 15N-labeled human cannabinoid receptor-2 domain in insect cell media. The domain was refolded by screening several membrane mimetic environments. Different q ratios of isotropic bicelles were screened for solubilizing transmembrane helix 6, 7 and 8 (TMH67H8). As the concentration of dimyristoylphosphocholine (DMPC) was increased such that the q ratio was between 0.16 and 0.42, there was less crowding in the cross peaks with increasing q ratio. In bicelles of q = 0.42, the maximum number of cross peaks were obtained and the cross peaks were uniformly dispersed. The receptor domain in bicelles beyond q = 0.42 resulted in peak crowding. These studies demonstrate that GPCRs folding especially in bicelles is protein-specific and requires the right mix of the longer chain and shorter chain lipids to provide the right environment for proper folding. These findings will allow further development of novel membrane mimetics to provide greater diversity of lipid mixtures than those currently being employed for GPCR stability and folding, which are critical for both X-ray and NMR studies of GPCRs.
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26
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The power, pitfalls and potential of the nanodisc system for NMR-based studies. Biol Chem 2016; 397:1335-1354. [DOI: 10.1515/hsz-2016-0224] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.
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27
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Neale C, Herce HD, Pomès R, García AE. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor? Biophys J 2016; 109:1652-62. [PMID: 26488656 DOI: 10.1016/j.bpj.2015.08.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane's cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - Henry D Herce
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Angel E García
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.
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28
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Kleist AB, Getschman AE, Ziarek JJ, Nevins AM, Gauthier PA, Chevigné A, Szpakowska M, Volkman BF. New paradigms in chemokine receptor signal transduction: Moving beyond the two-site model. Biochem Pharmacol 2016; 114:53-68. [PMID: 27106080 DOI: 10.1016/j.bcp.2016.04.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Abstract
Chemokine receptor (CKR) signaling forms the basis of essential immune cellular functions, and dysregulated CKR signaling underpins numerous disease processes of the immune system and beyond. CKRs, which belong to the seven transmembrane domain receptor (7TMR) superfamily, initiate signaling upon binding of endogenous, secreted chemokine ligands. Chemokine-CKR interactions are traditionally described by a two-step/two-site mechanism, in which the CKR N-terminus recognizes the chemokine globular core (i.e. site 1 interaction), followed by activation when the unstructured chemokine N-terminus is inserted into the receptor TM bundle (i.e. site 2 interaction). Several recent studies challenge the structural independence of sites 1 and 2 by demonstrating physical and allosteric links between these supposedly separate sites. Others contest the functional independence of these sites, identifying nuanced roles for site 1 and other interactions in CKR activation. These developments emerge within a rapidly changing landscape in which CKR signaling is influenced by receptor PTMs, chemokine and CKR dimerization, and endogenous non-chemokine ligands. Simultaneous advances in the structural and functional characterization of 7TMR biased signaling have altered how we understand promiscuous chemokine-CKR interactions. In this review, we explore new paradigms in CKR signal transduction by considering studies that depict a more intricate architecture governing the consequences of chemokine-CKR interactions.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Amanda M Nevins
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Pierre-Arnaud Gauthier
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Andy Chevigné
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Martyna Szpakowska
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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29
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Conductance of P2X4 purinergic receptor is determined by conformational equilibrium in the transmembrane region. Proc Natl Acad Sci U S A 2016; 113:4741-6. [PMID: 27071117 DOI: 10.1073/pnas.1600519113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ligand-gated ion channels are partially activated by their ligands, resulting in currents lower than the currents evoked by the physiological full agonists. In the case of P2X purinergic receptors, a cation-selective pore in the transmembrane region expands upon ATP binding to the extracellular ATP-binding site, and the currents evoked by α,β-methylene ATP are lower than the currents evoked by ATP. However, the mechanism underlying the partial activation of the P2X receptors is unknown although the crystal structures of zebrafish P2X4 receptor in the apo and ATP-bound states are available. Here, we observed the NMR signals from M339 and M351, which were introduced in the transmembrane region, and the endogenous alanine and methionine residues of the zebrafish P2X4 purinergic receptor in the apo, ATP-bound, and α,β-methylene ATP-bound states. Our NMR analyses revealed that, in the α,β-methylene ATP-bound state, M339, M351, and the residues that connect the ATP-binding site and the transmembrane region, M325 and A330, exist in conformational equilibrium between closed and open conformations, with slower exchange rates than the chemical shift difference (<100 s(-1)), suggesting that the small population of the open conformation causes the partial activation in this state. Our NMR analyses also revealed that the transmembrane region adopts the open conformation in the state bound to the inhibitor trinitrophenyl-ATP, and thus the antagonism is due to the closure of ion pathways, except for the pore in the transmembrane region: i.e., the lateral cation access in the extracellular region.
