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Baskakova KO, Kuzmichev PK, Karbyshev MS. Advanced applications of Nanodiscs-based platforms for antibodies discovery. Biophys Chem 2024; 313:107290. [PMID: 39002246 DOI: 10.1016/j.bpc.2024.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.
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Affiliation(s)
- Kristina O Baskakova
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Pavel K Kuzmichev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
| | - Mikhail S Karbyshev
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation; Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, Moscow, Russian Federation.
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2
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Wang G. Thermo-ring basis for heat unfolding-induced inactivation in TRPV1. RESEARCH SQUARE 2024:rs.3.rs-3280283. [PMID: 37674717 PMCID: PMC10479453 DOI: 10.21203/rs.3.rs-3280283/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Transient receptor potential vanilloid-1 (TRPV1) is a capsaicin receptor and employs the use-dependent desensitization to protect mammals from noxious heat damage in response to repeated or constant heat stimuli. However, the underlying structural factor or motif has not been resolved precisely. In this computational study, the graph theory-based grid thermodynamic model was used to reveal how the temperature-dependent noncovalent interactions as identified in the 3D structures of rat TRPV1 could develop a well-organized fluidic grid-like mesh network, featuring various topological grids constrained as the thermo-rings that range in size from the biggest to the smallest to govern distinct structural and functional traits of the channel in response to varying temperature degrees. Following the findings that the heat unfolding of three specific biggest grids, one in the closed state and two in the open state, was respectively responsible for the reversible activation at 43 °C and thermal inactivation from 56 °C to 61 °C, a random smaller grid was further identified for the irreversible inactivation and the relevant use-dependent desensitization from the pre-open closed state between 43 °C and 61 °C. Thus, these two distinct inactivation pathways of TRPV1 may be involved in protecting mammals against noxious heat damages.
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Affiliation(s)
- Guangyu Wang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
- Department of Drug Research and Development, Institute of Biophysical Medico-chemistry, Reno, NV 89523, USA
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3
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Nadezhdin KD, Neuberger A, Khosrof LS, Talyzina IA, Khau J, Yelshanskaya MV, Sobolevsky AI. TRPV3 activation by different agonists accompanied by lipid dissociation from the vanilloid site. SCIENCE ADVANCES 2024; 10:eadn2453. [PMID: 38691614 PMCID: PMC11062575 DOI: 10.1126/sciadv.adn2453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
TRPV3 represents both temperature- and ligand-activated transient receptor potential (TRP) channel. Physiologically relevant opening of TRPV3 channels by heat has been captured structurally, while opening by agonists has only been observed in structures of mutant channels. Here, we present cryo-EM structures that illuminate opening and inactivation of wild-type human TRPV3 in response to binding of two types of agonists: either the natural cannabinoid tetrahydrocannabivarin (THCV) or synthetic agonist 2-aminoethoxydiphenylborane (2-APB). We found that THCV binds to the vanilloid site, while 2-APB binds to the S1-S4 base and ARD-TMD linker sites. Despite binding to distally located sites, both agonists induce similar pore opening and cause dissociation of a lipid that occupies the vanilloid site in their absence. Our results uncover different but converging allosteric pathways through which small-molecule agonists activate TRPV3 and provide a framework for drug design and understanding the role of lipids in ion channel function.
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Affiliation(s)
- Kirill D. Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Lena S. Khosrof
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Irina A. Talyzina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jeffrey Khau
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Maria V. Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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4
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García-Ávila M, Tello-Marmolejo J, Rosenbaum T, Islas LD. Permeant cations modulate pore dynamics and gating of TRPV1 ion channels. J Gen Physiol 2024; 156:e202313422. [PMID: 38055192 PMCID: PMC10760480 DOI: 10.1085/jgp.202313422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/04/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
The transient receptor vanilloid 1 (TRPV1) is a non-selective ion channel, which is activated by several chemical ligands and heat. We have previously shown that activation of TRPV1 by different ligands results in single-channel openings with different conductance, suggesting that the selectivity filter is highly dynamic. TRPV1 is weakly voltage dependent; here, we sought to explore whether the permeation of different monovalent ions could influence the voltage dependence of this ion channel. By using single-channel recordings, we show that TRPV1 channels undergo rapid transitions to closed states that are directly connected to the open state, which may result from structural fluctuations of their selectivity filter. Moreover, we demonstrate that the rates of these transitions are influenced by the permeant ion, suggesting that ion permeation regulates the voltage dependence of these channels. Our data could be the basis for more detailed MD simulations exploring the permeation mechanism and how the occupancy of different ions alters the three-dimensional structure of the pore of TRPV1 channels.
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Affiliation(s)
- Miriam García-Ávila
- Department of Physiology, School of Medicine, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Javier Tello-Marmolejo
- Department of Physiology, School of Medicine, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Tamara Rosenbaum
- Department of Cognitive Neuroscience, Instituto de Fisiología Celular, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - León D. Islas
- Department of Physiology, School of Medicine, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
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5
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Wang G. Thermoring basis for the TRPV3 bio-thermometer. Sci Rep 2023; 13:21594. [PMID: 38062125 PMCID: PMC10703924 DOI: 10.1038/s41598-023-47100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
The thermosensitive transient receptor potential (TRP) channels are well-known as bio-thermometers with specific temperature thresholds and sensitivity. However, their precise structural origins are still mysterious. Here, graph theory was used to test how the temperature-dependent non-covalent interactions as identified in the 3D structures of thermo-gated TRPV3 could form a systematic fluidic grid-like mesh network with the constrained thermo-rings from the biggest grids to the smallest ones as necessary structural motifs for the variable temperature thresholds and sensitivity. The results showed that the heat-evoked melting of the biggest grids may control the specific temperature thresholds to initiate channel gating while the smaller grids may be required to secure heat efficacy. Together, all the grids along the lipid-dependent minimal gating pathway may be necessary to change with molar heat capacity for the specific temperature sensitivity. Therefore, this graph theory-based grid thermodynamic model may provide an extensive structural basis for the thermo-gated TRP channels.
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Affiliation(s)
- Guangyu Wang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, 95616, USA.
- Department of Drug Research and Development, Institute of Biophysical Medico-Chemistry, Reno, NV, 89523, USA.
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6
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Burns D, Venditti V, Potoyan DA. Temperature sensitive contact modes allosterically gate TRPV3. PLoS Comput Biol 2023; 19:e1011545. [PMID: 37831724 PMCID: PMC10599574 DOI: 10.1371/journal.pcbi.1011545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
TRPV Ion channels are sophisticated molecular sensors designed to respond to distinct temperature thresholds. The recent surge in cryo-EM structures has provided numerous insights into the structural rearrangements accompanying their opening and closing; however, the molecular mechanisms by which TRPV channels establish precise and robust temperature sensing remain elusive. In this work we employ molecular simulations, multi-ensemble contact analysis, graph theory, and machine learning techniques to reveal the temperature-sensitive residue-residue interactions driving allostery in TRPV3. We find that groups of residues exhibiting similar temperature-dependent contact frequency profiles cluster at specific regions of the channel. The dominant mode clusters on the ankyrin repeat domain and displays a linear melting trend while others display non-linear trends. These modes describe the residue-level temperature response patterns that underlie the channel's functional dynamics. With network analysis, we find that the community structure of the channel changes with temperature. And that a network of high centrality contacts connects distant regions of the protomer to the gate, serving as a means for the temperature-sensitive contact modes to allosterically regulate channel gating. Using a random forest model, we show that the contact states of specific temperature-sensitive modes are indeed predictive of the channel gate's state. Supporting the physical validity of these modes and networks are several residues identified with our analyses that are reported in literature to be functionally critical. Our results offer high resolution insight into thermo-TRP channel function and demonstrate the utility of temperature-sensitive contact analysis.
