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Elbahnsi A, Dudas B, Cisternino S, Declèves X, Miteva MA. Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations. Comput Struct Biotechnol J 2024; 23:2548-2564. [PMID: 38989058 PMCID: PMC11233806 DOI: 10.1016/j.csbj.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
P-glycoprotein (P-gp) plays a crucial role in cellular detoxification and drug efflux processes, transitioning between inward-facing (IF) open, occluded, and outward-facing (OF) states to facilitate substrate transport. Its role is critical in cancer therapy, where P-gp contributes to the multidrug resistance phenotype. In our study, classical and enhanced molecular dynamics (MD) simulations were conducted to dissect the structural and functional features of the P-gp conformational states. Our advanced MD simulations, including kinetically excited targeted MD (ketMD) and adiabatic biasing MD (ABMD), provided deeper insights into state transition and translocation mechanisms. Our findings suggest that the unkinking of TM4 and TM10 helices is a prerequisite for correctly achieving the outward conformation. Simulations of the IF-occluded conformations, characterized by kinked TM4 and TM10 helices, consistently demonstrated altered communication between the transmembrane domains (TMDs) and nucleotide binding domain 2 (NBD2), suggesting the implication of this interface in inhibiting P-gp's efflux function. A particular emphasis was placed on the unstructured linker segment connecting the NBD1 to TMD2 and its role in the transporter's dynamics. With the linker present, we specifically noticed a potential entrance of cholesterol (CHOL) through the TM4-TM6 portal, shedding light on crucial residues involved in accommodating CHOL. We therefore suggest that this entry mechanism could be employed for some P-gp substrates or inhibitors. Our results provide critical data for understanding P-gp functioning and developing new P-gp inhibitors for establishing more effective strategies against multidrug resistance.
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Affiliation(s)
- Ahmad Elbahnsi
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Salvatore Cisternino
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Xavier Declèves
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Maria A. Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
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2
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Bernetti M, Bosio S, Bresciani V, Falchi F, Masetti M. Probing allosteric communication with combined molecular dynamics simulations and network analysis. Curr Opin Struct Biol 2024; 86:102820. [PMID: 38688074 DOI: 10.1016/j.sbi.2024.102820] [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: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Understanding the allosteric mechanisms within biomolecules involved in diseases is of paramount importance for drug discovery. Indeed, characterizing communication pathways and critical hotspots in signal transduction can guide a rational approach to leverage allosteric modulation for therapeutic purposes. While the atomistic signatures of allosteric processes are difficult to determine experimentally, computational methods can be a remarkable resource. Network analysis built on Molecular Dynamics simulation data is particularly suited in this respect and is gradually becoming of routine use. Herein, we collect the recent literature in the field, discussing different aspects and available options for network construction and analysis. We further highlight interesting refinements and extensions, eventually providing our perspective on this topic.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
| | - Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/Stefano__Bosio
| | - Veronica Bresciani
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/V_Bresciani
| | - Federico Falchi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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3
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Ghorbani M, Wang ZJ, Chen X, Tiwari PB, Klauda JB, Brelidze TI. Chlorpromazine inhibits EAG1 channels by altering the coupling between the PAS, CNBH and pore domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581826. [PMID: 38464246 PMCID: PMC10925124 DOI: 10.1101/2024.02.23.581826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
EAG1 depolarization-activated potassium selective channels are important targets for treatment of cancer and neurological disorders. EAG1 channels are formed by a tetrameric subunit assembly with each subunit containing an N-terminal Per-Arnt-Sim (PAS) domain and C-terminal cyclic nucleotide-binding homology (CNBH) domain. The PAS and CNBH domains from adjacent subunits interact and form an intracellular tetrameric ring that regulates the EAG1 channel gating, including the movement of the voltage sensor domain (VSD) from closed to open states. Small molecule ligands can inhibit EAG1 channels by binding to their PAS domains. However, the allosteric pathways of this inhibition are not known. Here we show that chlorpromazine, a PAS domain small molecule binder, alters interactions between the PAS and CNBH domains and decreases the coupling between the intracellular tetrameric ring and the pore of the channel, while having little effect on the coupling between the PAS and VSD domains. In addition, chlorpromazine binding to the PAS domain did not alter Cole-Moore shift characteristic of EAG1 channels, further indicating that chlorpromazine has no effect on VSD movement from the deep closed to opened states. Our study provides a framework for understanding global pathways of EAG1 channel regulation by small molecule PAS domain binders.
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El Balkhi S, Rahali MA, Lakis R, Sauvage FL, Martin M, Janaszkiewicz A, Lawson R, Goncalves R, Carrier P, Loustaud-Ratti V, Guyot A, Marquet P, Di Meo F, Saint-Marcoux F. Early detection of liver injuries by the Serum enhanced binding test sensitive to albumin post-transcriptional modifications. Sci Rep 2024; 14:1434. [PMID: 38228668 PMCID: PMC10791642 DOI: 10.1038/s41598-024-51412-0] [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: 08/02/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
Early and sensitive biomarkers of liver dysfunction and drug-induced liver injury (DILI) are still needed, both for patient care and drug development. We developed the Serum Enhanced Binding (SEB) test to reveal post-transcriptional modifications (PTMs) of human serum albumin resulting from hepatocyte dysfunctions and further evaluated its performance in an animal model. The SEB test consists in spiking serum ex-vivo with ligands having specific binding sites related to the most relevant albumin PTMs and measuring their unbound fraction. To explore the hypothesis that albumin PTMs occur early during liver injury and can also be detected by the SEB test, we induced hepatotoxicity in male albino Wistar rats by administering high daily doses of ethanol and CCl4 over several days. Blood was collected for characterization and quantification of albumin isoforms by high-resolution mass spectrometry, for classical biochemical analyses as well as to apply the SEB test. In the exposed rats, the appearance of albumin isoforms paralleled the positivity of the SEB test ligands and histological injuries. These were observed as early as D3 in the Ethanol and CCl4 groups, whereas the classical liver tests (ALT, AST, PAL) significantly increased only at D7. The behavior of several ligands was supported by structural and molecular simulation analysis. The SEB test and albumin isoforms revealed hepatocyte damage early, before the current biochemical biomarkers. The SEB test should be easier to implement in the clinics than albumin isoform profiling.
