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Sanganna Gari RR, Tagiltsev G, Pumroy RA, Jiang Y, Blackledge M, Moiseenkova-Bell VY, Scheuring S. Intrinsically disordered regions in TRPV2 mediate protein-protein interactions. Commun Biol 2023; 6:966. [PMID: 37736816 PMCID: PMC10516966 DOI: 10.1038/s42003-023-05343-7] [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: 08/12/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
Transient receptor potential (TRP) ion channels are gated by diverse intra- and extracellular stimuli leading to cation inflow (Na+, Ca2+) regulating many cellular processes and initiating organismic somatosensation. Structures of most TRP channels have been solved. However, structural and sequence analysis showed that ~30% of the TRP channel sequences, mainly the N- and C-termini, are intrinsically disordered regions (IDRs). Unfortunately, very little is known about IDR 'structure', dynamics and function, though it has been shown that they are essential for native channel function. Here, we imaged TRPV2 channels in membranes using high-speed atomic force microscopy (HS-AFM). The dynamic single molecule imaging capability of HS-AFM allowed us to visualize IDRs and revealed that N-terminal IDRs were involved in intermolecular interactions. Our work provides evidence about the 'structure' of the TRPV2 IDRs, and that the IDRs may mediate protein-protein interactions.
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Affiliation(s)
| | - Grigory Tagiltsev
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yining Jiang
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, New York, USA
| | - Martin Blackledge
- Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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2
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Ives CM, Thomson NJ, Zachariae U. A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels. J Gen Physiol 2023; 155:213957. [PMID: 36943243 PMCID: PMC10038842 DOI: 10.1085/jgp.202213226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/15/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The selective exchange of ions across cellular membranes is a vital biological process. Ca2+-mediated signaling is implicated in a broad array of physiological processes in cells, while elevated intracellular concentrations of Ca2+ are cytotoxic. Due to the significance of this cation, strict Ca2+ concentration gradients are maintained across the plasma and organelle membranes. Therefore, Ca2+ signaling relies on permeation through selective ion channels that control the flux of Ca2+ ions. A key family of Ca2+-permeable membrane channels is the polymodal signal-detecting transient receptor potential (TRP) ion channels. TRP channels are activated by a wide variety of cues including temperature, small molecules, transmembrane voltage, and mechanical stimuli. While most members of this family permeate a broad range of cations non-selectively, TRPV5 and TRPV6 are unique due to their strong Ca2+ selectivity. Here, we address the question of how some members of the TRPV subfamily show a high degree of Ca2+ selectivity while others conduct a wider spectrum of cations. We present results from all-atom molecular dynamics simulations of ion permeation through two Ca2+-selective and two non-selective TRPV channels. Using a new method to quantify permeation cooperativity based on mutual information, we show that Ca2+-selective TRPV channel permeation occurs by a three-binding site knock-on mechanism, whereas a two-binding site knock-on mechanism is observed in non-selective TRPV channels. Each of the ion binding sites involved displayed greater affinity for Ca2+ over Na+. As such, our results suggest that coupling to an extra binding site in the Ca2+-selective TRPV channels underpins their increased selectivity for Ca2+ over Na+ ions. Furthermore, analysis of all available TRPV channel structures shows that the selectivity filter entrance region is wider for the non-selective TRPV channels, slightly destabilizing ion binding at this site, which is likely to underlie mechanistic decoupling.
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Affiliation(s)
- Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Neil J Thomson
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
- Biochemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee, UK
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3
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Biou V. Lipid-membrane protein interaction visualised by cryo-EM: A review. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184068. [PMID: 36216098 DOI: 10.1016/j.bbamem.2022.184068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Membrane proteins reside at interfaces between aqueous and lipid media and solving their molecular structure relies most of the time on removing them from the membrane using detergent. Luckily, this solubilization process does not strip them from all the associated lipids and single-particle cryo-transmission electron microscopy (SP-TEM) has proved a very good tool to visualise both protein high-resolution structure and, often, many of its associated lipids. In this review, we observe membrane protein structures from the Protein DataBank and their associated maps in the Electron Microscopy DataBase and determine how the SP-TEM maps allow lipid visualization, the type of binding sites, the influence of symmetry, resolution and other factors. We illustrate lipid visualization around and inside the protein core, show that some lipid bilayers in the core can be shifted with respect to the membrane and how some proteins can actively bend the lipid bilayer that binds to them. We conclude that resolution improvement in SP-TEM will likely enable many more discoveries regarding the role of lipids bound to proteins.