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Affiliation(s)
- Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Vincenzo Venditti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Davit A. Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
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7
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Burns D, Venditti V, Potoyan DA. Temperature-Sensitive Contact Modes Allosterically Gate TRPV3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522497. [PMID: 36711981 PMCID: PMC9881879 DOI: 10.1101/2023.01.02.522497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
TRPV Ion channels are sophisticated molecular sensors designed to respond to distinct temperature thresholds. The recent surge in cryo-EM structures has provided numerous insights into the structural rearrangements accompanying their opening and closing; however, the molecular mechanisms by which TRPV channels establish precise and robust temperature sensing remain elusive. In this work we employ molecular simulations, multi-ensemble contact analysis, graph theory, and machine learning techniques to reveal the temperature-sensitive residue-residue interactions driving allostery in TRPV3. We find that groups of residues exhibiting similar temperature-dependent contact frequency profiles cluster at specific regions of the channel. The dominant mode clusters on the ankyrin repeat domain and displays a linear melting trend while others display non-linear trends. These modes describe the residue-level temperature response patterns that underlie the channel's functional dynamics. With network analysis, we find that the community structure of the channel changes with temperature. And that a network of high centrality contacts connects distant regions of the protomer to the gate, serving as a means for the temperature-sensitive contact modes to allosterically regulate channel gating. Using a random forest model, we show that the contact states of specific temperature-sensitive modes are indeed predictive of the channel gate's state. Supporting the physical validity of these modes and networks are several residues identified with our analyses that are reported in literature to be functionally critical. Our results offer high resolution insight into thermo-TRP channel function and demonstrate the utility of temperature-sensitive contact analysis.
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8
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Wang G. Thermoring-based heat activation switches in the TRPV1 biothermometer. Int J Biol Macromol 2023; 248:125915. [PMID: 37481175 DOI: 10.1016/j.ijbiomac.2023.125915] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Non-covalent interactions in bio-macromolecules are individually weak but collectively important. How they take a concerted action in a complex biochemical reaction network to realize their thermal stability and activity is still challenging to study. Here graph theory was used to investigate how the temperature-dependent non-covalent interactions as identified in the 3D structures of the thermo-gated capsaicin receptor TRPV1 could form a systemic fluidic grid-like mesh network with topological grids constrained as the thermo-rings to govern heat-sensing. The results showed that the heat-evoked melting of the biggest grid initiated a matched temperature threshold to release the lipid from the active vanilloid site for channel activation. Meanwhile, smaller grids were required to stabilize heat efficacy. Altogether, the change in the total grid sizes upon the change in the total noncovalent interactions along the lipid-dependent gating pathway was necessary for the matched temperature sensitivity. Therefore, this grid thermodynamic model may be broadly significant for the structural thermostability and the functional thermoactivity of bio-macromolecules.
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Affiliation(s)
- Guangyu Wang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA; Department of Drug Research and Development, Institute of Biophysical Medico-chemistry, Reno, NV 89523, USA.
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9
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Zhang M, Ma Y, Ye X, Zhang N, Pan L, Wang B. TRP (transient receptor potential) ion channel family: structures, biological functions and therapeutic interventions for diseases. Signal Transduct Target Ther 2023; 8:261. [PMID: 37402746 DOI: 10.1038/s41392-023-01464-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/26/2023] [Accepted: 04/25/2023] [Indexed: 07/06/2023] Open
Abstract
Transient receptor potential (TRP) channels are sensors for a variety of cellular and environmental signals. Mammals express a total of 28 different TRP channel proteins, which can be divided into seven subfamilies based on amino acid sequence homology: TRPA (Ankyrin), TRPC (Canonical), TRPM (Melastatin), TRPML (Mucolipin), TRPN (NO-mechano-potential, NOMP), TRPP (Polycystin), TRPV (Vanilloid). They are a class of ion channels found in numerous tissues and cell types and are permeable to a wide range of cations such as Ca2+, Mg2+, Na+, K+, and others. TRP channels are responsible for various sensory responses including heat, cold, pain, stress, vision and taste and can be activated by a number of stimuli. Their predominantly location on the cell surface, their interaction with numerous physiological signaling pathways, and the unique crystal structure of TRP channels make TRPs attractive drug targets and implicate them in the treatment of a wide range of diseases. Here, we review the history of TRP channel discovery, summarize the structures and functions of the TRP ion channel family, and highlight the current understanding of the role of TRP channels in the pathogenesis of human disease. Most importantly, we describe TRP channel-related drug discovery, therapeutic interventions for diseases and the limitations of targeting TRP channels in potential clinical applications.
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Affiliation(s)
- Miao Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- The Center for Microbes, Development and Health; Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yueming Ma
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xianglu Ye
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ning Zhang
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Lei Pan
- The Center for Microbes, Development and Health; Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Bing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Center for Pharmaceutics Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai, 201203, China.
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10
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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11
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Wang G. Thermoring basis for the TRPV3 bio-thermometer. RESEARCH SQUARE 2023:rs.3.rs-2987105. [PMID: 37398446 PMCID: PMC10312932 DOI: 10.21203/rs.3.rs-2987105/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The thermosensitive transient receptor potential (TRP) channels are well-known as bio-thermometers with specific temperature thresholds and sensitivity. However, their structural origins are still mysterious. Here, graph theory was used to test how the temperature-dependent non-covalent interactions as identified in the 3D structures of thermo-gated TRPV3 could form a systematic fluidic grid-like mesh network with the thermal rings from the biggest grids to the smallest ones as necessary structural motifs for the variable temperature thresholds and sensitivity. The results showed that the heat-evoked melting of the biggest grids may control temperature thresholds to activate the channel while the smaller grids may act as thermo-stable anchors to secure the channel activity. Together, all the grids along the gating pathway may be necessary for the specific temperature sensitivity. Therefore, this grid thermodynamic model may provide an extensive structural basis for the thermo-gated TRP channels.
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12
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Novel Insights into the Role of Keratinocytes-Expressed TRPV3 in the Skin. Biomolecules 2023; 13:biom13030513. [PMID: 36979447 PMCID: PMC10046267 DOI: 10.3390/biom13030513] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
TRPV3 is a non-selective cation channel that is highly expressed in keratinocytes in the skin. Traditionally, keratinocytes-expressed TRPV3 is involved in multiple physiological and pathological functions of the skin, such as itching, heat pain, and hair development. Although the underlying mechanisms by which TRPV3 functions in vivo remain obscure, recent research studies suggest that several cytokines and EGFR signaling pathways may be involved. However, there have also been other studies with opposite results that question the role of TRPV3 in heat pain. In addition, an increasing number of studies have suggested a novel role of TRPV3 in promoting skin regeneration, indicating that TRPV3 may become a new potential target for regulating skin regeneration. This paper not only reviews the role of keratinocytes-expressed TRPV3 in the physiological and pathological processes of itching, heat pain, hair development, and skin regeneration, but also reviews the relationship between TRPV3 gene mutations and skin diseases such as atopic dermatitis (AD) and Olmsted syndrome (OS). This review will lay a foundation for further developing our understanding of the mechanisms by which TRPV3 is involved in itching, heat pain, and hair development, as well as the treatments for TRPV3-related skin diseases.
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13
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Saward BG, Leissing TM, Clifton IJ, Tumber A, Timperley CM, Hopkinson RJ, Schofield CJ. Biochemical and Structural Insights into FIH-Catalysed Hydroxylation of Transient Receptor Potential Ankyrin Repeat Domains. Chembiochem 2023; 24:e202200576. [PMID: 36448355 PMCID: PMC10946520 DOI: 10.1002/cbic.202200576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Transient receptor potential (TRP) channels have important roles in environmental sensing in animals. Human TRP subfamily A member 1 (TRPA1) is responsible for sensing allyl isothiocyanate (AITC) and other electrophilic sensory irritants. TRP subfamily vanilloid member 3 (TRPV3) is involved in skin maintenance. TRPV3 is a reported substrate of the 2-oxoglutarate oxygenase factor inhibiting hypoxia-inducible factor (FIH). We report biochemical and structural studies concerning asparaginyl hydroxylation of the ankyrin repeat domains (ARDs) of TRPA1 and TRPV3 catalysed by FIH. The results with ARD peptides support a previous report on FIH-catalysed TRPV3 hydroxylation and show that, of the 12 potential TRPA1 sequences investigated, one sequence (TRPA1 residues 322-348) undergoes hydroxylation at Asn336. Structural studies reveal that the TRPA1 and TRPV3 ARDs bind to FIH with a similar overall geometry to most other reported FIH substrates. However, the binding mode of TRPV3 to FIH is distinct from that of other substrates.