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Functional Stability of the Human Kappa Opioid Receptor Reconstituted in Nanodiscs Revealed by a Time-Resolved Scintillation Proximity Assay. PLoS One 2016; 11:e0150658. [PMID: 27035823 PMCID: PMC4817975 DOI: 10.1371/journal.pone.0150658] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/16/2016] [Indexed: 11/19/2022] Open
Abstract
Long-term functional stability of isolated membrane proteins is crucial for many in vitro applications used to elucidate molecular mechanisms, and used for drug screening platforms in modern pharmaceutical industry. Compared to soluble proteins, the understanding at the molecular level of membrane proteins remains a challenge. This is partly due to the difficulty to isolate and simultaneously maintain their structural and functional stability, because of their hydrophobic nature. Here we show, how scintillation proximity assay can be used to analyze time-resolved high-affinity ligand binding to membrane proteins solubilized in various environments. The assay was used to establish conditions that preserved the biological function of isolated human kappa opioid receptor. In detergent solution the receptor lost high-affinity ligand binding to a radiolabelled ligand within minutes at room temperature. After reconstitution in Nanodiscs made of phospholipid bilayer the half-life of high-affinity ligand binding to the majority of receptors increased 70-fold compared to detergent solubilized receptors—a level of stability that is appropriate for further downstream applications. Time-resolved scintillation proximity assay has the potential to screen numerous conditions in parallel to obtain high levels of stable and active membrane proteins, which are intrinsically unstable in detergent solution, and with minimum material consumption.
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Monneau Y, Arenzana-Seisdedos F, Lortat-Jacob H. The sweet spot: how GAGs help chemokines guide migrating cells. J Leukoc Biol 2015; 99:935-53. [DOI: 10.1189/jlb.3mr0915-440r] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/24/2015] [Indexed: 12/19/2022] Open
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Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I. Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ-Opioid Receptor. Angew Chem Int Ed Engl 2015; 54:15771-6. [PMID: 26568421 PMCID: PMC4722849 DOI: 10.1002/anie.201508794] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/19/2015] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptor (GPCR) ligands impart differing degrees of signaling in the G-protein and arrestin pathways, in phenomena called "biased signaling". However, the mechanism underlying the biased signaling of GPCRs is still unclear, although crystal structures of GPCRs bound to the G protein or arrestin are available. In this study, we observed the NMR signals from methionine residues of the μ-opioid receptor (μOR) in the balanced- and biased-ligand-bound states. We found that the intracellular cavity of μOR exists in an equilibrium between closed and multiple open conformations with coupled conformational changes on the transmembrane helices 3, 5, 6, and 7, and that the population of each open conformation determines the G-protein- and arrestin-mediated signaling levels in each ligand-bound state. These findings provide insight into the biased signaling of GPCRs and will be helpful for development of analgesics that stimulate μOR with reduced tolerance and dependence.
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Affiliation(s)
- Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0075 (Japan)
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Motohiko Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Naoyuki Nobuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Kento Onishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Masahiro Maeda
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561-0825 (Japan)
| | - Hideki Tsujishita
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561-0825 (Japan)
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan).
