1
|
Török F, Salamon S, Ortner NJ, Fernández-Quintero ML, Matthes J, Striessnig J. Inactivation induced by pathogenic Ca v1.3 L-type Ca 2+-channel variants enhances sensitivity for dihydropyridine Ca 2+ channel blockers. Br J Pharmacol 2024. [PMID: 39370994 DOI: 10.1111/bph.17357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 08/12/2024] [Accepted: 09/02/2024] [Indexed: 10/08/2024] Open
Abstract
BACKGROUND AND PURPOSE Pathogenic gain-of-function mutations in Cav1.3 L-type voltage-gated Ca2+-channels (CACNA1D) cause neurodevelopmental disorders with or without endocrine symptoms. We aimed to confirm a pathogenic gain-of function phenotype of CACNA1D de novo missense mutations A749T and L271H, and investigated the molecular mechanism causing their enhanced sensitivity for the Ca2+-channel blocker isradipine, a potential therapeutic for affected patients. EXPERIMENTAL APPROACH Wildtype and mutant channels were expressed in tsA-201 cells and their gating analysed using whole-cell and single-channel patch-clamp recordings. The voltage-dependence of isradipine action was quantified using protocols inducing variable fractions of inactivated channels. The molecular basis for altered channel gating in the mutants was investigated using in silico modelling and molecular dynamics simulations. KEY RESULTS Both mutations were confirmed pathogenic due to characteristic shifts of voltage-dependent activation and inactivation towards negative potentials (~20 mV). At negative holding potentials both mutations showed significantly higher isradipine sensitivity compared to wildtype. The affinity for wildtype and mutant channels increased with channel inactivation as predicted by the modulated receptor hypothesis (30- to 40-fold). The IC50 was indistinguishable for wildtype and mutants when >50% of channels were inactivated. CONCLUSIONS AND IMPLICATIONS Mutations A749T and L271H induce pathogenic gating changes. Like wildtype, isradipine inhibition is strongly voltage-dependent. Our data explains their apparent higher drug sensitivity at a given negative voltage by the availability of more inactivated channels due to their more negative inactivation voltage range. Low nanomolar isradipine concentrations will only inhibit Cav1.3 channels in neurons during prolonged depolarized states without selectivity for mutant channels.
Collapse
Affiliation(s)
- Ferenc Török
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Sarah Salamon
- Center of Pharmacology, Institute II, University of Cologne, Cologne, Germany
| | - Nadine J Ortner
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Jan Matthes
- Center of Pharmacology, Institute II, University of Cologne, Cologne, Germany
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
2
|
Ives CM, Şahin AT, Thomson NJ, Zachariae U. A hydrophobic funnel governs monovalent cation selectivity in the ion channel TRPM5. Biophys J 2024; 123:3304-3316. [PMID: 39086136 PMCID: PMC11480762 DOI: 10.1016/j.bpj.2024.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 06/18/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
A key capability of ion channels is the facilitation of selective permeation of certain ionic species across cellular membranes at high rates. Due to their physiological significance, ion channels are of great pharmaceutical interest as drug targets. The polymodal signal-detecting transient receptor potential (TRP) superfamily of ion channels forms a particularly promising group of drug targets. While most members of this family permeate a broad range of cations including Ca2+, TRPM4 and TRPM5 are unique due to their strong monovalent selectivity and impermeability for divalent cations. Here, we investigated the mechanistic basis for their unique monovalent selectivity by in silico electrophysiology simulations of TRPM5. Our simulations reveal an unusual mechanism of cation selectivity, which is underpinned by the function of the central channel cavity alongside the selectivity filter. Our results suggest that a subtle hydrophobic barrier at the cavity entrance ("hydrophobic funnel") enables monovalent but not divalent cations to pass and occupy the cavity at physiologically relevant membrane voltages. Monovalent cations then permeate efficiently by a cooperative, distant knock-on mechanism between two binding regions in the extracellular pore vestibule and the central cavity. By contrast, divalent cations do not enter or interact favorably with the channel cavity due to its raised hydrophobicity. Hydrophilic mutations in the transition zone between the selectivity filter and the central channel cavity abolish the barrier for divalent cations, enabling both monovalent and divalent cations to traverse TRPM5.