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Affiliation(s)
- Benjamin G. Saward
- Department of Chemistry and theIneos Oxford Institute for Antimicrobial ResearchChemistry Research LaboratoryMansfield RoadUniversity of OxfordOxfordOX1 3TAUK
| | - Thomas M. Leissing
- Department of Chemistry and theIneos Oxford Institute for Antimicrobial ResearchChemistry Research LaboratoryMansfield RoadUniversity of OxfordOxfordOX1 3TAUK
| | - Ian J. Clifton
- Department of Chemistry and theIneos Oxford Institute for Antimicrobial ResearchChemistry Research LaboratoryMansfield RoadUniversity of OxfordOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of Chemistry and theIneos Oxford Institute for Antimicrobial ResearchChemistry Research LaboratoryMansfield RoadUniversity of OxfordOxfordOX1 3TAUK
| | | | - Richard J. Hopkinson
- Department of Chemistry and theIneos Oxford Institute for Antimicrobial ResearchChemistry Research LaboratoryMansfield RoadUniversity of OxfordOxfordOX1 3TAUK
- Present address: Leicester Institute for Structural and Chemical Biology and School of ChemistryUniversity of LeicesterHenry Wellcome Building, Lancaster RoadLeicesterLE1 7RHUK
| | - Christopher J. Schofield
- Department of Chemistry and theIneos Oxford Institute for Antimicrobial ResearchChemistry Research LaboratoryMansfield RoadUniversity of OxfordOxfordOX1 3TAUK
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14
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Wang Y. Multidisciplinary Advances Address the Challenges in Developing Drugs against Transient Receptor Potential Channels to Treat Metabolic Disorders. ChemMedChem 2023; 18:e202200562. [PMID: 36530131 DOI: 10.1002/cmdc.202200562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Transient receptor potential (TRP) channels are cation channels that regulate key physiological and pathological processes in response to a broad range of stimuli. Moreover, they systemically regulate the release of hormones, metabolic homeostasis, and complications of diabetes, which positions them as promising therapeutic targets to combat metabolic disorders. Nevertheless, there are significant challenges in the design of TRP ligands with high potency and durability. Herein we summarize the four challenges as hydrophobicity, selectivity, mono-target therapy, and interspecies discrepancy. We present 1134 TRP ligands with diversified modes of TRP-ligand interaction and provide a detailed discussion of the latest strategies, especially cryogenic electron microscopy (cryo-EM) and computational methods. We propose solutions to address the challenges with a critical analysis of advances in membrane partitioning, polypharmacology, biased agonism, and biochemical screening of transcriptional modulators. They are fueled by the breakthrough from cryo-EM, chemoinformatics and bioinformatics. The discussion is aimed to shed new light on designing next-generation drugs to treat obesity, diabetes and its complications, with optimal hydrophobicity, higher mode selectivity, multi-targeting and consistent activities between human and rodents.
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Affiliation(s)
- Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai, 200438, P. R. China.,Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai, 200438, P. R. China
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15
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Gochman A, Tan X, Bae C, Chen H, Swartz KJ, Jara-Oseguera A. Cannabidiol sensitizes TRPV2 channels to activation by 2-APB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525817. [PMID: 36747846 PMCID: PMC9900902 DOI: 10.1101/2023.01.27.525817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The cation-permeable TRPV2 channel is essential for cardiac and immune cells. Cannabidiol (CBD), a non-psychoactive cannabinoid of clinical relevance, is one of the few molecules known to activate TRPV2. Using the patch-clamp technique we discover that CBD can sensitize current responses of the rat TRPV2 channel to the synthetic agonist 2-aminoethoxydiphenyl borate (2- APB) by over two orders of magnitude, without sensitizing channels to activation by moderate (40 ⁰C) heat. Using cryo-EM we uncover a new small-molecule binding site in the pore domain of rTRPV2 that can be occupied by CBD in addition to a nearby CBD site that had already been reported. The TRPV1 and TRPV3 channels share >40% sequence identity with TRPV2 are also activated by 2-APB and CBD, but we only find a strong sensitizing effect of CBD on the response of mouse TRPV3 to 2-APB. Mutations at non-conserved positions between rTRPV2 and rTRPV1 in either the pore domain or the CBD sites failed to confer strong sensitization by CBD in mutant rTRPV1 channels. Together, our results indicate that CBD-dependent sensitization of TRPV2 channels engages multiple channel regions and possibly involves more than one CBD and 2-APB sites. The remarkably robust effect of CBD on TRPV2 and TRPV3 channels offers a promising new tool to both understand and overcome one of the major roadblocks in the study of these channels - their resilience to activation.
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Affiliation(s)
- Aaron Gochman
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892 USA,Current affiliation: Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Xiaofeng Tan
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892 USA
| | - Chanhyung Bae
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892 USA,Current affiliation: Janssen R&D, Biologics Discovery, Spring House, PA, USA
| | - Helen Chen
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, TX, 78712 USA
| | - Kenton J. Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892 USA
| | - Andrés Jara-Oseguera
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, TX, 78712 USA.,Corresponding author: Andrés Jara-Oseguera ()
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16
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Rosenbaum T, Morales-Lázaro SL. Regulation of ThermoTRP Channels by PIP2 and Cholesterol. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:245-277. [PMID: 36988884 DOI: 10.1007/978-3-031-21547-6_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Transient receptor potential (TRP) ion channels are proteins that are expressed by diverse tissues and that play pivotal functions in physiology. These channels are polymodal and are activated by several stimuli. Among TRPs, some members of this family of channels respond to changes in ambient temperature and are known as thermoTRPs. These proteins respond to heat or cold in the noxious range and some of them to temperatures considered innocuous, as well as to mechanical, osmotic, and/or chemical stimuli. In addition to this already complex ability to respond to different signals, the activity of these ion channels can be fine-tuned by lipids. Two lipids well known to modulate ion channel activity are phosphatidylinositol 4,5-bisphosphate (PIP2) and cholesterol. These lipids can either influence the function of these proteins through direct interaction by binding to a site in the structure of the ion channel or through indirect mechanisms, which can include modifying membrane properties, such as curvature and rigidity, by regulating their expression or by modulating the actions of other molecules or signaling pathways that affect the physiology of ion channels. Here, we summarize the key aspects of the regulation of thermoTRP channels by PIP2 and cholesterol.
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Affiliation(s)
- Tamara Rosenbaum
- Departamento de Neurociencia Cognitiva, División Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
| | - Sara L Morales-Lázaro
- Departamento de Neurociencia Cognitiva, División Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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17
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Fan J, Hu L, Yue Z, Liao D, Guo F, Ke H, Jiang D, Yang Y, Lei X. Structural basis of TRPV3 inhibition by an antagonist. Nat Chem Biol 2023; 19:81-90. [PMID: 36302896 DOI: 10.1038/s41589-022-01166-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 09/08/2022] [Indexed: 12/31/2022]
Abstract
The TRPV3 channel plays vital roles in skin physiology. Dysfunction of TRPV3 causes skin diseases, including Olmsted syndrome. However, the lack of potent and selective inhibitors impedes the validation of TRPV3 as a therapeutic target. In this study, we identified Trpvicin as a potent and subtype-selective inhibitor of TRPV3. Trpvicin exhibits pharmacological potential in the inhibition of itch and hair loss in mouse models. Cryogenic electron microscopy structures of TRPV3 and the pathogenic G573S mutant complexed with Trpvicin reveal detailed ligand-binding sites, suggesting that Trpvicin inhibits the TRPV3 channel by stabilizing it in a closed state. Our G573S mutant structures demonstrate that the mutation causes a dilated pore, generating constitutive opening activity. Trpvicin accesses additional binding sites inside the central cavity of the G573S mutant to remodel the channel symmetry and block the channel. Together, our results provide mechanistic insights into the inhibition of TRPV3 by Trpvicin and support TRPV3-related drug development.