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Yoshiura C, Ueda T, Kofuku Y, Matsumoto M, Okude J, Kondo K, Shiraishi Y, Shimada I. Elucidation of the CCR1- and CCR5-binding modes of MIP-1α by application of an NMR spectra reconstruction method to the transferred cross-saturation experiments. JOURNAL OF BIOMOLECULAR NMR 2015; 63:333-340. [PMID: 26472202 PMCID: PMC4662715 DOI: 10.1007/s10858-015-9992-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/10/2015] [Indexed: 05/14/2023]
Abstract
C-C chemokine receptor 1 (CCR1) and CCR5 are involved in various inflammation and immune responses, and regulate the progression of the autoimmune diseases differently. However, the number of residues identified at the binding interface was not sufficient to clarify the differences in the CCR1- and CCR5-binding modes to MIP-1α, because the NMR measurement time for CCR1 and CCR5 samples was limited to 24 h, due to their low stability. Here we applied a recently developed NMR spectra reconstruction method, Conservation of experimental data in ANAlysis of FOuRier, to the amide-directed transferred cross-saturation experiments of chemokine receptors, CCR1 and CCR5, embedded in lipid bilayers of the reconstituted high density lipoprotein, and MIP-1α. Our experiments revealed that the residues on the N-loop and β-sheets of MIP-1α are close to both CCR1 and CCR5, and those in the C-terminal helix region are close to CCR5. These results suggest that the genetic influence of the single nucleotide polymorphisms of MIP-1α that accompany substitution of residues in the C-terminal helix region, E57 and V63, would provide clues toward elucidating how the CCR5-MIP-1α interaction affects the progress of autoimmune diseases.
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Affiliation(s)
- Chie Yoshiura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masahiko Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Japan Biological Informatics Consortium, Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Wiesner S, Sprangers R. Methyl groups as NMR probes for biomolecular interactions. Curr Opin Struct Biol 2015; 35:60-7. [DOI: 10.1016/j.sbi.2015.08.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 11/26/2022]
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Okude J, Ueda T, Kofuku Y, Sato M, Nobuyama N, Kondo K, Shiraishi Y, Mizumura T, Onishi K, Natsume M, Maeda M, Tsujishita H, Kuranaga T, Inoue M, Shimada I. Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ‐Opioid Receptor. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Junya Okude
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Chiyoda‐ku, Tokyo 102‐0075 (Japan)
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Motohiko Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Naoyuki Nobuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Keita Kondo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yutaro Shiraishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takuya Mizumura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Kento Onishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Mei Natsume
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Masahiro Maeda
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561‐0825 (Japan)
| | - Hideki Tsujishita
- Shionogi Co., Ltd., Discovery Research Laboratories, Osaka 561‐0825 (Japan)
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7‐3‐1, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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Milić D, Veprintsev DB. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front Pharmacol 2015; 6:66. [PMID: 25873898 PMCID: PMC4379943 DOI: 10.3389/fphar.2015.00066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/13/2015] [Indexed: 01/26/2023] Open
Abstract
Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.
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Affiliation(s)
- Dalibor Milić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland ; Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich Switzerland
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Martínez-Muñoz L, Barroso R, Paredes AG, Mellado M, Rodríguez-Frade JM. Methods to immobilize GPCR on the surface of SPR sensors. Methods Mol Biol 2015; 1272:173-188. [PMID: 25563184 DOI: 10.1007/978-1-4939-2336-6_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The G protein-coupled receptors (GPCRs) form one of the largest membrane receptor families. The nature of the ligands that interact with these receptors is highly diverse; they include light, peptides and hormones, neurotransmitters, and small molecular weight compounds. The GPCRs are involved in a wide variety of physiological processes and thus hold considerable therapeutic potential.GPCR function is usually determined in cell-based assays, whose complexity nonetheless limits their use. The use of alternative, cell-free assays is hampered by the difficulties in purifying these seven-transmembrane domain receptors without altering their functional properties. Several methods have been proposed to immobilize GPCR on biosensor surfaces which use antibodies or avidin-/biotin-based capture procedures, alone or with reconstitution of the GPCR physiological microenvironment. Here we propose a method for GPCR immobilization in their native membrane microenvironment that requires no manipulation of the target receptor and maintains the many conformations GPCR can adopt in the cell membrane.