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Affiliation(s)
- Valérie Biou
- Université de Paris, CNRS, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique, F-75005 Paris, France.
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4
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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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5
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Walker V, Vuister GW. Biochemistry and pathophysiology of the Transient Potential Receptor Vanilloid 6 (TRPV6) calcium channel. Adv Clin Chem 2023; 113:43-100. [PMID: 36858649 DOI: 10.1016/bs.acc.2022.11.002] [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] [Indexed: 01/15/2023]
Abstract
TRPV6 is a Transient Receptor Potential Vanilloid (TRPV) cation channel with high selectivity for Ca2+ ions. First identified in 1999 in a search for the gene which mediates intestinal Ca2+ absorption, its far more extensive repertoire as a guardian of intracellular Ca2+ has since become apparent. Studies on TRPV6-deficient mice demonstrated additional important roles in placental Ca2+ transport, fetal bone development and male fertility. The first reports of inherited deficiency in newborn babies appeared in 2018, revealing its physiological importance in humans. There is currently strong evidence that TRPV6 also contributes to the pathogenesis of some common cancers. The recently reported association of TRPV6 deficiency with non-alcoholic chronic pancreatitis suggests a role in normal pancreatic function. Over time and with greater awareness of TRPV6, other disease-associations are likely to emerge. Powerful analytical tools have provided invaluable insights into the structure and operation of TRPV6. Its roles in Ca2+ signaling and carcinogenesis, and the use of channel inhibitors in cancer treatment are being intensively investigated. This review first briefly describes the biochemistry and physiology of the channel, and analytical methods used to investigate these. The focus subsequently shifts to the clinical disorders associated with abnormal expression and the underlying pathophysiology. The aims of this review are to increase awareness of this channel, and to draw together findings from a wide range of sources which may help to formulate new ideas for further studies.
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Affiliation(s)
- Valerie Walker
- Department of Clinical Biochemistry, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, United Kingdom.
| | - Geerten W Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
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6
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Blanes-Mira C, Fernández-Aguado P, de Andrés-López J, Fernández-Carvajal A, Ferrer-Montiel A, Fernández-Ballester G. Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening. Molecules 2022; 28:molecules28010175. [PMID: 36615367 PMCID: PMC9821981 DOI: 10.3390/molecules28010175] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The rapid advances of 3D techniques for the structural determination of proteins and the development of numerous computational methods and strategies have led to identifying highly active compounds in computer drug design. Molecular docking is a method widely used in high-throughput virtual screening campaigns to filter potential ligands targeted to proteins. A great variety of docking programs are currently available, which differ in the algorithms and approaches used to predict the binding mode and the affinity of the ligand. All programs heavily rely on scoring functions to accurately predict ligand binding affinity, and despite differences in performance, none of these docking programs is preferable to the others. To overcome this problem, consensus scoring methods improve the outcome of virtual screening by averaging the rank or score of individual molecules obtained from different docking programs. The successful application of consensus docking in high-throughput virtual screening highlights the need to optimize the predictive power of molecular docking methods.
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7
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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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8
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Goretzki B, Tebbe F, Mitrovic SA, Hellmich UA. Backbone NMR assignments of the extensive human and chicken TRPV4 N-terminal intrinsically disordered regions as important players in ion channel regulation. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:205-212. [PMID: 35451798 PMCID: PMC9027025 DOI: 10.1007/s12104-022-10080-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Transient receptor potential (TRP) channels are important pharmacological targets due to their ability to act as sensory transducers on the organismic and cellular level, as polymodal signal integrators and because of their role in numerous diseases. However, a detailed molecular understanding of the structural dynamics of TRP channels and their integration into larger cellular signalling networks remains challenging, in part due to the systematic absence of highly dynamic regions pivotal for channel regulation from available structures. In human TRP vanilloid 4 (TRPV4), a ubiquitously expressed homotetrameric cation channel involved in temperature, osmo- and mechano-sensation and in a multitude of (patho)physiological processes, the intrinsically disordered N-terminus encompasses 150 amino acids and thus represents > 17% of the entire channel sequence. Its deletion renders the channel significantly less excitable to agonists supporting a crucial role in TRPV4 activation and regulation. For a structural understanding and a comparison of its properties across species, we determined the NMR backbone assignments of the human and chicken TRPV4 N-terminal IDRs.