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Affiliation(s)
- Junping Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Linghan Hu
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Zongwei Yue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | | | - Fusheng Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Han Ke
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Daohua Jiang
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yong Yang
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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18
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Feng S, Pumroy RA, Protopopova AD, Moiseenkova‐Bell VY, Im W. Modulation of TRPV2 by endogenous and exogenous ligands: A computational study. Protein Sci 2023; 32:e4490. [PMID: 36327382 PMCID: PMC9794027 DOI: 10.1002/pro.4490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/17/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Transient receptor potential vanilloid (TRPV) channels play various important roles in human physiology. As membrane proteins, these channels are modulated by their endogenous lipid environment as the recent wealth of structural studies has revealed functional and structural lipid binding sites. Additionally, it has been shown that exogenous ligands can exchange with some of these lipids to alter channel gating. Here, we used molecular dynamics simulations to examine how one member of the TRPV family, TRPV2, interacts with endogenous lipids and the pharmacological modulator cannabidiol (CBD). By computationally reconstituting TRPV2 into a typical plasma membrane environment, which includes phospholipids, cholesterol, and phosphatidylinositol (PIP) in the inner leaflet, we showed that most of the interacting surface lipids are phospholipids without strong specificity for headgroup types. Intriguingly, we observed that the C-terminal membrane proximal region of the channel binds preferentially to PIP lipids. We also modelled two structural lipids in the simulation: one in the vanilloid pocket and the other in the voltage sensor-like domain (VSLD) pocket. The simulation shows that the VSLD lipid dampens the fluctuation of the VSLD residues, while the vanilloid lipid exhibits heterogeneity both in its binding pose and in its influence on protein dynamics. Addition of CBD to our simulation system led to an open selectivity filter and a structural rearrangement that includes a clockwise rotation of the ankyrin repeat domains, TRP helix, and VSLD. Together, these results reveal the interplay between endogenous lipids and an exogenous ligand and their effect on TRPV2 stability and channel gating.
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Affiliation(s)
- Shasha Feng
- Departments of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Ruth A. Pumroy
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Anna D. Protopopova
- Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - Wonpil Im
- Departments of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
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19
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Structural mechanisms of TRPV2 modulation by endogenous and exogenous ligands. Nat Chem Biol 2023; 19:72-80. [PMID: 36163384 DOI: 10.1038/s41589-022-01139-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/10/2022] [Indexed: 12/31/2022]
Abstract
The transient receptor potential vanilloid 2 (TRPV2) ion channel is a polymodal receptor widely involved in many physiological and pathological processes. Despite many TRPV2 modulators being identified, whether and how TRPV2 is regulated by endogenous lipids remains elusive. Here, we report an endogenous cholesterol molecule inside the vanilloid binding pocket (VBP) of TRPV2, with a 'head down, tail up' configuration, resolved at 3.2 Å using cryo-EM. Cholesterol binding antagonizes ligand activation of TRPV2, which is removed from VBP by methyl-β-cyclodextrin (MβCD) as resolved at 2.9 Å. We also observed that estradiol (E2) potentiated TRPV2 activation by 2-aminoethoxydiphenyl borate (2-APB), a classic tool compound for TRP channels. Our cryo-EM structures (resolved at 2.8-3.3 Å) further suggest how E2 disturbed cholesterol binding and how 2-APB bound within the VBP with E2 or without both E2 and endogenous cholesterol, respectively. Therefore, our study has established the structural basis for ligand recognition of the inhibitory endogenous cholesterol and excitatory exogenous 2-APB in TRPV2.
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20
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Zhang L, Simonsen C, Zimova L, Wang K, Moparthi L, Gaudet R, Ekoff M, Nilsson G, Hellmich UA, Vlachova V, Gourdon P, Zygmunt PM. Cannabinoid non-cannabidiol site modulation of TRPV2 structure and function. Nat Commun 2022; 13:7483. [PMID: 36470868 PMCID: PMC9722916 DOI: 10.1038/s41467-022-35163-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
TRPV2 is a ligand-operated temperature sensor with poorly defined pharmacology. Here, we combine calcium imaging and patch-clamp electrophysiology with cryo-electron microscopy (cryo-EM) to explore how TRPV2 activity is modulated by the phytocannabinoid Δ9-tetrahydrocannabiorcol (C16) and by probenecid. C16 and probenecid act in concert to stimulate TRPV2 responses including histamine release from rat and human mast cells. Each ligand causes distinct conformational changes in TRPV2 as revealed by cryo-EM. Although the binding for probenecid remains elusive, C16 associates within the vanilloid pocket. As such, the C16 binding location is distinct from that of cannabidiol, partially overlapping with the binding site of the TRPV2 inhibitor piperlongumine. Taken together, we discover a new cannabinoid binding site in TRPV2 that is under the influence of allosteric control by probenecid. This molecular insight into ligand modulation enhances our understanding of TRPV2 in normal and pathophysiology.
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Affiliation(s)
- Liying Zhang
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden ,grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Simonsen
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Lucie Zimova
- grid.418095.10000 0001 1015 3316Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Kaituo Wang
- grid.5254.60000 0001 0674 042XDepartment of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lavanya Moparthi
- grid.5640.70000 0001 2162 9922Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden ,grid.5640.70000 0001 2162 9922Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Rachelle Gaudet
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Maria Ekoff
- grid.24381.3c0000 0000 9241 5705Division Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Gunnar Nilsson
- grid.24381.3c0000 0000 9241 5705Division Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Ute A. Hellmich
- grid.9613.d0000 0001 1939 2794Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry and Cluster of Excellence “Balance of the Microverse”, Friedrich Schiller University Jena, Jena, Germany ,grid.7839.50000 0004 1936 9721Center for Biomolecular Magnetic Resonance, Goethe-University, Frankfurt/Main, Germany
| | - Viktorie Vlachova
- grid.418095.10000 0001 1015 3316Department of Cellular Neurophysiology, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Pontus Gourdon
- grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter M. Zygmunt
- grid.4514.40000 0001 0930 2361Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
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21
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Wiedemann C, Goretzki B, Merz ZN, Tebbe F, Schmitt P, Hellmich UA. Extent of intrinsic disorder and NMR chemical shift assignments of the distal N-termini from human TRPV1, TRPV2 and TRPV3 ion channels. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:289-296. [PMID: 35666427 PMCID: PMC9510099 DOI: 10.1007/s12104-022-10093-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The mammalian Transient Receptor Potential Vanilloid (TRPV) channels are a family of six tetrameric ion channels localized at the plasma membrane. The group I members of the family, TRPV1 through TRPV4, are heat-activated and exhibit remarkable polymodality. The distal N-termini of group I TRPV channels contain large intrinsically disordered regions (IDRs), ranging from ~ 75 amino acids (TRPV2) to ~ 150 amino acids (TRPV4), the vast majority of which is invisible in the structural models published so far. These IDRs provide important binding sites for cytosolic partners, and their deletion is detrimental to channel activity and regulation. Recently, we reported the NMR backbone assignments of the distal TRPV4 N-terminus and noticed some discrepancies between the extent of disorder predicted solely based on protein sequence and from experimentally determined chemical shifts. Thus, for an analysis of the extent of disorder in the distal N-termini of all group I TRPV channels, we now report the NMR assignments for the human TRPV1, TRPV2 and TRPV3 IDRs.
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Affiliation(s)
- Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Benedikt Goretzki
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Zoe N Merz
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Frederike Tebbe
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Pauline Schmitt
- Department of Chemistry, Division Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becher-Weg 30, 55128, Mainz, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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22
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Structure of the Human BK Ion Channel in Lipid Environment. MEMBRANES 2022; 12:membranes12080758. [PMID: 36005673 PMCID: PMC9414842 DOI: 10.3390/membranes12080758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023]
Abstract
Voltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage sensing, ligand binding, and channel opening, the structures of ion channels in various functional states and in lipid membrane environments need to be determined. Here, the random spherically constrained (RSC) single-particle cryo-EM method was employed to study human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure was determined at 3.5 Å resolution in the absence of Ca2+. Instead of the common fourfold symmetry observed in ligand-modulated ion channels, a twofold symmetry was observed in hBK in liposomes. Compared with the structure of isolated hSlo1 Ca2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits also moved downwards relative to the two other subunits.