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Affiliation(s)
- Souleiman El Balkhi
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France.
- Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France.
- Pharmacology-Toxicology and Pharmacovigilance Department, Centre de Biologie Et de Recherche en Santé (CBRS), 2, Av. Martin Luther King, 87042, Limoges Cedex, France.
| | - Mohamad Ali Rahali
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
- Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
| | - Roy Lakis
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
| | | | | | | | - Roland Lawson
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
| | | | - Paul Carrier
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
- Department of Liver Disease, CHU Limoges, Limoges, France
| | - Veronique Loustaud-Ratti
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
- Department of Liver Disease, CHU Limoges, Limoges, France
| | - Anne Guyot
- Department of Pathology, CHU Limoges, Limoges, France
| | - Pierre Marquet
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
- Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
| | | | - Franck Saint-Marcoux
- P&T, UMR1248, Inserm, Univ. Limoges, Limoges, France
- Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, Limoges, France
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5
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González-Garrido A, López-Ramírez O, Cerda-Mireles A, Navarrete-Miranda T, Flores-Arenas AI, Rojo-Domínguez A, Arregui L, Iturralde P, Antúnez-Argüelles E, Domínguez-Pérez M, Jacobo-Albavera L, Carnevale A, Villarreal-Molina T. KCNQ1 p.D446E Variant as a Risk Allele for Arrhythmogenic Phenotypes: Electrophysiological Characterization Reveals a Complex Phenotype Affecting the Slow Delayed Rectifier Potassium Current (IKs) Voltage Dependence by Causing a Hyperpolarizing Shift and a Lack of Response to Protein Kinase A Activation. Int J Mol Sci 2024; 25:953. [PMID: 38256028 PMCID: PMC10816087 DOI: 10.3390/ijms25020953] [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: 11/27/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Genetic testing is crucial in inherited arrhythmogenic channelopathies; however, the clinical interpretation of genetic variants remains challenging. Incomplete penetrance, oligogenic, polygenic or multifactorial forms of channelopathies further complicate variant interpretation. We identified the KCNQ1/p.D446E variant in 2/63 patients with long QT syndrome, 30-fold more frequent than in public databases. We thus characterized the biophysical phenotypes of wildtype and mutant IKs co-expressing these alleles with the β-subunit minK in HEK293 cells. KCNQ1 p.446E homozygosity significantly shifted IKs voltage dependence to hyperpolarizing potentials in basal conditions (gain of function) but failed to shift voltage dependence to hyperpolarizing potentials (loss of function) in the presence of 8Br-cAMP, a protein kinase A activator. Basal IKs activation kinetics did not differ among genotypes, but in response to 8Br-cAMP, IKs 446 E/E (homozygous) activation kinetics were slower at the most positive potentials. Protein modeling predicted a slower transition of the 446E Kv7.1 tetrameric channel to the stabilized open state. In conclusion, biophysical and modelling evidence shows that the KCNQ1 p.D446E variant has complex functional consequences including both gain and loss of function, suggesting a contribution to the pathogenesis of arrhythmogenic phenotypes as a functional risk allele.
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Affiliation(s)
- Antonia González-Garrido
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Omar López-Ramírez
- Instituto de Oftalmología Fundación de Asistencia Privada Conde de la Valenciana, I.A.P., Mexico City 06800, Mexico;
| | - Abel Cerda-Mireles
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Thania Navarrete-Miranda
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Aranza Iztanami Flores-Arenas
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Arturo Rojo-Domínguez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Mexico City 05348, Mexico; (A.R.-D.); (L.A.)
| | - Leticia Arregui
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Mexico City 05348, Mexico; (A.R.-D.); (L.A.)
| | - Pedro Iturralde
- Departamento de Electrofisiología, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico;
| | | | - Mayra Domínguez-Pérez
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (M.D.-P.); (L.J.-A.)
| | - Leonor Jacobo-Albavera
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (M.D.-P.); (L.J.-A.)
| | - Alessandra Carnevale
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Teresa Villarreal-Molina
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (M.D.-P.); (L.J.-A.)
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6
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Huang Y, Ma D, Yang Z, Zhao Y, Guo J. Voltage-gated potassium channels KCNQs: Structures, mechanisms, and modulations. Biochem Biophys Res Commun 2023; 689:149218. [PMID: 37976835 DOI: 10.1016/j.bbrc.2023.149218] [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: 08/09/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
KCNQ (Kv7) channels are voltage-gated, phosphatidylinositol 4,5-bisphosphate- (PIP2-) modulated potassium channels that play essential roles in regulating the activity of neurons and cardiac myocytes. Hundreds of mutations in KCNQ channels are closely related to various cardiac and neurological disorders, such as long QT syndrome, epilepsy, and deafness, which makes KCNQ channels important drug targets. During the past several years, the application of single-particle cryo-electron microscopy (cryo-EM) technique in the structure determination of KCNQ channels has greatly advanced our understanding of their molecular mechanisms. In this review, we summarize the currently available structures of KCNQ channels, analyze their special voltage gating mechanism, and discuss their activation mechanisms by both the endogenous membrane lipid and the exogenous synthetic ligands. These structural studies of KCNQ channels will guide the development of drugs targeting KCNQ channels.
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Affiliation(s)
- Yuan Huang
- Department of Cardiology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Demin Ma
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhenni Yang
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yiwen Zhao
- The Key Laboratory of Neural and Vascular Biology, The Key Laboratory of New Drug Pharmacology and Toxicology, Department of Pharmacology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050011, China
| | - Jiangtao Guo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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7
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Abstract
Calcium ions (Ca2+) are the basis of a unique and potent array of cellular responses. Calmodulin (CaM) is a small but vital protein that is able to rapidly transmit information about changes in Ca2+ concentrations to its regulatory targets. CaM plays a critical role in cellular Ca2+ signaling, and interacts with a myriad of target proteins. Ca2+-dependent modulation by CaM is a major component of a diverse array of processes, ranging from gene expression in neurons to the shaping of the cardiac action potential in heart cells. Furthermore, the protein sequence of CaM is highly evolutionarily conserved, and identical CaM proteins are encoded by three independent genes (CALM1-3) in humans. Mutations within any of these three genes may lead to severe cardiac deficits including severe long QT syndrome (LQTS) and/or catecholaminergic polymorphic ventricular tachycardia (CPVT). Research into disease-associated CaM variants has identified several proteins modulated by CaM that are likely to underlie the pathogenesis of these calmodulinopathies, including the cardiac L-type Ca2+ channel (LTCC) CaV1.2, and the sarcoplasmic reticulum Ca2+ release channel, ryanodine receptor 2 (RyR2). Here, we review the research that has been done to identify calmodulinopathic CaM mutations and evaluate the mechanisms underlying their role in disease.
