1
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Ma XB, Yue CX, Liu Y, Yang Y, Wang J, Yang XN, Huang LD, Zhu MX, Hattori M, Li CZ, Yu Y, Guo CR. A shared mechanism for TNP-ATP recognition by members of the P2X receptor family. Comput Struct Biotechnol J 2024; 23:295-308. [PMID: 38173879 PMCID: PMC10762375 DOI: 10.1016/j.csbj.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show that a common mechanism of TNP-ATP recognition exists for the P2X family members by combining enhanced conformation sampling, engineered disulfide bond analysis, and covalent occupancy. In this model, the polar triphosphate moiety of TNP-ATP interacts with the orthosteric site, while its TNP-moiety is deeply embedded in the head and dorsal fin (DF) interface, creating a restrictive allostery in these two domains that results in a partly enlarged yet ion-impermeable pore. Similar results were obtained from multiple P2X subtypes of different species, including ckP2X7, hP2X3, rat P2X2 (rP2X2), and human P2X1 (hP2X1). Thus, TNP-ATP uses a common mechanism for P2X recognition and modulation by restricting the movements of the head and DF domains which are essential for P2X activation. This knowledge is applicable to the development of new P2X inhibitors.
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Affiliation(s)
- Xiao-Bo Ma
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chen-Xi Yue
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Na Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Dong Huang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Michael X. Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chang-Zhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Ye Yu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Chang-Run Guo
- School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR. MEMBRANES 2021; 11:membranes11080604. [PMID: 34436367 PMCID: PMC8398610 DOI: 10.3390/membranes11080604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 01/02/2023]
Abstract
A primary biological function of multi-spanning membrane proteins is to transfer information and/or materials through a membrane by changing their conformations. Therefore, particular dynamics of the membrane proteins are tightly associated with their function. The semi-atomic resolution dynamics information revealed by NMR is able to discriminate function-related dynamics from random fluctuations. This review will discuss several studies in which quantitative dynamics information by solution NMR has contributed to revealing the structural basis of the function of multi-spanning membrane proteins, such as ion channels, GPCRs, and transporters.
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Lokale Deuterierung ermöglicht NMR‐Messung von Methylgruppen in Proteinen aus eukaryotischen und Zell‐freien Expressionssystemen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Thibault Viennet
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Sandeep Chhabra
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Shantha Elter
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Jan Borggräfe
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Aldino Viegas
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Radosław P. Nowak
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Ognyan Petrov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Eric S. Fischer
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Manuel Etzkorn
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Haribabu Arthanari
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
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4
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Local Deuteration Enables NMR Observation of Methyl Groups in Proteins from Eukaryotic and Cell-Free Expression Systems. Angew Chem Int Ed Engl 2021; 60:13783-13787. [PMID: 33768661 PMCID: PMC8251921 DOI: 10.1002/anie.202016070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Indexed: 01/13/2023]
Abstract
Therapeutically relevant proteins such as GPCRs, antibodies and kinases face clear limitations in NMR studies due to the challenges in site-specific isotope labeling and deuteration in eukaryotic expression systems. Here we describe an efficient and simple method to observe the methyl groups of leucine residues in proteins expressed in bacterial, eukaryotic or cell-free expression systems without modification of the expression protocol. The method relies on simple stereo-selective 13 C-labeling and deuteration of leucine that alleviates the need for additional deuteration of the protein. The spectroscopic benefits of "local" deuteration are examined in detail through Forbidden Coherence Transfer (FCT) experiments and simulations. The utility of this labeling method is demonstrated in the cell-free synthesis of bacteriorhodopsin and in the insect-cell expression of the RRM2 domain of human RBM39.
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Affiliation(s)
- Abhinav Dubey
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Thibault Viennet
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Sandeep Chhabra
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Shantha Elter
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Jan Borggräfe
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Aldino Viegas
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Radosław P. Nowak
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Ognyan Petrov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Eric S. Fischer
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Manuel Etzkorn
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Vladimir Gelev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Haribabu Arthanari
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
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5
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Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH. Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose. Glycobiology 2021; 31:425-435. [PMID: 32902634 PMCID: PMC8091466 DOI: 10.1093/glycob/cwaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/02/2023] Open
Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and some unexpected truncation of the amino acid sequence. The labeling of both the protein (through alanines) and the glycans in a single culture requiring no additional technical expertise past standard mammalian expression requirements is anticipated to have several applications, including structural and functional screening of the many glycosylated proteins important to human health.