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23
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Wang Y, Tan L, Jiao K, Xue C, Tang Q, Jiang S, Ren Y, Chen H, El-Aziz TMA, Abdelazeem KNM, Yu Y, Zhao F, Zhu MX, Cao Z. Scutellarein Attenuates Atopic Dermatitis by Selectively Inhibiting Transient Receptor Potential Vanilloid 3. Br J Pharmacol 2022; 179:4792-4808. [PMID: 35771623 DOI: 10.1111/bph.15913] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/08/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Atopic dermatitis (AD) is one of the most common chronic inflammatory cutaneous diseases with unmet clinical needs. As a common ingredient found in several medicinal herbs with efficacy on cutaneous inflammatory diseases, Scutellarein (Scu) has been shown to possess anti-inflammatory and anti-proliferative activities. We aimed to evaluate the therapeutic efficacy of Scu against AD and its underlying molecular mechanism. EXPERIMENTAL APPROACH Efficacy of Scu on AD was evaluated in 2,4-dinitrofluorobenzene (DNFB) and carvacrol-induced dermatitis mouse models. Cytokine mRNA and serum IgE levels were examined using qPCR and ELISA, respectively. Voltage clamp recordings were used to measure currents mediated by transient receptor potential (TRP) channels. In silico docking, site-direct mutagenesis, and covalent modification were used to explore the binding pocket of Scu on TRPV3. KEY RESULTS Subcutaneous administration of Scu efficaciously suppresses DNFB and carvacrol-induced pruritus, epidermal hyperplasia and skin inflammation in wild type mice but has no additional benefit in Trpv3 knockout mice in the carvacrol model. Scu is a potent and selective TRPV3 channel allosteric negative modulator with an apparent affinity of 1.18 μM. Molecular docking coupled with site-direct mutagenesis and covalent modification of incorporated cysteine residues demonstrate that Scu targets the cavity formed between the pore helix and transmembrane helix S6. Moreover, Scu attenuates endogenous TRPV3 activity in human keratinocytes and inhibits carvacrol-induced proliferative and proinflammatory responses. CONCLUSIONS AND IMPLICATIONS Collectively, these data demonstrate that Scu ameliorates carvacrol-induced skin inflammation by directly inhibiting TRPV3, and TRPV3 represents a viable therapeutic target for AD treatment.
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Affiliation(s)
- Yujing Wang
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Liaoxi Tan
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Kejun Jiao
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Chu Xue
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qinglian Tang
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Shan Jiang
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Younan Ren
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hao Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | | | - Khalid N M Abdelazeem
- Radiation Biology Research Department, National Centre for Radiation Research and Technology, Atomic Energy Authority, Cairo, Egypt
| | - Ye Yu
- Department of Basic Medicine, School of Basic Medicine and Clinic Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fang Zhao
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Michael X Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhengyu Cao
- State Key Laboratory of Natural Medicines and Department of TCM Pharmacology, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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24
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Neuberger A, Nadezhdin KD, Sobolevsky AI. Structural mechanism of TRPV3 channel inhibition by the anesthetic dyclonine. Nat Commun 2022; 13:2795. [PMID: 35589741 PMCID: PMC9120478 DOI: 10.1038/s41467-022-30537-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/05/2022] [Indexed: 02/02/2023] Open
Abstract
Skin diseases are common human illnesses that occur in all cultures, at all ages, and affect between 30% and 70% of individuals globally. TRPV3 is a cation-permeable TRP channel predominantly expressed in skin keratinocytes, implicated in cutaneous sensation and associated with numerous skin diseases. TRPV3 is inhibited by the local anesthetic dyclonine, traditionally used for topical applications to relieve pain and itch. However, the structural basis of TRPV3 inhibition by dyclonine has remained elusive. Here we present a cryo-EM structure of a TRPV3-dyclonine complex that reveals binding of the inhibitor in the portals which connect the membrane environment surrounding the channel to the central cavity of the channel pore. We propose a mechanism of TRPV3 inhibition in which dyclonine molecules stick out into the channel pore, creating a barrier for ion conductance. The allosteric binding site of dyclonine can serve as a template for the design of new TRPV3-targeting drugs.
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Affiliation(s)
- Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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25
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Yelshanskaya MV, Sobolevsky AI. Ligand-Binding Sites in Vanilloid-Subtype TRP Channels. Front Pharmacol 2022; 13:900623. [PMID: 35652046 PMCID: PMC9149226 DOI: 10.3389/fphar.2022.900623] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 02/02/2023] Open
Abstract
Vanilloid-subfamily TRP channels TRPV1-6 play important roles in various physiological processes and are implicated in numerous human diseases. Advances in structural biology, particularly the "resolution revolution" in cryo-EM, have led to breakthroughs in molecular characterization of TRPV channels. Structures with continuously improving resolution uncover atomic details of TRPV channel interactions with small molecules and protein-binding partners. Here, we provide a classification of structurally characterized binding sites in TRPV channels and discuss the progress that has been made by structural biology combined with mutagenesis, functional recordings, and molecular dynamics simulations toward understanding of the molecular mechanisms of ligand action. Given the similarity in structural architecture of TRP channels, 16 unique sites identified in TRPV channels may be shared between TRP channel subfamilies, although the chemical identity of a particular ligand will likely depend on the local amino-acid composition. The characterized binding sites and molecular mechanisms of ligand action create a diversity of druggable targets to aid in the design of new molecules for tuning TRP channel function in disease conditions.
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Affiliation(s)
| | - Alexander I. Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
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26
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Pumroy RA, Protopopova AD, Fricke TC, Lange IU, Haug FM, Nguyen PT, Gallo PN, Sousa BB, Bernardes GJL, Yarov-Yarovoy V, Leffler A, Moiseenkova-Bell VY. Structural insights into TRPV2 activation by small molecules. Nat Commun 2022; 13:2334. [PMID: 35484159 PMCID: PMC9051106 DOI: 10.1038/s41467-022-30083-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022] Open
Abstract
Transient receptor potential vanilloid 2 (TRPV2) is involved in many critical physiological and pathophysiological processes, making it a promising drug target. Here we present cryo-electron microscopy (cryo-EM) structures of rat TRPV2 in lipid nanodiscs activated by 2-aminoethoxydiphenyl borate (2-APB) and propose a TRPV2-specific 2-ABP binding site at the interface of S5 of one monomer and the S4-S5 linker of the adjacent monomer. In silico docking and electrophysiological studies confirm the key role of His521 and Arg539 in 2-APB activation of TRPV2. Additionally, electrophysiological experiments show that the combination of 2-APB and cannabidiol has a synergetic effect on TRPV2 activation, and cryo-EM structures demonstrate that both drugs were able to bind simultaneously. Together, our cryo-EM structures represent multiple functional states of the channel, providing a native picture of TRPV2 activation by small molecules and a structural framework for the development of TRPV2-specific activators.
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Affiliation(s)
- Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Anna D Protopopova
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Tabea C Fricke
- Department of Anesthesiology and Intensive Care Medicine, Hannover Medical School, Hannover, 30625, Germany
| | - Iris U Lange
- Department of Anesthesiology and Intensive Care Medicine, Hannover Medical School, Hannover, 30625, Germany
| | - Ferdinand M Haug
- Department of Anesthesiology and Intensive Care Medicine, Hannover Medical School, Hannover, 30625, Germany
| | - Phuong T Nguyen
- Department of Physiology and Membrane Biology, University of California, Davis, CA, 95616, United States
| | - Pamela N Gallo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Bárbara B Sousa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA, 95616, United States
| | - Andreas Leffler
- Department of Anesthesiology and Intensive Care Medicine, Hannover Medical School, Hannover, 30625, Germany
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States.