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Affiliation(s)
- John W. Hussey
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Worawan B. Limpitikul
- Department of Medicine, Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
| | - Ivy E. Dick
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
- CONTACT Ivy E. Dick School of Medicine, University of Maryland, Baltimore, MD21210
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8
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Tóth Á, Crespi V, Janaszkiewicz A, Di Meo F. Computational and structural insights into the pre- and post-hydrolysis states of bovine multidrug resistance-associated protein 1. Basic Clin Pharmacol Toxicol 2023; 133:508-525. [PMID: 37038087 DOI: 10.1111/bcpt.13871] [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: 12/29/2022] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/12/2023]
Abstract
ATP-binding cassette C-family drug membrane transporters play an important role in local pharmacokinetics, that is, drug concentration in cellular compartments. From the structural point of view, only the bovine ortholog of the multidrug resistance-associated protein 1 (bMRP1) has been resolved. We here used μs-scaled molecular dynamics simulations to investigate the structure and dynamics of the bovine multidrug resistance-associated protein 1 in pre- and post-hydrolysis functional states. The present work aims to examine the slight but likely relevant structural differences between pre- and post-hydrolysis states of outward-facing conformations as well as the interactions between the multidrug resistance-associated protein 1 and the surrounding lipid bilayer. Global conformational dynamics show unfavourable extracellular opening associated with nucleotide-binding domain dimerization indicating that the post-hydrolysis state adopts a close-cleft conformation rather than an outward-open conformation. Our present simulations also highlight persistent interactions with annular cholesterol molecules and the expected active role of lipid bilayer in the allosteric communication between distant domains of the transporter.
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Affiliation(s)
- Ágota Tóth
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| | - Veronica Crespi
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
| | | | - Florent Di Meo
- Inserm UMR 1248 Pharmacology & Transplantation, Univ. Limoges, Limoges, France
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9
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Kang PW, Woodbury L, Angsutararux P, Sambare N, Shi J, Marras M, Abella C, Bedi A, Zinn D, Cui J, Silva JR. Arrhythmia-associated calmodulin variants interact with KCNQ1 to confer aberrant membrane trafficking and function. PNAS NEXUS 2023; 2:pgad335. [PMID: 37965565 PMCID: PMC10642763 DOI: 10.1093/pnasnexus/pgad335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023]
Abstract
Missense variants in calmodulin (CaM) predispose patients to arrhythmias associated with high mortality rates ("calmodulinopathy"). As CaM regulates many key cardiac ion channels, an understanding of disease mechanism associated with CaM variant arrhythmias requires elucidating individual CaM variant effects on distinct channels. One key CaM regulatory target is the KCNQ1 (KV7.1) voltage-gated potassium channel that carries the IKs current. Yet, relatively little is known as to how CaM variants interact with KCNQ1 or affect its function. Here, we take a multipronged approach employing a live-cell fluorescence resonance energy transfer binding assay, fluorescence trafficking assay, and functional electrophysiology to characterize >10 arrhythmia-associated CaM variants for effect on KCNQ1 CaM binding, membrane trafficking, and channel function. We identify one variant (G114W) that exhibits severely weakened binding to KCNQ1 but find that most other CaM variants interact with similar binding affinity to KCNQ1 when compared with CaM wild-type over physiological Ca2+ ranges. We further identify several CaM variants that affect KCNQ1 and IKs membrane trafficking and/or baseline current activation kinetics, thereby delineating KCNQ1 dysfunction in calmodulinopathy. Lastly, we identify CaM variants with no effect on KCNQ1 function. This study provides extensive functional data that reveal how CaM variants contribute to creating a proarrhythmic substrate by causing abnormal KCNQ1 membrane trafficking and current conduction. We find that CaM variant regulation of KCNQ1 is not uniform with effects varying from benign to significant loss of function, suggesting how CaM variants predispose patients to arrhythmia via the dysregulation of multiple cardiac ion channels. Classification: Biological, Health, and Medical Sciences, Physiology.
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Affiliation(s)
- Po wei Kang
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Lucy Woodbury
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Paweorn Angsutararux
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Namit Sambare
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Jingyi Shi
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Martina Marras
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Carlota Abella
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Anish Bedi
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - DeShawn Zinn
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Jianmin Cui
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
| | - Jonathan R Silva
- Department of Biomedical Engineering, Washington University in St.Louis, St. Louis, MO 63130, USA
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10
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McCormick L, Wadmore K, Milburn A, Gupta N, Morris R, Held M, Prakash O, Carr J, Barrett‐Jolley R, Dart C, Helassa N. Long QT syndrome-associated calmodulin variants disrupt the activity of the slowly activating delayed rectifier potassium channel. J Physiol 2023; 601:3739-3764. [PMID: 37428651 PMCID: PMC10952621 DOI: 10.1113/jp284994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/21/2023] [Indexed: 07/12/2023] Open
Abstract
Calmodulin (CaM) is a highly conserved mediator of calcium (Ca2+ )-dependent signalling and modulates various cardiac ion channels. Genotyping has revealed several CaM mutations associated with long QT syndrome (LQTS). LQTS patients display prolonged ventricular recovery times (QT interval), increasing their risk of incurring life-threatening arrhythmic events. Loss-of-function mutations to Kv7.1 (which drives the slow delayed rectifier potassium current, IKs, a key ventricular repolarising current) are the largest contributor to congenital LQTS (>50% of cases). CaM modulates Kv7.1 to produce a Ca2+ -sensitive IKs, but little is known about the consequences of LQTS-associated CaM mutations on Kv7.1 function. Here, we present novel data characterising the biophysical and modulatory properties of three LQTS-associated CaM variants (D95V, N97I and D131H). We showed that mutations induced structural alterations in CaM and reduced affinity for Kv7.1, when compared with wild-type (WT). Using HEK293T cells expressing Kv7.1 channel subunits (KCNQ1/KCNE1) and patch-clamp electrophysiology, we demonstrated that LQTS-associated CaM variants reduced current density at systolic Ca2+ concentrations (1 μm), revealing a direct QT-prolonging modulatory effect. Our data highlight for the first time that LQTS-associated perturbations to CaM's structure impede complex formation with Kv7.1 and subsequently result in reduced IKs. This provides a novel mechanistic insight into how the perturbed structure-function relationship of CaM variants contributes to the LQTS phenotype. KEY POINTS: Calmodulin (CaM) is a ubiquitous, highly conserved calcium (Ca2+ ) sensor playing a key role in cardiac muscle contraction. Genotyping has revealed several CaM mutations associated with long QT syndrome (LQTS), a life-threatening cardiac arrhythmia syndrome. LQTS-associated CaM variants (D95V, N97I and D131H) induced structural alterations, altered binding to Kv7.1 and reduced IKs. Our data provide a novel mechanistic insight into how the perturbed structure-function relationship of CaM variants contributes to the LQTS phenotype.