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Affiliation(s)
- Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology
| | | | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
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6
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Zhang WJ, Zhu ZM, Liu ZX. The role of P2X4 receptor in neuropathic pain and its pharmacological properties. Pharmacol Res 2020; 158:104875. [PMID: 32407956 DOI: 10.1016/j.phrs.2020.104875] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/02/2020] [Accepted: 04/24/2020] [Indexed: 12/21/2022]
Abstract
Neuropathic pain (NPP) is a common symptom of most diseases in clinic, which seriously affects the mental health of patients and brings certain pain to patients. Due to its pathological mechanism is very complicated, and thus, its treatment has been one of the challenges in the field of medicine. Therefore, exploring the pathogenesis and treatment approach of NPP has aroused the interest of many researchers. ATP is an important energy information substance, which participates in the signal transmission in the body. The P2 × 4 receptor (P2 × 4R) is dependent on ATP ligand-gated cationic channel receptor, which can be activated by ATP and plays an important role in the transmission of information in the nervous system and the formation of pain. In this paper, we provide a comprehensive review of the structure and function of the P2 × 4R gene. We also discuss the pathogenesis of NPP and the intrinsic relationship between P2 × 4R and NPP. Moreover, we explore the pharmacological properties of P2 × 4R antagonists or inhibitors used as targeted therapies for NPP.
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Affiliation(s)
- Wen-Jun Zhang
- The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi province, 343000, China.
| | - Zheng-Ming Zhu
- The Second Affiliated Hospital, Nanchang University, Nanchang City, Jiangxi province, 343000, China.
| | - Zeng-Xu Liu
- Basic Medicine, Nanchang University, Nanchang City, Jiangxi province, 343000, China
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7
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Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR. Int J Mol Sci 2020; 21:ijms21051829. [PMID: 32155847 PMCID: PMC7084655 DOI: 10.3390/ijms21051829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.
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8
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Conformational equilibrium defines the variable induction of the multidrug-binding transcriptional repressor QacR. Proc Natl Acad Sci U S A 2019; 116:19963-19972. [PMID: 31527244 DOI: 10.1073/pnas.1906129116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
QacR, a multidrug-binding transcriptional repressor in pathogenic bacteria Staphylococcus aureus, modulates the transcriptional level of the multidrug transporter gene, qacA, in response to engaging a set of diverse ligands. However, the structural basis that defines the variable induction level remains unknown. Here, we reveal that the conformational equilibrium between the repressive and inducive conformations in QacR defines the induction level of the transporter gene. In addition, the unligated QacR is already partly populated in the inducive conformation, allowing the basal expression of the transporter. We also showed that, in the known constitutively active QacR mutants, the equilibrium is shifted more toward the inducive conformation, even in the unligated state. These results highlight the unexpected structural mechanism, connecting the promiscuous multidrug binding to the variable transcriptional regulation of QacR, which provide clues to dysfunctioning of the multidrug resistance systems.
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9
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Ueda T, Kofuku Y, Okude J, Imai S, Shiraishi Y, Shimada I. Function-related conformational dynamics of G protein-coupled receptors revealed by NMR. Biophys Rev 2019; 11:409-418. [PMID: 31102199 PMCID: PMC6557943 DOI: 10.1007/s12551-019-00539-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/26/2019] [Indexed: 11/26/2022] Open
Abstract
G protein-coupled receptors (GPCRs) function as receptors for various neurotransmitters, hormones, cytokines, and metabolites. GPCR ligands impart differing degrees of signaling in the G protein and arrestin pathways, in phenomena called biased signaling, and each ligand for a given GPCR has a characteristic level of ability to activate or deactivate its target, which is referred to as its efficacy. The ligand efficacies and biased signaling of GPCRs remarkably affect the therapeutic properties of the ligands. However, these features of GPCRs can only be partially understood from the crystallography data, although numerous GPCR structures have been solved. NMR analyses have revealed that GPCRs have multiple interconverting substates, exchanging on various timescales, and that the exchange rates are related to the ligand efficacies and biased signaling. In addition, NMR analyses of GPCRs in the lipid bilayer environment of rHDLs revealed that the exchange rates are modulated by the lipid bilayer environment, highlighting the importance of the function-related dynamics in the lipid bilayer. In this review, we will describe several solution NMR studies that have clarified the conformational dynamics related to the ligand efficacy and biased signaling of GPCRs.