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27
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Tikhonov DB, Zhorov BS. P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models. MEMBRANES 2022; 12:membranes12020229. [PMID: 35207150 PMCID: PMC8876033 DOI: 10.3390/membranes12020229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 01/27/2023]
Abstract
The superfamily of P-loop channels includes potassium, sodium, and calcium channels, as well as TRP channels and ionotropic glutamate receptors. A rapidly increasing number of crystal and cryo-EM structures have revealed conserved and variable elements of the channel structures. Intriguing differences are seen in transmembrane helices of channels, which may include π-helical bulges. The bulges reorient residues in the helices and thus strongly affect their intersegment contacts and patterns of ligand-sensing residues. Comparison of the experimental structures suggests that some π-bulges are dynamic: they may appear and disappear upon channel gating and ligand binding. The AlphaFold2 models represent a recent breakthrough in the computational prediction of protein structures. We compared some crystal and cryo-EM structures of P-loop channels with respective AlphaFold2 models. Folding of the regions, which are resolved experimentally, is generally similar to that predicted in the AlphaFold2 models. The models also reproduce some subtle but significant differences between various P-loop channels. However, patterns of π-bulges do not necessarily coincide in the experimental and AlphaFold2 structures. Given the importance of dynamic π-bulges, further studies involving experimental and theoretical approaches are necessary to understand the cause of the discrepancy.
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28
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Cai R, Chen XZ. Roles of Intramolecular Interactions in the Regulation of TRP Channels. Rev Physiol Biochem Pharmacol 2022; 186:29-56. [PMID: 35882668 DOI: 10.1007/112_2022_74] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The transient receptor potential (TRP) channels, classified into six (-A, -V, -P, -C, -M, -ML, -N and -Y) subfamilies, are important membrane sensors and mediators of diverse stimuli including pH, light, mechano-force, temperature, pain, taste, and smell. The mammalian TRP superfamily of 28 members share similar membrane topology with six membrane-spanning helices (S1-S6) and cytosolic N-/C-terminus. Abnormal function or expression of TRP channels is associated with cancer, skeletal dysplasia, immunodeficiency, and cardiac, renal, and neuronal diseases. The majority of TRP members share common functional regulators such as phospholipid PIP2, 2-aminoethoxydiphenyl borate (2-APB), and cannabinoid, while other ligands are more specific, such as allyl isothiocyanate (TRPA1), vanilloids (TRPV1), menthol (TRPM8), ADP-ribose (TRPM2), and ML-SA1 (TRPML1). The mechanisms underlying the gating and regulation of TRP channels remain largely unclear. Recent advances in cryogenic electron microscopy provided structural insights into 19 different TRP channels which all revealed close proximity of the C-terminus with the N-terminus and intracellular S4-S5 linker. Further studies found that some highly conserved residues in these regions of TRPV, -P, -C and -M members mediate functionally critical intramolecular interactions (i.e., within one subunit) between these regions. This review provides an overview on (1) intramolecular interactions in TRP channels and their effect on channel function; (2) functional roles of interplays between PIP2 (and other ligands) and TRP intramolecular interactions; and (3) relevance of the ligand-induced modulation of intramolecular interaction to diseases.
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Affiliation(s)
- Ruiqi Cai
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, ON, Canada.,Department of Physiology, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Department of Physiology, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada.
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29
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Neuberger A, Nadezhdin KD, Zakharian E, Sobolevsky AI. Structural mechanism of TRPV3 channel inhibition by the plant-derived coumarin osthole. EMBO Rep 2021; 22:e53233. [PMID: 34472684 PMCID: PMC8567229 DOI: 10.15252/embr.202153233] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/09/2022] Open
Abstract
TRPV3, a representative of the vanilloid subfamily of TRP channels, is predominantly expressed in skin keratinocytes and has been implicated in cutaneous sensation and associated with numerous skin pathologies and cancers. TRPV3 is inhibited by the natural coumarin derivative osthole, an active ingredient of Cnidium monnieri, which has been used in traditional Chinese medicine for the treatment of a variety of human diseases. However, the structural basis of channel inhibition by osthole has remained elusive. Here we present cryo-EM structures of TRPV3 in complex with osthole, revealing two types of osthole binding sites in the transmembrane region of TRPV3 that coincide with the binding sites of agonist 2-APB. Osthole binding converts the channel pore into a previously unidentified conformation with a widely open selectivity filter and closed intracellular gate. Our structures provide insight into competitive inhibition of TRPV3 by osthole and can serve as a template for the design of osthole chemistry-inspired drugs targeting TRPV3-associated diseases.
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Affiliation(s)
- Arthur Neuberger
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Eleonora Zakharian
- Department of Cancer Biology & PharmacologyUniversity of Illinois College of MedicinePeoriaILUSA
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30
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Thermodynamic and structural basis of temperature-dependent gating in TRP channels. Biochem Soc Trans 2021; 49:2211-2219. [PMID: 34623379 DOI: 10.1042/bst20210301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022]
Abstract
Living organisms require detecting the environmental thermal clues for survival, allowing them to avoid noxious stimuli or find prey moving in the dark. In mammals, the Transient Receptor Potential ion channels superfamily is constituted by 27 polymodal receptors whose activity is controlled by small ligands, peptide toxins, protons and voltage. The thermoTRP channels subgroup exhibits unparalleled temperature dependence -behaving as heat and cold sensors. Functional studies have dissected their biophysical features in detail, and the advances of single-particle Cryogenic Electron microscopy provided the structural framework required to propose detailed channel gating mechanisms. However, merging structural and functional evidence for temperature-driven gating of thermoTRP channels has been a hard nut to crack, remaining an open question nowadays. Here we revisit the highlights on the study of heat and cold sensing in thermoTRP channels in the light of the structural data that has emerged during recent years.
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31
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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32
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Zhao Y, McVeigh BM, Moiseenkova-Bell VY. Structural Pharmacology of TRP Channels. J Mol Biol 2021; 433:166914. [PMID: 33676926 PMCID: PMC8338738 DOI: 10.1016/j.jmb.2021.166914] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Transient receptor potential (TRP) ion channels are a super-family of ion channels that mediate transmembrane cation flux with polymodal activation, ranging from chemical to physical stimuli. Furthermore, due to their ubiquitous expression and role in human diseases, they serve as potential pharmacological targets. Advances in cryo-EM TRP channel structural biology has revealed general, as well as diverse, architectural elements and regulatory sites among TRP channel subfamilies. Here, we review the endogenous and pharmacological ligand-binding sites of TRP channels and their regulatory mechanisms.
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Affiliation(s)
- Yaxian Zhao
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bridget M McVeigh
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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33
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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34
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Nadezhdin KD, Neuberger A, Trofimov YA, Krylov NA, Sinica V, Kupko N, Vlachova V, Zakharian E, Efremov RG, Sobolevsky AI. Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel. Nat Struct Mol Biol 2021; 28:564-572. [PMID: 34239124 PMCID: PMC8283911 DOI: 10.1038/s41594-021-00615-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open states. The heat-induced transformations of TRPV3 are accompanied by changes in the secondary structure of the S2-S3 linker and the N and C termini and represent a conformational wave that links these parts of the protein to a lipid occupying the vanilloid binding site. State-dependent differences in the behavior of bound lipids suggest their active role in thermo-TRP temperature-dependent gating. Our structural data, supported by physiological recordings and molecular dynamics simulations, provide an insight for understanding the molecular mechanism of temperature sensing.