Collapse
Affiliation(s)
- Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alp Tegin Şahin
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom; School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Neil J Thomson
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom; Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom.
| |
Collapse
|
3
|
Pelizzari S, Heiss MC, Fernández-Quintero ML, El Ghaleb Y, Liedl KR, Tuluc P, Campiglio M, Flucher BE. Ca V1.1 voltage-sensing domain III exclusively controls skeletal muscle excitation-contraction coupling. Nat Commun 2024; 15:7440. [PMID: 39198449 PMCID: PMC11358481 DOI: 10.1038/s41467-024-51809-5] [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: 12/04/2023] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
Skeletal muscle contractions are initiated by action potentials, which are sensed by the voltage-gated calcium channel (CaV1.1) and are conformationally coupled to calcium release from intracellular stores. Notably, CaV1.1 contains four separate voltage-sensing domains (VSDs), which activate channel gating and excitation-contraction (EC-) coupling at different voltages and with distinct kinetics. Here we show that a single VSD of CaV1.1 controls skeletal muscle EC-coupling. Whereas mutations in VSDs I, II and IV affect the current properties but not EC-coupling, only mutations in VSD III alter the voltage-dependence of depolarization-induced calcium release. Molecular dynamics simulations reveal comprehensive, non-canonical state transitions of VSD III in response to membrane depolarization. Identifying the voltage sensor that activates EC-coupling and detecting its unique conformational changes opens the door to unraveling the downstream events linking VSD III motion to the opening of the calcium release channel, and thus resolving the signal transduction mechanism of skeletal muscle EC-coupling.
Collapse
Affiliation(s)
- Simone Pelizzari
- Institute of Physiology, Department of Physiology and Medical Biophysics, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Martin C Heiss
- Institute of Physiology, Department of Physiology and Medical Biophysics, Medical University Innsbruck, 6020, Innsbruck, Austria
| | | | - Yousra El Ghaleb
- Institute of Physiology, Department of Physiology and Medical Biophysics, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020, Innsbruck, Austria
| | - Marta Campiglio
- Institute of Physiology, Department of Physiology and Medical Biophysics, Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Bernhard E Flucher
- Institute of Physiology, Department of Physiology and Medical Biophysics, Medical University Innsbruck, 6020, Innsbruck, Austria.
| |
Collapse
|
4
|
Huang J, Pan X, Yan N. Structural biology and molecular pharmacology of voltage-gated ion channels. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00763-7. [PMID: 39103479 DOI: 10.1038/s41580-024-00763-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2024] [Indexed: 08/07/2024]
Abstract
Voltage-gated ion channels (VGICs), including those for Na+, Ca2+ and K+, selectively permeate ions across the cell membrane in response to changes in membrane potential, thus participating in physiological processes involving electrical signalling, such as neurotransmission, muscle contraction and hormone secretion. Aberrant function or dysregulation of VGICs is associated with a diversity of neurological, psychiatric, cardiovascular and muscular disorders, and approximately 10% of FDA-approved drugs directly target VGICs. Understanding the structure-function relationship of VGICs is crucial for our comprehension of their working mechanisms and role in diseases. In this Review, we discuss how advances in single-particle cryo-electron microscopy have afforded unprecedented structural insights into VGICs, especially on their interactions with clinical and investigational drugs. We present a comprehensive overview of the recent advances in the structural biology of VGICs, with a focus on how prototypical drugs and toxins modulate VGIC activities. We explore how these structures elucidate the molecular basis for drug actions, reveal novel pharmacological sites, and provide critical clues to future drug discovery.
Collapse
Affiliation(s)
- Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Xiaojing Pan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong, China.
| | - Nieng Yan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.
| |
Collapse
|
5
|
Ceccarelli M, Milenkovic S, Bodrenko IV. The Effect of Lipopolysaccharides on the Electrostatic Properties of Gram-Negative General Porins from Enterobacteriaceae. Chemphyschem 2024; 25:e202400147. [PMID: 38625051 DOI: 10.1002/cphc.202400147] [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: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
We investigated, by using all-atom molecular dynamics simulations, the effect of the outer membrane of Gram-negative bacteria, composed in the outer leaflet by polar/charged lipopolysaccharides (LPS), on the electrostatic properties of general porins from the Enterobacteriaceae family. General porins constitute the main path for the facilitated diffusion of polar antibiotics through the outer membrane. As model system we selected OmpK36 from Klebsiella pneumoniae, the ortholog of OmpC from Escherichia coli. This species presents high variability of amino acid composition of porins, with the effect to increase its resistance to the penetration of antibiotics. The various properties we analyzed seem to indicate that LPS acts as an independent layer without affecting the internal electrostatic properties of OmpK36. The only apparent effect on the microsecond time scale we sampled is the appearance of calcium ions, when present at moderate concentration in solution, inside the pore. However, we noticed increased fluctuations of the polarization density and only minor changes on its average value.