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Affiliation(s)
- 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, Kawaguchi, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Junya Okude
- 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
| | - 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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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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11
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Clark L, Dikiy I, Rosenbaum DM, Gardner KH. On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies. JOURNAL OF BIOMOLECULAR NMR 2018; 71:203-211. [PMID: 30121871 PMCID: PMC7282444 DOI: 10.1007/s10858-018-0204-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 05/21/2023]
Abstract
NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. We review the different expression systems for production of isotopically labeled membrane proteins and highlight the use of the yeast Pichia pastoris to achieve perdeuteration and 13C methyl probe incorporation within isoleucine sidechains. We further illustrate the use of this method for labeling of several biomedically significant GPCRs.
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Affiliation(s)
- Lindsay Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA.
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY, 10016, USA.
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12
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Structural basis for the ethanol action on G-protein-activated inwardly rectifying potassium channel 1 revealed by NMR spectroscopy. Proc Natl Acad Sci U S A 2018; 115:3858-3863. [PMID: 29581303 DOI: 10.1073/pnas.1722257115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Ethanol consumption leads to a wide range of pharmacological effects by acting on the signaling proteins in the human nervous system, such as ion channels. Despite its familiarity and biological importance, very little is known about the molecular mechanisms underlying the ethanol action, due to extremely weak binding affinity and the dynamic nature of the ethanol interaction. In this research, we focused on the primary in vivo target of ethanol, G-protein-activated inwardly rectifying potassium channel (GIRK), which is responsible for the ethanol-induced analgesia. By utilizing solution NMR spectroscopy, we characterized the changes in the structure and dynamics of GIRK induced by ethanol binding. We demonstrated here that ethanol binds to GIRK with an apparent dissociation constant of 1.0 M and that the actual physiological binding site of ethanol is located on the cavity formed between the neighboring cytoplasmic regions of the GIRK tetramer. From the methyl-based NMR relaxation analyses, we revealed that ethanol activates GIRK by shifting the conformational equilibrium processes, which are responsible for the gating of GIRK, to stabilize an open conformation of the cytoplasmic ion gate. We suggest that the dynamic molecular mechanism of the ethanol-induced activation of GIRK represents a general model of the ethanol action on signaling proteins in the human nervous system.
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13
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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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14
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Chien CTH, Helfinger LR, Bostock MJ, Solt A, Tan YL, Nietlispach D. An Adaptable Phospholipid Membrane Mimetic System for Solution NMR Studies of Membrane Proteins. J Am Chem Soc 2017; 139:14829-14832. [PMID: 28990386 PMCID: PMC6109379 DOI: 10.1021/jacs.7b06730] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on the saposin-A (SapA) scaffold protein, we demonstrate the suitability of a size-adaptable phospholipid membrane-mimetic system for solution NMR studies of membrane proteins (MPs) under close-to-native conditions. The Salipro nanoparticle size can be tuned over a wide pH range by adjusting the saposin-to-lipid stoichiometry, enabling maintenance of sufficiently high amounts of phospholipid in the Salipro nanoparticle to mimic a realistic membrane environment while controlling the overall size to enable solution NMR for a range of MPs. Three representative MPs, including one G-protein-coupled receptor, were successfully incorporated into SapA-dimyristoylphosphatidylcholine nanoparticles and studied by solution NMR spectroscopy.
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Affiliation(s)
- Chih-Ta Henry Chien
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Lukas R. Helfinger
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Mark J. Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Andras Solt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
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15
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Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel. Nat Commun 2017; 8:876. [PMID: 29026074 PMCID: PMC5638823 DOI: 10.1038/s41467-017-00887-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 08/02/2017] [Indexed: 12/29/2022] Open
Abstract
P2X receptors are non-selective cation channels gated by extracellular ATP, and the P2X7 receptor subtype plays a crucial role in the immune and nervous systems. Altered expression and dysfunctions of P2X7 receptors caused by genetic deletions, mutations, and polymorphic variations have been linked to various diseases, such as rheumatoid arthritis and hypertension. Despite the availability of crystal structures of P2X receptors, the mechanism of competitive antagonist action for P2X receptors remains controversial. Here, we determine the crystal structure of the chicken P2X7 receptor in complex with the competitive P2X antagonist, TNP-ATP. The structure reveals an expanded, incompletely activated conformation of the channel, and identified the unique recognition manner of TNP-ATP, which is distinct from that observed in the previously determined human P2X3 receptor structure. A structure-based computational analysis furnishes mechanistic insights into the TNP-ATP-dependent inhibition. Our work provides structural insights into the functional mechanism of the P2X competitive antagonist. P2X receptors are nonselective cation channels that are gated by extracellular ATP. Here the authors present the crystal structure of chicken P2X7 with its bound competitive antagonist TNP-ATP and give mechanistic insights into TNP-ATP dependent inhibition through further computational analysis and electrophysiology measurements.