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Affiliation(s)
- Liam McCormick
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory HubSaint Mary's HospitalManchesterUK
| | - Kirsty Wadmore
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Amy Milburn
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Nitika Gupta
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Rachael Morris
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Marie Held
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Ohm Prakash
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Joseph Carr
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Richard Barrett‐Jolley
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Caroline Dart
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
| | - Nordine Helassa
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life SciencesUniversity of LiverpoolLiverpoolUK
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11
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Costa F, Ocello R, Guardiani C, Giacomello A, Masetti M. Integrated Approach Including Docking, MD Simulations, and Network Analysis Highlights the Action Mechanism of the Cardiac hERG Activator RPR260243. J Chem Inf Model 2023; 63:4888-4899. [PMID: 37504578 PMCID: PMC10428221 DOI: 10.1021/acs.jcim.3c00596] [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: 04/19/2023] [Indexed: 07/29/2023]
Abstract
hERG is a voltage-gated potassium channel involved in the heart contraction whose defections are associated with the cardiac arrhythmia Long QT Syndrome type 2. The activator RPR260243 (RPR) represents a possible candidate to pharmacologically treat LQTS2 because it enhances the opening of the channel. However, the molecular detail of its action mechanism remains quite elusive. Here, we address the problem using a combination of docking, molecular dynamics simulations, and network analysis. We show that the drug preferably binds at the interface between the voltage sensor and the pore, enhancing the canonical activation path and determining a whole-structure rearrangement of the channel that slightly impairs inactivation.
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Affiliation(s)
- Flavio Costa
- Dipartimento
di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184 Rome, Italy
| | - Riccardo Ocello
- Department
of Pharmacy and Biotechnology, Alma Mater
Studiorum−Università di Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Carlo Guardiani
- Dipartimento
di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184 Rome, Italy
| | - Alberto Giacomello
- Dipartimento
di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184 Rome, Italy
| | - Matteo Masetti
- Department
of Pharmacy and Biotechnology, Alma Mater
Studiorum−Università di Bologna, via Belmeloro 6, 40126 Bologna, Italy
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12
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Konovalov KA, Wu CG, Qiu Y, Balakrishnan VK, Parihar PS, O’Connor MS, Xing Y, Huang X. Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A. J Chem Phys 2023; 158:215101. [PMID: 37260014 PMCID: PMC10238128 DOI: 10.1063/5.0150272] [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: 03/13/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Mutations in protein phosphatase 2A (PP2A) are connected to intellectual disability and cancer. It has been hypothesized that these mutations might disrupt the autoinhibition and phosphorylation-induced activation of PP2A. Since they are located far from both the active and substrate binding sites, it is unclear how they exert their effect. We performed allosteric pathway analysis based on molecular dynamics simulations and combined it with biochemical experiments to investigate the autoinhibition of PP2A. In the wild type (WT), the C-arm of the regulatory subunit B56δ obstructs the active and substrate binding sites exerting a dual autoinhibition effect. We find that the disease mutant, E198K, severely weakens the allosteric pathways that stabilize the C-arm in the WT. Instead, the strongest allosteric pathways in E198K take a different route that promotes exposure of the substrate binding site. To facilitate the allosteric pathway analysis, we introduce a path clustering algorithm for lumping pathways into channels. We reveal remarkable similarities between the allosteric channels of E198K and those in phosphorylation-activated WT, suggesting that the autoinhibition can be alleviated through a conserved mechanism. In contrast, we find that another disease mutant, E200K, which is in spatial proximity of E198, does not repartition the allosteric pathways leading to the substrate binding site; however, it may still induce exposure of the active site. This finding agrees with our biochemical data, allowing us to predict the activity of PP2A with the phosphorylated B56δ and provide insight into how disease mutations in spatial proximity alter the enzymatic activity in surprisingly different mechanisms.
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Affiliation(s)
- Kirill A. Konovalov
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Yunrui Qiu
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Vijaya Kumar Balakrishnan
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Pankaj Singh Parihar
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Michael S. O’Connor
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yongna Xing
- Authors to whom correspondence should be addressed: and
| | - Xuhui Huang
- Authors to whom correspondence should be addressed: and
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13
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Okamura Y, Yoshioka D. What voltage-sensing phosphatases can reveal about the mechanisms of ion channel regulation by phosphoinositides. Biochem Soc Trans 2023; 51:827-839. [PMID: 37052219 DOI: 10.1042/bst20221065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]
Abstract
Many membrane proteins including ion channels and ion transporters are regulated by membrane phospholipids such as phosphoinositides in cell membranes and organelles. Voltage-sensing phosphatase, VSP, is a voltage-sensitive phosphoinositide phosphatase which dephosphorylates PI(4,5)P2 into PI(4)P. VSP rapidly reduces the level of PI(4,5)P2 upon membrane depolarization, thus serving as a useful tool to quantitatively study phosphoinositide-regulation of ion channels and ion transporters using a cellular electrophysiology system. In this review, we focus on the application of VSPs to Kv7 family potassium channels, which have been important research targets in biophysics, pharmacology and medicine.