Collapse
Affiliation(s)
- Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, IT
| | - Stefan Milenkovic
- Department of Physics, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, IT
| | - Igor V Bodrenko
- Istituto Nanoscienze, CNR, piazza San Silvestro 12, 56127, Pisa, Italy
- Lab NEST, Scuola Normale Superiore, piazza San Silvestro 12, 56127, Pisa, Italy
| |
Collapse
|
6
|
Farci D, Milenkovic S, Iesu L, Tanas M, Ceccarelli M, Piano D. Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans. J Biol Chem 2024; 300:105537. [PMID: 38072042 PMCID: PMC10828601 DOI: 10.1016/j.jbc.2023.105537] [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: 10/05/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024] Open
Abstract
The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) stands out as a pivotal structural component. We used cryo-electron microscopy to reveal unique features, such as an unconventional protein belt (DR_1364) around the main secretin (GspD), and a cap (DR_0940) found to be a separated subunit rather than integrated with GspD. Furthermore, a novel region at the N-terminus of the GspD constitutes an additional second gate, supplementing the one typically found in the outer membrane region. This T2SS was found to contribute to envelope integrity, while also playing a role in nucleic acid and nutrient trafficking. Studies on intact cell envelopes show a consistent T2SS structure repetition, highlighting its significance within the cellular framework.
Collapse
Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; R&D Department, ReGenFix Laboratories, Sardara, Italy.
| | - Stefan Milenkovic
- Department of Physics and IOM/CNR, Università degli Studi di Cagliari, Monserrato, Italy
| | - Luca Iesu
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Marta Tanas
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, Università degli Studi di Cagliari, Monserrato, Italy
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; R&D Department, ReGenFix Laboratories, Sardara, Italy.
| |
Collapse
|
7
|
Liu C, Xue L, Song C. Calcium binding and permeation in TRPV channels: Insights from molecular dynamics simulations. J Gen Physiol 2023; 155:e202213261. [PMID: 37728593 PMCID: PMC10510737 DOI: 10.1085/jgp.202213261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 05/21/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023] Open
Abstract
Some calcium channels selectively permeate Ca2+, despite the high concentration of monovalent ions in the surrounding environment, which is essential for many physiological processes. Without atomistic and dynamical ion permeation details, the underlying mechanism of Ca2+ selectivity has long been an intensively studied, yet controversial, topic. This study takes advantage of the homologous Ca2+-selective TRPV6 and non-selective TRPV1 and utilizes the recently solved open-state structures and a newly developed multisite calcium model to investigate the ion binding and permeation features in TRPV channels by molecular dynamics simulations. Our results revealed that the open-state TRPV6 and TRPV1 show distinct ion binding patterns in the selectivity filter, which lead to different ion permeation features. Two Ca2+ ions simultaneously bind to the selectivity filter of TRPV6 compared with only one Ca2+ in the case of TRPV1. Multiple Ca2+ binding at the selectivity filter of TRPV6 permeated in a concerted manner, which could efficiently block the permeation of Na+. Cations of various valences differentiate between the binding sites at the entrance of the selectivity filter in TRPV6. Ca2+ preferentially binds to the central site with a higher probability of permeation, repelling Na+ to a peripheral site. Therefore, we believe that ion binding competition at the selectivity filter of calcium channels, including the binding strength and number of binding sites, determines Ca2+ selectivity under physiological conditions.
Collapse
Affiliation(s)
- Chunhong Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lingfeng Xue
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| |
Collapse
|
8
|
Medeiros-Silva J, Dregni AJ, Somberg NH, Duan P, Hong M. Atomic structure of the open SARS-CoV-2 E viroporin. SCIENCE ADVANCES 2023; 9:eadi9007. [PMID: 37831764 PMCID: PMC10575589 DOI: 10.1126/sciadv.adi9007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.
Collapse
Affiliation(s)
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | |
Collapse
|
9
|
Zhang J, Song D, Schackert FK, Li J, Xiang S, Tian C, Gong W, Carloni P, Alfonso-Prieto M, Shi C. Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR. SCIENCE ADVANCES 2023; 9:eadg9709. [PMID: 37611110 PMCID: PMC10446490 DOI: 10.1126/sciadv.adg9709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) methods can probe the motions of membrane proteins in liposomes at the atomic level and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we report our study on the fluoride channel Fluc-Ec1 in phospholipid bilayers based on ssNMR and molecular dynamics simulations. Previously unidentified fluoride binding sites in the aqueous vestibules were experimentally verified by 19F-detected ssNMR. One of the two fluoride binding sites in the polar track was identified as a water molecule by 1H-detected ssNMR. Meanwhile, a dynamic hotspot at loop 1 was observed by comparing the spectra of wild-type Fluc-Ec1 in variant buffer conditions or with its mutants. Therefore, we propose that fluoride conduction in the Fluc channel occurs via a "water-mediated knock-on" permeation mechanism and that loop 1 is a key molecular determinant for channel gating.
Collapse
Affiliation(s)
- Jin Zhang
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Dan Song
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Florian Karl Schackert
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52428 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Juan Li
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Shengqi Xiang
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Changlin Tian
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Weimin Gong
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Paolo Carloni
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52428 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Chaowei Shi
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| |
Collapse
|