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Affiliation(s)
- Kirill D. Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Yuri A. Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,National Research Nuclear University Moscow Engineering Physics Institute, Moscow, Russia,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,National Research University Higher School of Economics, Moscow, Russia
| | - Viktor Sinica
- Department of Cellular Neurophysiology, Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic
| | - Nikita Kupko
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Viktorie Vlachova
- Department of Cellular Neurophysiology, Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic
| | - Eleonora Zakharian
- Department of Cancer Biology & Pharmacology, University of Illinois College of Medicine, Peoria, Illinois, USA
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia,National Research University Higher School of Economics, Moscow, Russia
| | - Alexander I. Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA,Correspondence and requests for materials should be addressed to A.I.S. (; Tel: 212-305-4249)
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35
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Zhang F, Lin Y, Min W, Hou Y, Yuan K, Wang J, Yang P. Computational discovery, structural optimization and biological evaluation of novel inhibitors targeting transient receptor potential vanilloid type 3 (TRPV3). Bioorg Chem 2021; 114:105093. [PMID: 34182309 DOI: 10.1016/j.bioorg.2021.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/24/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
Transient receptor potential vanilloid type 3 (TRPV3) is a Ca2+ permeable nonselective cation channel and expressed abundantly in skin keratinocytes. TRPV3 emerges as an attractive target for treatment of pruritic, inflammatory, pain and skin-related diseases. However, only a few reports of TRPV3 inhibitors exist at present besides some patents. Therefore, TRPV3 research has always been fraught with challenges. Through a combination of virtual screening and biological evaluation, compound P1 (10 μM) was identified as a top hit with 34.5% inhibitory effect on 2-APB (1 mM)-evoked currents of mTRPV3-WT. Further structural optimization provided the inhibitor PC5 with the best activity (IC50 = 2.63 ± 0.28 μM), and point mutation assays indicated that amino acids V629 and F633 are crucial for the binding of PC5 and TRPV3. In summary, these newly discovered inhibitors could serve as promising lead compounds for the development of TRPV3 inhibitors in the future.
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Affiliation(s)
- Fang Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yiyu Lin
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Hou
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jin Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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36
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Baker MR, Fan G, Seryshev AB, Agosto MA, Baker ML, Serysheva II. Cryo-EM structure of type 1 IP 3R channel in a lipid bilayer. Commun Biol 2021; 4:625. [PMID: 34035440 PMCID: PMC8149723 DOI: 10.1038/s42003-021-02156-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) is the predominant Ca2+-release channel in neurons. IP3R1 mediates Ca2+ release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IP3R1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IP3R1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IP3R1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating. 3D structure of full-length rat type 1 inositol 1,4,5-trisphosphate receptor reconstituted in lipid nanodisc is determined using single-particle cryo-electron microscopy. The study suggests conserved locations of protein-bound lipids among structurally diverse, homo-tetrameric ion channels.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alexander B Seryshev
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Melina A Agosto
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA.
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37
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Gladkikh IN, Sintsova OV, Leychenko EV, Kozlov SA. TRPV1 Ion Channel: Structural Features, Activity Modulators, and Therapeutic Potential. BIOCHEMISTRY (MOSCOW) 2021; 86:S50-S70. [PMID: 33827400 DOI: 10.1134/s0006297921140054] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although TRPV1 ion channel has been attracting researchers' attention for many years, its functions in animal organisms, the principles of regulation, and the involvement in pathological processes have not yet been fully clarified. Mutagenesis experiments and structural studies have identified the structural features of the channel and binding sites for its numerous ligands; however, these studies are far from conclusion. This review summarizes recent achievements in the TRPV1 research with special focus on structural and functional studies of the channel and on its ligands, which are extremely diverse in their nature and interaction specificity to TRPV1. Particular attention was given to the effects of numerous endogenous agonists and antagonists that can fine-tune the channel sensitivity to its usual activators, such as capsaicin, heat, acids, or their combination. In addition to the pain sensing not covered in this review, the TRPV1 channel was found to be involved in the regulation of many important physiological and pathological processes and, therefore, can be considered as a promising therapeutic target in the treatment of various diseases, such as pneumonia, ischemia, diabetes, epilepsy, schizophrenia, psoriasis, etc.
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Affiliation(s)
- Irina N Gladkikh
- Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Oksana V Sintsova
- Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Elena V Leychenko
- Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Sergey A Kozlov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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38
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A unique mode of keratinocyte death requires intracellular acidification. Proc Natl Acad Sci U S A 2021; 118:2020722118. [PMID: 33893234 DOI: 10.1073/pnas.2020722118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The stratum corneum (SC), the outermost epidermal layer, consists of nonviable anuclear keratinocytes, called corneocytes, which function as a protective barrier. The exact modes of cell death executed by keratinocytes of the upper stratum granulosum (SG1 cells) remain largely unknown. Here, using intravital imaging combined with intracellular Ca2+- and pH-responsive fluorescent probes, we aimed to dissect the SG1 death process in vivo. We found that SG1 cell death was preceded by prolonged (∼60 min) Ca2+ elevation and rapid induction of intracellular acidification. Once such intracellular ionic changes were initiated, they became sustained, irreversibly committing the SG1 cells to corneocyte conversion. Time-lapse imaging of isolated murine SG1 cells revealed that intracellular acidification was essential for the degradation of keratohyalin granules and nuclear DNA, phenomena specific to SC corneocyte formation. Furthermore, intravital imaging showed that the number of SG1 cells exhibiting Ca2+ elevation and the timing of intracellular acidification were both tightly regulated by the transient receptor potential cation channel V3. The functional activity of this protein was confirmed in isolated SG1 cells using whole-cell patch-clamp analysis. These findings provide a theoretical framework for improved understanding of the unique molecular mechanisms underlying keratinocyte-specific death mode, namely corneoptosis.
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39
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Liu Q, Wang J, Wei X, Hu J, Ping C, Gao Y, Xie C, Wang P, Cao P, Cao Z, Yu Y, Li D, Yao J. Therapeutic inhibition of keratinocyte TRPV3 sensory channel by local anesthetic dyclonine. eLife 2021; 10:e68128. [PMID: 33876725 PMCID: PMC8112869 DOI: 10.7554/elife.68128] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
The multimodal sensory channel transient receptor potential vanilloid-3 (TRPV3) is expressed in epidermal keratinocytes and implicated in chronic pruritus, allergy, and inflammation-related skin disorders. Gain-of-function mutations of TRPV3 cause hair growth disorders in mice and Olmsted syndrome in humans. Nevertheless, whether and how TRPV3 could be therapeutically targeted remains to be elucidated. We here report that mouse and human TRPV3 channel is targeted by the clinical medication dyclonine that exerts a potent inhibitory effect. Accordingly, dyclonine rescued cell death caused by gain-of-function TRPV3 mutations and suppressed pruritus symptoms in vivo in mouse model. At the single-channel level, dyclonine inhibited TRPV3 open probability but not the unitary conductance. By molecular simulations and mutagenesis, we further uncovered key residues in TRPV3 pore region that could toggle the inhibitory efficiency of dyclonine. The functional and mechanistic insights obtained on dyclonine-TRPV3 interaction will help to conceive therapeutics for skin inflammation.
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Affiliation(s)
- Qiang Liu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Jin Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical UniversityNanjingChina
| | - Xin Wei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Juan Hu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Conghui Ping
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Yue Gao
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Chang Xie
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Peiyu Wang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Peng Cao
- Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zhengyu Cao
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical UniversityNanjingChina
| | - Ye Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical UniversityNanjingChina
| | - Dongdong Li
- Sorbonne Université, Institute of Biology Paris Seine, Neuroscience Paris Seine, CNRS UMR8246, Inserm U1130ParisFrance
| | - Jing Yao
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
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40
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Anada C, Ikeda K, Egawa A, Fujiwara T, Nakao H, Nakano M. Temperature- and composition-dependent conformational transitions of amphipathic peptide-phospholipid nanodiscs. J Colloid Interface Sci 2021; 588:522-530. [PMID: 33429348 DOI: 10.1016/j.jcis.2020.12.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022]
Abstract
Nanodiscs are discoidal particles in which a lipid bilayer is encircled by amphipathic molecules such as proteins, peptides, or synthetic polymers. The apolipoprotein-A-I-derived peptide 18A is known to form nanodiscs in the presence of phospholipids, but the detailed mechanism of the formation and deformation of these nanodiscs in response to changes in the surrounding environment is not well understood. Here, we investigated the temperature- and composition-dependent structural changes of 18A-phosphatidylcholine complexes using fluorescence spectroscopy, dynamic light scattering, circular dichroism, static 31P NMR, and electron microscopy. We found that the nanodiscs in fast isotropic rotational motion increased in size above the gel-to-liquid-crystalline phase transition temperature of the lipid bilayers, resulting in the formation of enlarged nanodiscs and a lamellar phase. The lamellar phase was found to be oriented along the magnetic field. Further increase in temperature induced the formation of lipid vesicles. These transformations were explained using a transition model based on the migration of the peptide from the rim of the nanodiscs to the liquid-crystalline bilayer phase. The study outcomes provide a basis for understanding the design principles of discoidal nanostructures for structural biology and nanomedicine applications.