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Affiliation(s)
- Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Yamada Oka 2-2, Suita, Osaka 565-0871, Japan
| | - Daisuke Yoshioka
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Yamada Oka 2-2, Suita, Osaka 565-0871, Japan
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14
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Kameyama M, Minobe E, Shao D, Xu J, Gao Q, Hao L. Regulation of Cardiac Cav1.2 Channels by Calmodulin. Int J Mol Sci 2023; 24:ijms24076409. [PMID: 37047381 PMCID: PMC10094977 DOI: 10.3390/ijms24076409] [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: 01/25/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Cav1.2 Ca2+ channels, a type of voltage-gated L-type Ca2+ channel, are ubiquitously expressed, and the predominant Ca2+ channel type, in working cardiac myocytes. Cav1.2 channels are regulated by the direct interactions with calmodulin (CaM), a Ca2+-binding protein that causes Ca2+-dependent facilitation (CDF) and inactivation (CDI). Ca2+-free CaM (apoCaM) also contributes to the regulation of Cav1.2 channels. Furthermore, CaM indirectly affects channel activity by activating CaM-dependent enzymes, such as CaM-dependent protein kinase II and calcineurin (a CaM-dependent protein phosphatase). In this article, we review the recent progress in identifying the role of apoCaM in the channel ‘rundown’ phenomena and related repriming of channels, and CDF, as well as the role of Ca2+/CaM in CDI. In addition, the role of CaM in channel clustering is reviewed.
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Affiliation(s)
- Masaki Kameyama
- Department of Physiology, Graduate School of Medical & Dental Sciences, Kagoshima University, Sakura-ga-oka, Kagoshima 890-8544, Japan
- Correspondence:
| | - Etsuko Minobe
- Department of Physiology, Graduate School of Medical & Dental Sciences, Kagoshima University, Sakura-ga-oka, Kagoshima 890-8544, Japan
| | - Dongxue Shao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110012, China (L.H.)
| | - Jianjun Xu
- Department of Physiology, Graduate School of Medical & Dental Sciences, Kagoshima University, Sakura-ga-oka, Kagoshima 890-8544, Japan
| | - Qinghua Gao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110012, China (L.H.)
| | - Liying Hao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang 110012, China (L.H.)
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15
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Erlandsdotter LM, Giammarino L, Halili A, Nikesjö J, Gréen H, Odening KE, Liin SI. Long-QT mutations in KCNE1 modulate the 17β-estradiol response of Kv7.1/KCNE1. SCIENCE ADVANCES 2023; 9:eade7109. [PMID: 36921038 PMCID: PMC10017040 DOI: 10.1126/sciadv.ade7109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Estradiol (17[Formula: see text]-E2) is implicated in higher arrhythmia risk of women with congenital or acquired long-QT syndrome (LQTS) compared to men. However, the underlying mechanisms remain poorly understood, and little is known about the impact of LQTS-associated mutations. We show that 17[Formula: see text]-E2 inhibits the human cardiac Kv7.1/KCNE1 channel expressed in Xenopus oocytes. We find that the 17[Formula: see text]-E2 effect depends on the Kv7.1 to KCNE1 stoichiometry, and we reveal a critical function of the KCNE1 carboxyl terminus for the effect. LQTS-associated mutations in the KCNE1 carboxyl terminus show a range of responses to 17[Formula: see text]-E2, from a wild-type like response to impaired or abolished response. Together, this study increases our understanding of the mechanistic basis for 17[Formula: see text]-E2 inhibition of Kv7.1/KCNE1 and demonstrates mutation-dependent responses to 17[Formula: see text]-E2. These findings suggest that the 17[Formula: see text]-E2 effect on Kv7.1/KCNE1 might contribute to the higher arrhythmia risk of women, particularly in carriers with specific LQTS-associated mutations.
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Affiliation(s)
| | - Lucilla Giammarino
- Translational Cardiology, Department of Cardiology, Inselspital, University Hospital Bern and Department of Physiology, University of Bern, Bern, Switzerland
| | - Azemine Halili
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johan Nikesjö
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Henrik Gréen
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Katja E. Odening
- Translational Cardiology, Department of Cardiology, Inselspital, University Hospital Bern and Department of Physiology, University of Bern, Bern, Switzerland
| | - Sara I. Liin
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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16
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O'Neill MJ, Sala L, Denjoy I, Wada Y, Kozek K, Crotti L, Dagradi F, Kotta MC, Spazzolini C, Leenhardt A, Salem JE, Kashiwa A, Ohno S, Tao R, Roden DM, Horie M, Extramiana F, Schwartz PJ, Kroncke BM. Continuous Bayesian variant interpretation accounts for incomplete penetrance among Mendelian cardiac channelopathies. Genet Med 2023; 25:100355. [PMID: 36496179 PMCID: PMC9992222 DOI: 10.1016/j.gim.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The congenital Long QT Syndrome (LQTS) and Brugada Syndrome (BrS) are Mendelian autosomal dominant diseases that frequently precipitate fatal cardiac arrhythmias. Incomplete penetrance is a barrier to clinical management of heterozygotes harboring variants in the major implicated disease genes KCNQ1, KCNH2, and SCN5A. We apply and evaluate a Bayesian penetrance estimation strategy that accounts for this phenomenon. METHODS We generated Bayesian penetrance models for KCNQ1-LQT1 and SCN5A-LQT3 using variant-specific features and clinical data from the literature, international arrhythmia genetic centers, and population controls. We analyzed the distribution of posterior penetrance estimates across 4 genotype-phenotype relationships and compared continuous estimates with ClinVar annotations. Posterior estimates were mapped onto protein structure. RESULTS Bayesian penetrance estimates of KCNQ1-LQT1 and SCN5A-LQT3 are empirically equivalent to 10 and 5 clinically phenotype heterozygotes, respectively. Posterior penetrance estimates were bimodal for KCNQ1-LQT1 and KCNH2-LQT2, with a higher fraction of missense variants with high penetrance among KCNQ1 variants. There was a wide distribution of variant penetrance estimates among identical ClinVar categories. Structural mapping revealed heterogeneity among "hot spot" regions and featured high penetrance estimates for KCNQ1 variants in contact with calmodulin and the S6 domain. CONCLUSIONS Bayesian penetrance estimates provide a continuous framework for variant interpretation.