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16
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Suurväli J, Boudinot P, Kanellopoulos J, Rüütel Boudinot S. P2X4: A fast and sensitive purinergic receptor. Biomed J 2017; 40:245-256. [PMID: 29179879 PMCID: PMC6138603 DOI: 10.1016/j.bj.2017.06.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 01/31/2023] Open
Abstract
Extracellular nucleotides have been recognized as important mediators of activation, triggering multiple responses via plasma membrane receptors known as P2 receptors. P2 receptors comprise P2X ionotropic receptors and G protein-coupled P2Y receptors. P2X receptors are expressed in many tissues, where they are involved in a number of functions including synaptic transmission, muscle contraction, platelet aggregation, inflammation, macrophage activation, differentiation and proliferation, neuropathic and inflammatory pain. P2X4 is one of the most sensitive purinergic receptors (at nanomolar ATP concentrations), about one thousand times more than the archetypal P2X7. P2X4 is widely expressed in central and peripheral neurons, in microglia, and also found in various epithelial tissues and endothelial cells. It localizes on the plasma membrane, but also in intracellular compartments. P2X4 is preferentially localized in lysosomes, where it is protected from proteolysis by its glycosylation. High ATP concentration in the lysosomes does not activate P2X4 at low pH; P2X4 gets activated by intra-lysosomal ATP only in its fully dissociated tetra-anionic form, when the pH increases to 7.4. Thus, P2X4 is functioning as a Ca2+-channel after the fusion of late endosomes and lysosomes. P2X4 modulates major neurotransmitter systems and regulates alcohol-induced responses in microglia. P2X4 is one of the key receptors mediating neuropathic pain. However, injury-induced upregulation of P2X4 expression is gender dependent and plays a key role in pain difference between males and females. P2X4 is also involved in inflammation. Extracellular ATP being a pro-inflammatory molecule, P2X4 can trigger inflammation in response to high ATP release. It is therefore involved in multiple pathologies, like post-ischemic inflammation, rheumatoid arthritis, airways inflammation in asthma, neurodegenerative diseases and even metabolic syndrome. Although P2X4 remains poorly characterized, more studies are needed as it is likely to be a potential therapeutic target in these multiple pathologies.
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Affiliation(s)
- Jaanus Suurväli
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean Kanellopoulos
- Institute for Integrative Biology of the Cell (I2BC) CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Sirje Rüütel Boudinot
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
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17
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Wang J, Sun LF, Cui WW, Zhao WS, Ma XF, Li B, Liu Y, Yang Y, Hu YM, Huang LD, Cheng XY, Li L, Lu XY, Tian Y, Yu Y. Intersubunit physical couplings fostered by the left flipper domain facilitate channel opening of P2X4 receptors. J Biol Chem 2017; 292:7619-7635. [PMID: 28302727 DOI: 10.1074/jbc.m116.771121] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/03/2017] [Indexed: 12/14/2022] Open
Abstract
P2X receptors are ATP-gated trimeric channels with important roles in diverse pathophysiological functions. A detailed understanding of the mechanism underlying the gating process of these receptors is thus fundamentally important and may open new therapeutic avenues. The left flipper (LF) domain of the P2X receptors is a flexible loop structure, and its coordinated motions together with the dorsal fin (DF) domain are crucial for the channel gating of the P2X receptors. However, the mechanism underlying the crucial role of the LF domain in the channel gating remains obscure. Here, we propose that the ATP-induced allosteric changes of the LF domain enable it to foster intersubunit physical couplings among the DF and two lower body domains, which are pivotal for the channel gating of P2X4 receptors. Metadynamics analysis indicated that these newly established intersubunit couplings correlate well with the ATP-bound open state of the receptors. Moreover, weakening or strengthening these physical interactions with engineered intersubunit metal bridges remarkably decreased or increased the open probability of the receptors, respectively. Further disulfide cross-linking and covalent modification confirmed that the intersubunit physical couplings among the DF and two lower body domains fostered by the LF domain at the open state act as an integrated structural element that is stringently required for the channel gating of P2X4 receptors. Our observations provide new mechanistic insights into P2X receptor activation and will stimulate development of new allosteric modulators of P2X receptors.