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Affiliation(s)
- Laura Martínez-Muñoz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain
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Kofuku Y, Ueda T, Okude J, Shiraishi Y, Kondo K, Mizumura T, Suzuki S, Shimada I. Functional Dynamics of Deuterated β2-Adrenergic Receptor in Lipid Bilayers Revealed by NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406603] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Kofuku Y, Ueda T, Okude J, Shiraishi Y, Kondo K, Mizumura T, Suzuki S, Shimada I. Functional dynamics of deuterated β2 -adrenergic receptor in lipid bilayers revealed by NMR spectroscopy. Angew Chem Int Ed Engl 2014; 53:13376-9. [PMID: 25284766 DOI: 10.1002/anie.201406603] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/13/2014] [Indexed: 11/11/2022]
Abstract
G-protein-coupled receptors (GPCRs) exist in conformational equilibrium between active and inactive states, and the former population determines the efficacy of signaling. However, the conformational equilibrium of GPCRs in lipid bilayers is unknown owing to the low sensitivities of their NMR signals. To increase the signal intensities, a deuteration method was developed for GPCRs expressed in an insect cell/baculovirus expression system. The NMR sensitivities of the methionine methyl resonances from the β2 -adrenergic receptor (β2 AR) in lipid bilayers of reconstituted high-density lipoprotein (rHDL) increased by approximately 5-fold upon deuteration. NMR analyses revealed that the exchange rates for the conformational equilibrium of β2 AR in rHDLs were remarkably different from those measured in detergents. The timescales of GPCR signaling, calculated from the exchange rates, are faster than those of receptor tyrosine kinases and thus enable rapid neurotransmission and sensory perception.
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Affiliation(s)
- Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 (Japan)
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Abstract
Structural analyses of protein-protein interactions are required to reveal their functional mechanisms, and accurate protein-protein complex models, based on experimental results, are the starting points for drug development. In addition, structural information about proteins under physiologically relevant conditions is crucially important for understanding biological events. However, for proteins such as those embedded in lipid bilayers and transiently complexed with their effectors under physiological conditions, structural analyses by conventional methods are generally difficult, due to their large molecular weights and inhomogeneity. We have developed the cross-saturation (CS) method, which is an nuclear magnetic resonance measurement technique for the precise identification of the interfaces of protein-protein complexes. In addition, we have developed an extended version of the CS method, termed transferred cross-saturation (TCS), which enables the identification of the residues of protein ligands in close proximity to huge (>150 kDa) and heterogeneous complexes under fast exchange conditions (>0.1 s(-1)). Here, we discuss the outline, basic theory, and practical considerations of the CS and TCS methods. In addition, we will review the recent progress in the construction of models of protein-protein complexes, based on CS and TCS experiments, and applications of TCS to in situ analyses of biologically and medically important proteins in physiologically relevant states.
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Nishida N, Osawa M, Takeuchi K, Imai S, Stampoulis P, Kofuku Y, Ueda T, Shimada I. Functional dynamics of cell surface membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:86-96. [PMID: 24331735 DOI: 10.1016/j.jmr.2013.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 06/03/2023]
Abstract
Cell surface receptors are integral membrane proteins that receive external stimuli, and transmit signals across plasma membranes. In the conventional view of receptor activation, ligand binding to the extracellular side of the receptor induces conformational changes, which convert the structure of the receptor into an active conformation. However, recent NMR studies of cell surface membrane proteins have revealed that their structures are more dynamic than previously envisioned, and they fluctuate between multiple conformations in an equilibrium on various timescales. In addition, NMR analyses, along with biochemical and cell biological experiments indicated that such dynamical properties are critical for the proper functions of the receptors. In this review, we will describe several NMR studies that revealed direct linkage between the structural dynamics and the functions of the cell surface membrane proteins, such as G-protein coupled receptors (GPCRs), ion channels, membrane transporters, and cell adhesion molecules.