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Affiliation(s)
- Matthew J O'Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Luca Sala
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Isabelle Denjoy
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Krystian Kozek
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Lia Crotti
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Federica Dagradi
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Maria-Christina Kotta
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Carla Spazzolini
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Antoine Leenhardt
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Joe-Elie Salem
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Asami Kashiwa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Fabrice Extramiana
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Peter J Schwartz
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN.
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17
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Nuñez E, Jones F, Muguruza-Montero A, Urrutia J, Aguado A, Malo C, Bernardo-Seisdedos G, Domene C, Millet O, Gamper N, Villarroel A. Redox regulation of K V7 channels through EF3 hand of calmodulin. eLife 2023; 12:e81961. [PMID: 36803414 PMCID: PMC9988260 DOI: 10.7554/elife.81961] [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: 07/18/2022] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Neuronal KV7 channels, important regulators of cell excitability, are among the most sensitive proteins to reactive oxygen species. The S2S3 linker of the voltage sensor was reported as a site-mediating redox modulation of the channels. Recent structural insights reveal potential interactions between this linker and the Ca2+-binding loop of the third EF-hand of calmodulin (CaM), which embraces an antiparallel fork formed by the C-terminal helices A and B, constituting the calcium responsive domain (CRD). We found that precluding Ca2+ binding to the EF3 hand, but not to EF1, EF2, or EF4 hands, abolishes oxidation-induced enhancement of KV7.4 currents. Monitoring FRET (Fluorescence Resonance Energy Transfer) between helices A and B using purified CRDs tagged with fluorescent proteins, we observed that S2S3 peptides cause a reversal of the signal in the presence of Ca2+ but have no effect in the absence of this cation or if the peptide is oxidized. The capacity of loading EF3 with Ca2+ is essential for this reversal of the FRET signal, whereas the consequences of obliterating Ca2+ binding to EF1, EF2, or EF4 are negligible. Furthermore, we show that EF3 is critical for translating Ca2+ signals to reorient the AB fork. Our data are consistent with the proposal that oxidation of cysteine residues in the S2S3 loop relieves KV7 channels from a constitutive inhibition imposed by interactions between the EF3 hand of CaM which is crucial for this signaling.
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Affiliation(s)
| | - Frederick Jones
- School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | | | | | | | | | | | - Carmen Domene
- Department of Chemistry, University of BathBathUnited Kingdom
- Department of Chemistry, University of OxfordOxfordUnited Kingdom
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNEDerioSpain
| | - Nikita Gamper
- School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
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18
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Tóth Á, Janaszkiewicz A, Crespi V, Di Meo F. On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter. Commun Biol 2023; 6:149. [PMID: 36737455 PMCID: PMC9898250 DOI: 10.1038/s42003-023-04537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Multidrug resistance-associated proteins are ABC C-family exporters. They are crucial in pharmacology as they transport various substrates across membranes. However, the role of the degenerate nucleotide-binding site (NBS) remains unclear likewise the interplay with the surrounding lipid environment. Here, we propose a dynamic and structural overview of MRP1 from ca. 110 μs molecular dynamics simulations. ATP binding to NBS1 is likely maintained along several transport cycles. Asymmetric NBD behaviour is ensured by lower signal transduction from NBD1 to the rest of the protein owing to the absence of ball-and-socket conformation between NBD1 and coupling helices. Even though surrounding lipids play an active role in the allosteric communication between the substrate-binding pocket and NBDs, our results suggest that lipid composition has a limited impact, mostly by affecting transport kinetics. We believe that our work can be extended to other degenerate NBS ABC proteins and provide hints for deciphering mechanistic differences among ABC transporters.
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Affiliation(s)
- Ágota Tóth
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Angelika Janaszkiewicz
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Veronica Crespi
- grid.9966.00000 0001 2165 4861Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute—Univ. Limoges, 2 rue du Prof. Descottes, 87000 F Limoges, France
| | - Florent Di Meo
- Inserm U1248 Pharmacology & Transplantation, ΩHealth Institute-Univ. Limoges, 2 rue du Prof. Descottes, 87000 F, Limoges, France.
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19
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Kang PW, Woodbury L, Angsutararux P, Sambare N, Shi J, Marras M, Abella C, Bedi A, Zinn D, Cui J, Silva JR. Arrhythmia-associated Calmodulin Variants Interact with KCNQ1 to Confer Aberrant Membrane Trafficking and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.28.526031. [PMID: 36747728 PMCID: PMC9900995 DOI: 10.1101/2023.01.28.526031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Rationale Missense variants in calmodulin (CaM) predispose patients to arrhythmias associated with high mortality rates. As CaM regulates several key cardiac ion channels, a mechanistic understanding of CaM variant-associated arrhythmias requires elucidating individual CaM variant effect on distinct channels. One key CaM regulatory target is the KCNQ1 (K V 7.1) voltage-gated potassium channel that underlie the I Ks current. Yet, relatively little is known as to how CaM variants interact with KCNQ1 or affect its function. Objective To observe how arrhythmia-associated CaM variants affect binding to KCNQ1, channel membrane trafficking, and KCNQ1 function. Methods and Results We combine a live-cell FRET binding assay, fluorescence trafficking assay, and functional electrophysiology to characterize >10 arrhythmia-associated CaM variants effect on KCNQ1. We identify one variant (G114W) that exhibits severely weakened binding to KCNQ1 but find that most other CaM variants interact with similar binding affinity to KCNQ1 when compared to CaM wild-type over physiological Ca 2+ ranges. We further identify several CaM variants that affect KCNQ1 and I Ks membrane trafficking and/or baseline current activation kinetics, thereby contextualizing KCNQ1 dysfunction in calmodulinopathy. Lastly, we delineate CaM variants with no effect on KCNQ1 function. Conclusions This study provides comprehensive functional data that reveal how CaM variants contribute to creating a pro-arrhythmic substrate by causing abnormal KCNQ1 membrane trafficking and current conduction. We find that CaM variant regulation of KCNQ1 is not uniform with effects varying from benign to significant loss of function. This study provides a new approach to collecting details of CaM binding that are key for understanding how CaM variants predispose patients to arrhythmia via the dysregulation of multiple cardiac ion channels.