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Affiliation(s)
- Benedikt Goretzki
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry and Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, Humboldtstrasse 10, 07443, Jena, Germany
- Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Frederike Tebbe
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry and Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, Humboldtstrasse 10, 07443, Jena, Germany
| | - Sarah-Ana Mitrovic
- 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 and Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, Humboldtstrasse 10, 07443, Jena, Germany.
- Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
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9
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Ionic channels in nerve membranes, 50 years on. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:12-20. [PMID: 34856230 PMCID: PMC8977236 DOI: 10.1016/j.pbiomolbio.2021.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022]
Abstract
This retrospective traces the hypothesis of ion channels from an early statement in a 1970 essay in this journal (Hille, B., 1970, Prog. Biophys. Mol. Biol. 21, 1-32) to its realization today in biophysical, molecular, biochemical, and structural terms. The Na+ and K+ channels of the action potential have been isolated, reconstituted, cloned, mutated, and expressed. They are conformationally flexible, multi-pass glycosylated membrane proteins. Refined atomic structures of several conformational states are known. The discoveries over this half century history illustrate the growth of a field from initial ideas to a mature discipline of biology, physiology, and biomedical science.
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10
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Zhang K, Julius D, Cheng Y. Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Cell 2021; 184:5138-5150.e12. [PMID: 34496225 DOI: 10.1016/j.cell.2021.08.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022]
Abstract
Many transient receptor potential (TRP) channels respond to diverse stimuli and conditionally conduct small and large cations. Such functional plasticity is presumably enabled by a uniquely dynamic ion selectivity filter that is regulated by physiological agents. What is currently missing is a "photo series" of intermediate structural states that directly address this hypothesis and reveal specific mechanisms behind such dynamic channel regulation. Here, we exploit cryoelectron microscopy (cryo-EM) to visualize conformational transitions of the capsaicin receptor, TRPV1, as a model to understand how dynamic transitions of the selectivity filter in response to algogenic agents, including protons, vanilloid agonists, and peptide toxins, permit permeation by small and large organic cations. These structures also reveal mechanisms governing ligand binding substates, as well as allosteric coupling between key sites that are proximal to the selectivity filter and cytoplasmic gate. These insights suggest a general framework for understanding how TRP channels function as polymodal signal integrators.
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Affiliation(s)
- Kaihua Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - David Julius
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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11
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Li T, Chen J, Zeng Z. Pathophysiological role of calcium channels and transporters in the multiple myeloma. Cell Commun Signal 2021; 19:99. [PMID: 34579758 PMCID: PMC8477534 DOI: 10.1186/s12964-021-00781-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/28/2021] [Indexed: 12/11/2022] Open
Abstract
Multiple myeloma (MM) is a common malignant tumor of plasma cells. Despite several treatment approaches in the past two decades, MM remains an aggressive and incurable disease in dire need of new treatment strategies. Approximately 70–80% of patients with MM have myeloma bone disease (MBD), often accompanied by pathological fractures and hypercalcemia, which seriously affect the prognosis of the patients. Calcium channels and transporters can mediate Ca2+ balance inside and outside of the membrane, indicating that they may be closely related to the prognosis of MM. Therefore, this review focuses on the roles of some critical calcium channels and transporters in MM prognosis, which located in the plasma membrane, endoplasmic reticulum and mitochondria. The goal of this review is to facilitate the identification of new targets for the treatment and prognosis of MM.![]() Video Abstract
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Affiliation(s)
- Tingting Li
- Department of Hematology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, Fujian, 350005, People's Republic of China.,Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Junmin Chen
- Department of Hematology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, Fujian, 350005, People's Republic of China. .,Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China.
| | - Zhiyong Zeng
- Department of Hematology, The First Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou, Fujian, 350005, People's Republic of China. .,Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China.