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Affiliation(s)
- Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koh Takeuchi
- Molecular Profiling Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Shunsuke Imai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Pavlos Stampoulis
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Expression, surface immobilization, and characterization of functional recombinant cannabinoid receptor CB2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2045-56. [PMID: 23777860 DOI: 10.1016/j.bbapap.2013.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 06/05/2013] [Accepted: 06/07/2013] [Indexed: 11/23/2022]
Abstract
Human peripheral cannabinoid receptor CB2, a G protein-coupled receptor (GPCR) involved in regulation of immune response has become an important target for pharmaceutical drug development. Structural and functional studies on CB2 may benefit from immobilization of the purified and functional receptor onto a suitable surface at a controlled density and, preferably in a uniform orientation. The goal of this project was to develop a generic strategy for preparation of functional recombinant CB2 and immobilization at solid interfaces. Expression of CB2 as a fusion with Rho-tag (peptide composed of the last nine amino acids of rhodopsin) in E. coli was evaluated in terms of protein levels, accessibility of the tag, and activity of the receptor. The structural integrity of CB2 was tested by ligand binding to the receptor solubilized in detergent micelles, captured on tag-specific monoclonal 1D4 antibody-coated resin. Highly pure and functional CB2 was obtained by sequential chromatography on a 1D4- and Ni-NTA-resin and its affinity to the 1D4 antibody characterized by surface plasmon resonance (SPR). Either the purified receptor or fusion CB2 from the crude cell extract was captured onto a 1D4-coated CM4 chip (Biacore) in a quantitative fashion at uniform orientation as demonstrated by the SPR signal. Furthermore, the accessibility of the extracellular surface of immobilized CB2 and the affinity of interaction with a novel monoclonal antibody NAA-1 was studied by SPR. In summary, we present an integral strategy for purification, surface immobilization, ligand- and antibody binding studies of functional cannabinoid receptor CB2.
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Vega B, Calle A, Sánchez A, Lechuga LM, Ortiz AM, Armelles G, Rodríguez-Frade JM, Mellado M. Real-time detection of the chemokine CXCL12 in urine samples by surface plasmon resonance. Talanta 2013; 109:209-15. [PMID: 23618162 DOI: 10.1016/j.talanta.2013.02.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 11/25/2022]
Abstract
Surface plasmon resonance (SPR)-based biosensors are established tools for measuring biomolecular interactions between unlabeled analytes in real time, and are thus an ideal method to evaluate G protein-coupled receptor (GPCR) binding interactions. Using as a vehicle lentiviral particles bearing the chemokine receptor CXCR4 in its native plasma membrane context, SPR analysis can be performed using the particles as specific receptors to monitor the CXCR4 interaction with its ligand, CXCL12. The method shows linear correlation in the 5-40 nM range, with low intra- and inter-assay variation, a relative standard deviation <10%, chip-to-chip variation <12%, with stability of the sensor response for more than 150 measurements in the same chip over a four-week period. Our objective was to develop a method for rapid detection and quantification of analytes such as CXCL12 in biological samples, with no need for pretreatment. As a proof of concept, we tested for CXCL12 in urine samples from rheumatoid arthritis patients, who have elevated levels of this chemokine in plasma and synovial fluid. The biosensor method allowed sensitive, reproducible CXCL12 detection in the physiological range, suggesting its value for the diagnosis of autoimmune disorders.