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20
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Calmodulin variant E140G associated with long QT syndrome impairs CaMKIIδ autophosphorylation and L-type calcium channel inactivation. J Biol Chem 2023; 299:102777. [PMID: 36496072 PMCID: PMC9830374 DOI: 10.1016/j.jbc.2022.102777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Long QT syndrome (LQTS) is a human inherited heart condition that can cause life-threatening arrhythmia including sudden cardiac death. Mutations in the ubiquitous Ca2+-sensing protein calmodulin (CaM) are associated with LQTS, but the molecular mechanism by which these mutations lead to irregular heartbeats is not fully understood. Here, we use a multidisciplinary approach including protein biophysics, structural biology, confocal imaging, and patch-clamp electrophysiology to determine the effect of the disease-associated CaM mutation E140G on CaM structure and function. We present novel data showing that mutant-regulated CaMKIIδ kinase activity is impaired with a significant reduction in enzyme autophosphorylation rate. We report the first high-resolution crystal structure of a LQTS-associated CaM variant in complex with the CaMKIIδ peptide, which shows significant structural differences, compared to the WT complex. Furthermore, we demonstrate that the E140G mutation significantly disrupted Cav1.2 Ca2+/CaM-dependent inactivation, while cardiac ryanodine receptor (RyR2) activity remained unaffected. In addition, we show that the LQTS-associated mutation alters CaM's Ca2+-binding characteristics, secondary structure content, and interaction with key partners involved in excitation-contraction coupling (CaMKIIδ, Cav1.2, RyR2). In conclusion, LQTS-associated CaM mutation E140G severely impacts the structure-function relationship of CaM and its regulation of CaMKIIδ and Cav1.2. This provides a crucial insight into the molecular factors contributing to CaM-mediated arrhythmias with a central role for CaMKIIδ.
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21
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Beghi S, Furmanik M, Jaminon A, Veltrop R, Rapp N, Wichapong K, Bidar E, Buschini A, Schurgers LJ. Calcium Signalling in Heart and Vessels: Role of Calmodulin and Downstream Calmodulin-Dependent Protein Kinases. Int J Mol Sci 2022; 23:ijms232416139. [PMID: 36555778 PMCID: PMC9783221 DOI: 10.3390/ijms232416139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Cardiovascular disease is the major cause of death worldwide. The success of medication and other preventive measures introduced in the last century have not yet halted the epidemic of cardiovascular disease. Although the molecular mechanisms of the pathophysiology of the heart and vessels have been extensively studied, the burden of ischemic cardiovascular conditions has risen to become a top cause of morbidity and mortality. Calcium has important functions in the cardiovascular system. Calcium is involved in the mechanism of excitation-contraction coupling that regulates numerous events, ranging from the production of action potentials to the contraction of cardiomyocytes and vascular smooth muscle cells. Both in the heart and vessels, the rise of intracellular calcium is sensed by calmodulin, a protein that regulates and activates downstream kinases involved in regulating calcium signalling. Among them is the calcium calmodulin kinase family, which is involved in the regulation of cardiac functions. In this review, we present the current literature regarding the role of calcium/calmodulin pathways in the heart and vessels with the aim to summarize our mechanistic understanding of this process and to open novel avenues for research.
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Affiliation(s)
- Sofia Beghi
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11A, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-3408473527
| | - Malgorzata Furmanik
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Armand Jaminon
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Rogier Veltrop
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Nikolas Rapp
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kanin Wichapong
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Elham Bidar
- Department of Cardiothoracic Surgery, Heart and Vascular Centre, Maastricht University Medical Centre+, 6229 HX Maastricht, The Netherlands
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11A, 43124 Parma, Italy
| | - Leon J. Schurgers
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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22
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Zhang G, Xu X, Jia Z, Geng Y, Liang H, Shi J, Marras M, Abella C, Magleby KL, Silva JR, Chen J, Zou X, Cui J. An allosteric modulator activates BK channels by perturbing coupling between Ca 2+ binding and pore opening. Nat Commun 2022; 13:6784. [PMID: 36351900 PMCID: PMC9646747 DOI: 10.1038/s41467-022-34359-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
BK type Ca2+-activated K+ channels activate in response to both voltage and Ca2+. The membrane-spanning voltage sensor domain (VSD) activation and Ca2+ binding to the cytosolic tail domain (CTD) open the pore across the membrane, but the mechanisms that couple VSD activation and Ca2+ binding to pore opening are not clear. Here we show that a compound, BC5, identified from in silico screening, interacts with the CTD-VSD interface and specifically modulates the Ca2+ dependent activation mechanism. BC5 activates the channel in the absence of Ca2+ binding but Ca2+ binding inhibits BC5 effects. Thus, BC5 perturbs a pathway that couples Ca2+ binding to pore opening to allosterically affect both, which is further supported by atomistic simulations and mutagenesis. The results suggest that the CTD-VSD interaction makes a major contribution to the mechanism of Ca2+ dependent activation and is an important site for allosteric agonists to modulate BK channel activation.
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Affiliation(s)
- Guohui Zhang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA
| | - Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri - Columbia, Columbia, MO, USA.,Department of Physics and Astronomy, University of Missouri - Columbia, Columbia, MO, USA.,Department of Biochemistry, University of Missouri - Columbia, Columbia, MO, USA.,Institute for Data Science and Informatics, University of Missouri - Columbia, Columbia, MO, USA
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA.,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Yanyan Geng
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hongwu Liang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA
| | - Martina Marras
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA
| | - Carlota Abella
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA
| | - Karl L Magleby
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan R Silva
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA.