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12
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CryoEM reconstructions of membrane proteins solved in several amphipathic solvents, nanodisc, amphipol and detergents, yield amphipathic belts of similar sizes corresponding to a common ordered solvent layer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183693. [PMID: 34271006 DOI: 10.1016/j.bbamem.2021.183693] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
To maintain membrane proteins soluble in aqueous solution, amphipathic compounds are used to shield the hydrophobic patch of their membrane insertion, which forms a belt around the protein. This amphipathic belt is seldom looked at due to the difficulty to visualize it. Cryo-EM is now offering this possibility, where belts are visible in 3D reconstructions. We investigated membrane proteins solved in nanodiscs, amphipols or detergents to analyze whether the nature of the amphipathic compound influences the belt size in 3D reconstructions. We identified belt boundaries in map-density distributions and measured distances for every reconstruction. We showed that all the belts create on average similar reconstructions, whether they originate from the same protein, or from protein from different shapes and structures. There is no difference among detergents or types of nanodisc used. These observations illustrate that the belt observed in 3D reconstructions corresponds to the minimum ordered layer around membrane proteins.
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13
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Valencia-Guzmán CJ, Castro-Ruiz JE, García-Gasca T, Rojas-Molina A, Romo-Mancillas A, Luna-Vázquez FJ, Rojas-Molina JI, Ibarra-Alvarado C. Endothelial TRP channels and cannabinoid receptors are involved in affinin-induced vasodilation. Fitoterapia 2021; 153:104985. [PMID: 34237389 DOI: 10.1016/j.fitote.2021.104985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023]
Abstract
Affinin is mainly recognized by its antinociceptive effect. Recently, our research group demonstrated that this compound produces vasodilation via activation of the gasotransmitters signaling pathways. However, the molecular targets of affinin were not identified. Considering the structural similarity of this alkamide with anandamide, we hypothesized that affinin-induced vasodilation could involve participation of TRP channels and cannabinoid receptors. In this work, by using the isolated rat aorta assay, we assessed involvement of TRP channels, the cannabinoid system, and the HNO-CGRP-TRPA1 pathway on the mechanism of action of affinin. Additionally, we measured NO and H2S levels elicited by affinin on rat aorta homogenates and carried out computer simulations of molecular interactions between affinin and the TRPA1 and TRPV1 channels and the CB1 receptor. Our results indicated that affinin induces an increase in aortic NO and H2S levels. We found evidence that the vasodilator effect induced by affinin involves activation of TRPA1 and TRPV1 channels and the CB1 and eCB receptors. In silico analyses showed that affinin is able to bind with high affinity to these molecular targets. Moreover, we also proved that affinin-induced vasodilation is partly mediated via activation of the HNO-TRPA1-CGRP pathway. Based on these results we propose a novel mechanism of action to explain the vasodilatory effect of affinin, which could be developed as an alternative drug to treat cardiovascular diseases.
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Affiliation(s)
- Christian J Valencia-Guzmán
- Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Jesús E Castro-Ruiz
- Laboratorio de Biología Celular y Molecular, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Campus Juriquilla, Querétaro 76230, Mexico.
| | - Teresa García-Gasca
- Laboratorio de Biología Celular y Molecular, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Campus Juriquilla, Querétaro 76230, Mexico.
| | - Alejandra Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Antonio Romo-Mancillas
- Laboratorio de Diseño Asistido por Computadora y Síntesis de Fármacos, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
| | - Francisco J Luna-Vázquez
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico
| | - Juana I Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico
| | - César Ibarra-Alvarado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Centro Universitario, Querétaro 76010, Mexico.