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Affiliation(s)
- Beatriz Vega
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Campus de Cantoblanco, Madrid, Spain
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Chemokine oligomerization in cell signaling and migration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:531-78. [PMID: 23663982 DOI: 10.1016/b978-0-12-386931-9.00020-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemokines are small proteins best known for their role in controlling the migration of diverse cells, particularly leukocytes. Upon binding to their G-protein-coupled receptors on the leukocytes, chemokines stimulate the signaling events that cause cytoskeletal rearrangements involved in cell movement, and migration of the cells along chemokine gradients. Depending on the cell type, chemokines also induce many other types of cellular responses including those related to defense mechanisms, cell proliferation, survival, and development. Historically, most research efforts have focused on the interaction of chemokines with their receptors, where monomeric forms of the ligands are the functionally relevant state. More recently, however, the importance of chemokine interactions with cell surface glycosaminoglycans has come to light, and in most cases appears to involve oligomeric chemokine structures. This review summarizes existing knowledge relating to the structure and function of chemokine oligomers, and emerging methodology for determining structures of complex chemokine assemblies in the future.
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Xie XQ, Chowdhury A. Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors. Methods Enzymol 2013; 520:153-74. [PMID: 23332699 DOI: 10.1016/b978-0-12-391861-1.00007-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design.
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Affiliation(s)
- Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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Nguyen LT, Vogel HJ. Structural perspectives on antimicrobial chemokines. Front Immunol 2012; 3:384. [PMID: 23293636 PMCID: PMC3531597 DOI: 10.3389/fimmu.2012.00384] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/30/2012] [Indexed: 12/14/2022] Open
Abstract
Chemokines are best known as signaling proteins in the immune system. Recently however, a large number of human chemokines have been shown to exert direct antimicrobial activity. This moonlighting activity appears to be related to the net high positive charge of these immune signaling proteins. Chemokines can be divided into distinct structural elements and some of these have been studied as isolated peptide fragments that can have their own antimicrobial activity. Such peptides often encompass the α-helical region found at the C-terminal end of the parent chemokines, which, similar to other antimicrobial peptides, adopt a well-defined membrane-bound amphipathic structure. Because of their relatively small size, intact chemokines can be studied effectively by NMR spectroscopy to examine their structures in solution. In addition, NMR relaxation experiments of intact chemokines can provide detailed information about the intrinsic dynamic behavior; such analyses have helped for example to understand the activity of TC-1, an antimicrobial variant of CXCL7/NAP-2. With chemokine dimerization and oligomerization influencing their functional properties, the use of NMR diffusion experiments can provide information about monomer-dimer equilibria in solution. Furthermore, NMR chemical shift perturbation experiments can be used to map out the interface between self-associating subunits. Moreover, the unusual case of XCL1/lymphotactin presents a chemokine that can interconvert between two distinct folds in solution, both of which have been elucidated. Finally, recent advances have allowed for the determination of the structures of chemokines in complex with glycosaminoglycans, a process that could interfere with their antimicrobial activity. Taken together, these studies highlight several different structural facets that contribute to the way in which chemokines exert their direct microbicidal actions.