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Affiliation(s)
- Jin Wang
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Liang-Fei Sun
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wen-Wen Cui
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wen-Shan Zhao
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xue-Fei Ma
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China, and
| | - Bin Li
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China, and
| | - Yan Liu
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - You-Min Hu
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Li-Dong Huang
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Yang Cheng
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingyong Li
- the Department of Anesthesiology and Perioperative Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Xiang-Yang Lu
- the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China, and
| | - Yun Tian
- the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China, and
| | - Ye Yu
- From the Department of Pharmacology and Chemical Biology, Institute of Medical Sciences and Hongqiao International Institute of Medicine of Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China, .,the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China, and
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18
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Mansoor SE, Lü W, Oosterheert W, Shekhar M, Tajkhorshid E, Gouaux E. X-ray structures define human P2X(3) receptor gating cycle and antagonist action. Nature 2016; 538:66-71. [PMID: 27626375 DOI: 10.1038/nature19367] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/12/2016] [Indexed: 12/19/2022]
Abstract
P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.
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Affiliation(s)
- Steven E Mansoor
- Vollum Institute, Oregon Health &Science University, Portland, Oregon 97239, USA.,Knight Cardiovascular Institute, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Wei Lü
- Vollum Institute, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Wout Oosterheert
- Vollum Institute, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Mrinal Shekhar
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health &Science University, Portland, Oregon 97239, USA.,Howard Hughes Medical Institute, Oregon Health &Science University, Portland, Oregon 97239, USA
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19
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Fryatt AG, Dayl S, Cullis PM, Schmid R, Evans RJ. Mechanistic insights from resolving ligand-dependent kinetics of conformational changes at ATP-gated P2X1R ion channels. Sci Rep 2016; 6:32918. [PMID: 27616669 PMCID: PMC5018734 DOI: 10.1038/srep32918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/12/2016] [Indexed: 01/05/2023] Open
Abstract
Structural studies of P2X receptors show a novel U shaped ATP orientation following binding. We used voltage clamp fluorometry (VCF) and molecular dynamics (MD) simulations to investigate agonist action. For VCF the P2X1 receptor (P2X1R) K190C mutant (adjacent to the agonist binding pocket) was labelled with the fluorophore MTS-TAMRA and changes in fluorescence on agonist treatment provided a real time measure of conformational changes. Studies with heteromeric channels incorporating a key lysine mutation (K68A) in the ATP binding site demonstrate that normally three molecules of ATP activate the receptor. The time-course of VCF responses to ATP, 2'-deoxy ATP, 3'-deoxy ATP, Ap5A and αβmeATP were agonist dependent. Comparing the properties of the deoxy forms of ATP demonstrated the importance of the 2' hydroxyl group on the ribose ring in determining agonist efficacy consistent with MD simulations showing that it forms a hydrogen bond with the γ-phosphate oxygen stabilizing the U-shaped conformation. Comparison of the recovery of fluorescence on agonist washout, with channel activation to a second agonist application for the partial agonists Ap5A and αβmeATP, showed a complex relationship between conformational change and desensitization. These results highlight that different agonists induce distinct conformational changes, kinetics and recovery from desensitization at P2X1Rs.
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Affiliation(s)
- Alistair G. Fryatt
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Sudad Dayl
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
- Department of Chemistry, College of Science, University of Baghdad, Baghdad, Iraq
| | - Paul M. Cullis
- Department of Chemistry, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ralf Schmid
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Richard J. Evans
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
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20
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Zhang H, van Ingen H. Isotope-labeling strategies for solution NMR studies of macromolecular assemblies. Curr Opin Struct Biol 2016; 38:75-82. [PMID: 27295425 DOI: 10.1016/j.sbi.2016.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 12/21/2022]
Abstract
Proteins come together in macromolecular assemblies, recognizing and binding to each other through their structures, and operating on their substrates through their motions. Detailed characterization of these processes is particularly suited to NMR, a high-resolution technique sensitive to structure, dynamics, and interactions. Advances in isotope-labeling have enabled such studies to an ever-increasing range of systems. Here we highlight recent applications and bring to the fore the range of options to produce labeled proteins and to control the specific placement of isotopes. The increased labeling control and affordability, together with the possibility to combine strategies will further deepen and extend the range of protein assembly investigations.
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Affiliation(s)
- Heyi Zhang
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, The Netherlands
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, The Netherlands.
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