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Affiliation(s)
- Chiharu Anada
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
| | - Ayako Egawa
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita 565-0871, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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41
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Zheng W, Wen H. Predicting lipid and ligand binding sites in TRPV1 channel by molecular dynamics simulation and machine learning. Proteins 2021; 89:966-977. [PMID: 33739482 DOI: 10.1002/prot.26075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 11/06/2022]
Abstract
As a key cellular sensor, the TRPV1 channel undergoes a gating transition from a closed state to an open state in response to many physical and chemical stimuli. This transition is regulated by small-molecule ligands including lipids and various agonists/antagonists, but the underlying molecular mechanisms remain obscure. Thanks to recent revolution in cryo-electron microscopy, a growing list of new structures of TRPV1 and other TRPV channels have been solved in complex with various ligands including lipids. Toward elucidating how ligand binding correlates with TRPV1 gating, we have performed extensive molecular dynamics simulations (with cumulative time of 20 μs), starting from high-resolution structures of TRPV1 in both the closed and open states. By comparing between the open and closed state ensembles, we have identified state-dependent binding sites for small-molecule ligands in general and lipids in particular. We further use machine learning to predict top ligand-binding sites as important features to classify the closed vs open states. The predicted binding sites are thoroughly validated by matching homologous sites in all structures of TRPV channels bound to lipids and other ligands, and with previous functional/mutational studies of ligand binding in TRPV1. Taken together, this study has integrated rich structural, dynamic, and functional data to inform future design of small-molecular drugs targeting TRPV1.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, New York, USA
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42
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Goretzki B, Guhl C, Tebbe F, Harder JM, Hellmich UA. Unstructural Biology of TRP Ion Channels: The Role of Intrinsically Disordered Regions in Channel Function and Regulation. J Mol Biol 2021; 433:166931. [PMID: 33741410 DOI: 10.1016/j.jmb.2021.166931] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 12/13/2022]
Abstract
The first genuine high-resolution single particle cryo-electron microscopy structure of a membrane protein determined was a transient receptor potential (TRP) ion channel, TRPV1, in 2013. This methodical breakthrough opened up a whole new world for structural biology and ion channel aficionados alike. TRP channels capture the imagination due to the sheer endless number of tasks they carry out in all aspects of animal physiology. To date, structures of at least one representative member of each of the six mammalian TRP channel subfamilies as well as of a few non-mammalian families have been determined. These structures were instrumental for a better understanding of TRP channel function and regulation. However, all of the TRP channel structures solved so far are incomplete since they miss important information about highly flexible regions found mostly in the channel N- and C-termini. These intrinsically disordered regions (IDRs) can represent between a quarter to almost half of the entire protein sequence and act as important recruitment hubs for lipids and regulatory proteins. Here, we analyze the currently available TRP channel structures with regard to the extent of these "missing" regions and compare these findings to disorder predictions. We discuss select examples of intra- and intermolecular crosstalk of TRP channel IDRs with proteins and lipids as well as the effect of splicing and post-translational modifications, to illuminate their importance for channel function and to complement the prevalently discussed structural biology of these versatile and fascinating proteins with their equally relevant 'unstructural' biology.
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Affiliation(s)
- Benedikt Goretzki
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Charlotte Guhl
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany; TransMED - Mainz Research School of Translational Medicine, Johannes Gutenberg-University, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Frederike Tebbe
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jean-Martin Harder
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany; TransMED - Mainz Research School of Translational Medicine, Johannes Gutenberg-University, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany; Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, 07743 Jena, Germany.
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Neuberger A, Nadezhdin KD, Sobolevsky AI. TRPV3 expression and purification for structure determination by Cryo-EM. Methods Enzymol 2021; 652:31-48. [PMID: 34059288 DOI: 10.1016/bs.mie.2021.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The transient receptor potential vanilloid-superfamily member 3 (TRPV3) channel is implicated in a variety of physiological processes, including temperature sensing, nociception and itch, maintenance of the skin barrier, wound healing, hair growth, and embryonic development. TRPV3 is also associated with various skin diseases, including Olmsted syndrome, atopic dermatitis, and rosacea. Studies of TRPV3 are of fundamental importance for structural pharmacology aimed at the design of drugs targeting this channel and for understanding the molecular basis of temperature sensing. Here we describe a detailed protocol for expression and purification of chemically pure and stable TRPV3 protein that is suitable for structural and functional characterization of this channel, in particular for cryo-EM sample preparation and high-resolution 3D reconstruction.
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Affiliation(s)
- Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.
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Structural basis for promiscuous action of monoterpenes on TRP channels. Commun Biol 2021; 4:293. [PMID: 33674682 PMCID: PMC7935860 DOI: 10.1038/s42003-021-01776-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023] Open
Abstract
Monoterpenes are major constituents of plant-derived essential oils and have long been widely used for therapeutic and cosmetic applications. The monoterpenes menthol and camphor are agonists or antagonists for several TRP channels such as TRPM8, TRPV1, TRPV3 and TRPA1. However, which regions within TRPV1 and TRPV3 confer sensitivity to monoterpenes or other synthesized chemicals such as 2-APB are unclear. In this study we identified conserved arginine and glycine residues in the linker between S4 and S5 that are related to the action of these chemicals and validated these findings in molecular dynamics simulations. The involvement of these amino acids differed between TRPV3 and TRPV1 for chemical-induced and heat-evoked activation. These findings provide the basis for characterization of physiological function and biophysical properties of ion channels.
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45
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Wang H, Yang P, Lu Y, Wang J, Jeon J, Wang Q, Tian JB, Zang B, Yu Y, Zhu MX. Mechanisms of proton inhibition and sensitization of the cation channel TRPV3. J Gen Physiol 2020; 153:211594. [PMID: 33320167 PMCID: PMC7745752 DOI: 10.1085/jgp.202012663] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/07/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
TRPV3 is a temperature-sensitive, nonselective cation channel expressed prominently in skin keratinocytes. TRPV3 plays important roles in hair morphogenesis and maintenance of epidermal barrier function. Gain-of-function mutations of TRPV3 have been found in both humans and rodents and are associated with hair loss, pruritus, and dermatitis. Here, we study the mechanisms of acid regulation of TRPV3 by using site-directed mutagenesis, fluorescent intracellular calcium measurement, and whole-cell patch-clamp recording techniques. We show that, whereas extracellular acid inhibits agonist-induced TRPV3 activation through an aspartate residue (D641) in the selectivity filter, intracellular protons sensitize the channel through cytoplasmic C-terminal glutamate and aspartate residues (E682, E689, and D727). Neutralization of the three C-terminal residues presensitizes the channel to agonist stimulation. Molecular dynamic simulations revealed that charge neutralization of the three C-terminal residues stabilized the sensitized channel conformation and enhanced the probability of α-helix formation in the linker between the S6 transmembrane segment and TRP domain. We conclude that acid inhibits TRPV3 function from the extracellular side but facilitates it from the intracellular side. These novel mechanisms of TRPV3 proton sensing can offer new insights into the role of TRPV3 in the regulation of epidermal barrier permeability and skin disorders under conditions of tissue acidosis.
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Affiliation(s)
- Haiyuan Wang
- Department of Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Pu Yang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yungang Lu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jin Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jaepyo Jeon
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Qiaochu Wang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Jin-Bin Tian
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Bin Zang
- Department of Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ye Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, Guilin, China
| | - Michael X Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
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46
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Zubcevic L. Temperature‐sensitive transient receptor potential vanilloid channels: structural insights into ligand‐dependent activation. Br J Pharmacol 2020; 179:3542-3559. [DOI: 10.1111/bph.15310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Lejla Zubcevic
- Department of Biochemistry and Molecular Biology The University of Kansas School of Medicine Kansas City KS USA
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