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Affiliation(s)
- Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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Ziarek JJ, Volkman BF. NMR in the Analysis of Functional Chemokine Interactions and Drug Discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e227-314. [PMID: 23166561 DOI: 10.1016/j.ddtec.2012.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The involvement of chemokines and chemokine receptors in a great variety of pathological indications underscores their utility as therapeutic targets. In general, chemokine-mediated migration and signaling requires three distinct interactions: self-association, glycosaminoglycan (GAG) binding, and activation of G protein-coupled receptors (GPCRs). Solution-state nuclear magnetic resonance (NMR) spectroscopy has long been used to determine the apo structure of chemokines and monitor complex formation; however, it has never contributed directly to drug discovery efforts that are traditionally focused on the previously inaccessible chemokine receptors. Our lab recently demonstrated that NMR structures can be successfully utilized to direct drug discovery against chemokines. The ease of collecting chemokine structural data coupled with the increased efficiency of structure-based drug discovery campaigns makes chemokine-directed therapies particularly attractive. In addition, recent advances in sample preparation, spectrometer hardware, and pulse program development are allowing researchers to examine interactions with previously inaccessible partners - including full-length chemokine receptors. These developments will facilitate exploration of novel ways to modulate chemokine activity using structure-guided drug discovery.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biochemistry, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, Wisconsin 53226 USA
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48
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HDL-like discs for assaying membrane proteins in drug discovery. Biophys Chem 2012; 165-166:56-61. [DOI: 10.1016/j.bpc.2012.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 03/09/2012] [Indexed: 01/03/2023]
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Mase Y, Yokogawa M, Osawa M, Shimada I. Structural basis for modulation of gating property of G protein-gated inwardly rectifying potassium ion channel (GIRK) by i/o-family G protein α subunit (Gαi/o). J Biol Chem 2012; 287:19537-49. [PMID: 22511772 DOI: 10.1074/jbc.m112.353888] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-gated inwardly rectifying potassium channel (GIRK) plays a crucial role in regulating heart rate and neuronal excitability. The gating of GIRK is regulated by the association and dissociation of G protein βγ subunits (Gβγ), which are released from pertussis toxin-sensitive G protein α subunit (Gα(i/o)) upon GPCR activation in vivo. Several lines of evidence indicate that Gα(i/o) also interacts directly with GIRK, playing functional roles in the signaling efficiency and the modulation of the channel activity. However, the underlying mechanism for GIRK regulation by Gα(i/o) remains to be elucidated. Here, we performed NMR analyses of the interaction between the cytoplasmic region of GIRK1 and Gα(i3) in the GTP-bound state. The NMR spectral changes of Gα upon the addition of GIRK as well as the transferred cross-saturation (TCS) results indicated their direct binding mode, where the K(d) value was estimated as ∼1 mm. The TCS experiments identified the direct binding sites on Gα and GIRK as the α2/α3 helices on the GTPase domain of Gα and the αA helix of GIRK. In addition, the TCS and paramagnetic relaxation enhancement results suggested that the helical domain of Gα transiently interacts with the αA helix of GIRK. Based on these results, we built a docking model of Gα and GIRK, suggesting the molecular basis for efficient GIRK deactivation by Gα(i/o).
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Affiliation(s)
- Yoko Mase
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Stampoulis P, Ueda T, Matsumoto M, Terasawa H, Miyano K, Sumimoto H, Shimada I. Atypical membrane-embedded phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2)-binding site on p47(phox) Phox homology (PX) domain revealed by NMR. J Biol Chem 2012; 287:17848-17859. [PMID: 22493288 DOI: 10.1074/jbc.m111.332874] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Phox homology (PX) domain is a functional module that targets membranes through specific interactions with phosphoinositides. The p47(phox) PX domain preferably binds phosphatidylinositol 3,4-bisphosphate (PI(3,4)P(2)) and plays a pivotal role in the assembly of phagocyte NADPH oxidase. We describe the PI(3,4)P(2) binding mode of the p47(phox) PX domain as identified by a transferred cross-saturation experiment. The identified PI(3,4)P(2)-binding site, which includes the residues of helices α1 and α1' and the following loop up to the distorted left-handed PP(II) helix, is located at a unique position, as compared with the phosphoinositide-binding sites of all other PX domains characterized thus far. Mutational analyses corroborated the results of the transferred cross-saturation experiments. Moreover, experiments with intact cells demonstrated the importance of this unique binding site for the function of the NADPH oxidase. The low affinity and selectivity of the atypical phosphoinositide-binding site on the p47(phox) PX domain suggest that different types of phosphoinositides sequentially bind to the p47(phox) PX domain, allowing the regulation of the multiple events that characterize the assembly and activation of phagocyte NADPH oxidase.
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Affiliation(s)
- Pavlos Stampoulis
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033; Japan Biological Informatics Consortium, Tokyo 104-0032
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033
| | - Masahiko Matsumoto
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033
| | - Hiroaki Terasawa
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033
| | - Kei Miyano
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582
| | - Hideki Sumimoto
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033; Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.
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