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14
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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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15
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Chen PF, Ma XF, Sun LF, Tian Y, Fan YZ, Li P, Xiao Z, Zhu MX, Guo CR, Li C, Yu Y, Wang J. A conserved residue in the P2X4 receptor has a nonconserved function in ATP recognition. J Biol Chem 2021; 296:100655. [PMID: 33901491 PMCID: PMC8166750 DOI: 10.1016/j.jbc.2021.100655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
Highly conserved amino acids are generally anticipated to have similar functions across a protein superfamily, including that of the P2X ion channels, which are gated by extracellular ATP. However, whether and how these functions are conserved becomes less clear when neighboring amino acids are not conserved. Here, we investigate one such case, focused on the highly conserved residue from P2X4, E118 (rat P2X4 numbering, rP2X4), a P2X subtype associated with human neuropathic pain. When we compared the crystal structures of P2X4 with those of other P2X subtypes, including P2X3, P2X7, and AmP2X, we observed a slightly altered side-chain orientation of E118. We used protein chimeras, double-mutant cycle analysis, and molecular modeling to reveal that E118 forms specific contacts with amino acids in the "beak" region, which facilitates ATP binding to rP2X4. These contacts are not present in other subtypes because of sequence variance in the beak region, resulting in decoupling of this conserved residue from ATP recognition and/or channel gating of P2X receptors. Our study provides an example of a conserved residue with a specific role in functional proteins enabled by adjacent nonconserved residues. The unique role established by the E118-beak region contact provides a blueprint for the development of subtype-specific inhibitors of P2X4.
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Affiliation(s)
- Ping-Fang Chen
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xue-Fei Ma
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Liang-Fei Sun
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Ying-Zhe Fan
- Putuo Hospital, Shanghai University of Chinese Traditional Medicine, Shanghai, China
| | - Peiwang Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Zhihong Xiao
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Michael X Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Chang-Run Guo
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China.
| | - Ye Yu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China; State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, China.
| | - Jin Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.
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16
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Ji C, McCulloch CA. TRPV4 integrates matrix mechanosensing with Ca 2+ signaling to regulate extracellular matrix remodeling. FEBS J 2020; 288:5867-5887. [PMID: 33300268 DOI: 10.1111/febs.15665] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/23/2020] [Indexed: 12/23/2022]
Abstract
In healthy connective tissues, mechanosensors trigger the generation of Ca2+ signals, which enable cells to maintain the structure of the fibrillar collagen matrix through actomyosin contractile forces. Transient receptor potential vanilloid type 4 (TRPV4) is a mechanosensitive Ca2+ -permeable channel that, when expressed in cell-matrix adhesions of the plasma membrane, regulates extracellular matrix (ECM) remodeling. In high prevalence disorders such as fibrosis and tumor metastasis, dysregulated matrix remodeling is associated with disruptions of Ca2+ homeostasis and TRPV4 function. Here, we consider that ECM polymers transmit cell-activating mechanical signals to TRPV4 in cell adhesions. When activated, TRPV4 regulates fibrillar collagen remodeling, thereby altering the mechanical properties of the ECM. In this review, we integrate functionally connected processes of matrix remodeling to highlight how TRPV4 in cell adhesions and matrix mechanics are reciprocally regulated through Ca2+ signaling.
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Affiliation(s)
- Chenfan Ji
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, ON, Canada
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17
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van Goor MK, de Jager L, Cheng Y, van der Wijst J. High-resolution structures of transient receptor potential vanilloid channels: Unveiling a functionally diverse group of ion channels. Protein Sci 2020; 29:1569-1580. [PMID: 32232875 PMCID: PMC7314393 DOI: 10.1002/pro.3861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022]
Abstract
Transient receptor potential vanilloid (TRPV) channels are part of the superfamily of TRP ion channels and play important roles in widespread physiological processes including both neuronal and non‐neuronal pathways. Various diseases such as skeletal abnormalities, chronic pain, and cancer are associated with dysfunction of a TRPV channel. In order to obtain full understanding of disease pathogenesis and create opportunities for therapeutic intervention, it is essential to unravel how these channels function at a molecular level. In the past decade, incredible progress has been made in biochemical sample preparation of large membrane proteins and structural biology techniques, including cryo‐electron microscopy. This has resulted in high resolution structures of all TRPV channels, which has provided novel insights into the molecular mechanisms of channel gating and regulation that will be summarized in this review.
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Affiliation(s)
- Mark K van Goor
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leanne de Jager
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States.,Howard Hughes Medical Institute, University of California, San Francisco, California, United States
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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