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA. .,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri - Columbia, Columbia, MO, USA. .,Department of Physics and Astronomy, University of Missouri - Columbia, Columbia, MO, USA. .,Department of Biochemistry, University of Missouri - Columbia, Columbia, MO, USA. .,Institute for Data Science and Informatics, University of Missouri - Columbia, Columbia, MO, USA.
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO, USA.
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23
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Westerlund AM, Sridhar A, Dahl L, Andersson A, Bodnar AY, Delemotte L. Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin. PLoS Comput Biol 2022; 18:e1010583. [PMID: 36206305 PMCID: PMC9581412 DOI: 10.1371/journal.pcbi.1010583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/19/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Calmodulin (CaM) is a calcium sensor which binds and regulates a wide range of target-proteins. This implicitly enables the concentration of calcium to influence many downstream physiological responses, including muscle contraction, learning and depression. The antipsychotic drug trifluoperazine (TFP) is a known CaM inhibitor. By binding to various sites, TFP prevents CaM from associating to target-proteins. However, the molecular and state-dependent mechanisms behind CaM inhibition by drugs such as TFP are largely unknown. Here, we build a Markov state model (MSM) from adaptively sampled molecular dynamics simulations and reveal the structural and dynamical features behind the inhibitory mechanism of TFP-binding to the C-terminal domain of CaM. We specifically identify three major TFP binding-modes from the MSM macrostates, and distinguish their effect on CaM conformation by using a systematic analysis protocol based on biophysical descriptors and tools from machine learning. The results show that depending on the binding orientation, TFP effectively stabilizes features of the calcium-unbound CaM, either affecting the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the bound domain. The conclusions drawn from this work may in the future serve to formulate a complete model of pharmacological modulation of CaM, which furthers our understanding of how these drugs affect signaling pathways as well as associated diseases. Calmodulin (CaM) is a calcium-sensing protein which makes other proteins dependent on the surrounding calcium concentration by binding to these proteins. Such protein-protein interactions with CaM are vital for calcium to control many physiological pathways within the cell. The antipsychotic drug trifluoperazine (TFP) inhibits CaM’s ability to bind and regulate other proteins. Here, we use molecular dynamics simulations together with Markov state modeling and machine learning to understand the structural and dynamical features by which TFP bound to the one domain of CaM prevents association to other proteins. We find that TFP encourages CaM to adopt a conformation that is like the one stabilized in absence of calcium: depending on the binding orientation of TFP, the drug indeed either affects the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the domain. Understanding TFP binding is a first step towards designing better drugs targeting CaM.
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Affiliation(s)
- Annie M. Westerlund
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Leo Dahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Alma Andersson
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- Division of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna-Yaroslava Bodnar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- * E-mail:
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24
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Bauer CK, Holling T, Horn D, Laço MN, Abdalla E, Omar OM, Alawi M, Kutsche K. Clinically Relevant KCNQ1 Variants Causing KCNQ1-KCNE2 Gain-of-Function Affect the Ca2+ Sensitivity of the Channel. Int J Mol Sci 2022; 23:ijms23179690. [PMID: 36077086 PMCID: PMC9456291 DOI: 10.3390/ijms23179690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Dominant KCNQ1 variants are well-known for underlying cardiac arrhythmia syndromes. The two heterozygous KCNQ1 missense variants, R116L and P369L, cause an allelic disorder characterized by pituitary hormone deficiency and maternally inherited gingival fibromatosis. Increased K+ conductance upon co-expression of KCNQ1 mutant channels with the beta subunit KCNE2 is suggested to underlie the phenotype; however, the reason for KCNQ1-KCNE2 (Q1E2) channel gain-of-function is unknown. We aimed to discover the genetic defect in a single individual and three family members with gingival overgrowth and identified the KCNQ1 variants P369L and V185M, respectively. Patch-clamp experiments demonstrated increased constitutive K+ conductance of V185M-Q1E2 channels, confirming the pathogenicity of the novel variant. To gain insight into the pathomechanism, we examined all three disease-causing KCNQ1 mutants. Manipulation of the intracellular Ca2+ concentration prior to and during whole-cell recordings identified an impaired Ca2+ sensitivity of the mutant KCNQ1 channels. With low Ca2+, wild-type KCNQ1 currents were efficiently reduced and exhibited a pre-pulse-dependent cross-over of current traces and a high-voltage-activated component. These features were absent in mutant KCNQ1 channels and in wild-type channels co-expressed with calmodulin and exposed to high intracellular Ca2+. Moreover, co-expression of calmodulin with wild-type Q1E2 channels and loading the cells with high Ca2+ drastically increased Q1E2 current amplitudes, suggesting that KCNE2 normally limits the resting Q1E2 conductance by an increased demand for calcified calmodulin to achieve effective channel opening. Our data link impaired Ca2+ sensitivity of the KCNQ1 mutants R116L, V185M and P369L to Q1E2 gain-of-function that is associated with a particular KCNQ1 channelopathy.
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Affiliation(s)
- Christiane K. Bauer
- Department of Cellular and Integrative Physiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Correspondence:
| | - Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Denise Horn
- Department of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, 13353 Berlin, Germany
| | - Mário Nôro Laço
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3004-561 Coimbra, Portugal
| | - Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria 5422031, Egypt
- Genetics Department, Armed Forces College of Medicine (AFCM), Cairo 4460015, Egypt
| | - Omneya Magdy Omar
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria 5422031, Egypt
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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25
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Yang ND, Kanyo R, Zhao L, Li J, Kang PW, Dou AK, White KM, Shi J, Nerbonne JM, Kurata HT, Cui J. Electro-mechanical coupling of KCNQ channels is a target of epilepsy-associated mutations and retigabine. SCIENCE ADVANCES 2022; 8:eabo3625. [PMID: 35857840 PMCID: PMC9299555 DOI: 10.1126/sciadv.abo3625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
KCNQ2 and KCNQ3 form the M-channels that are important in regulating neuronal excitability. Inherited mutations that alter voltage-dependent gating of M-channels are associated with neonatal epilepsy. In the homolog KCNQ1 channel, two steps of voltage sensor activation lead to two functionally distinct open states, the intermediate-open (IO) and activated-open (AO), which define the gating, physiological, and pharmacological properties of KCNQ1. However, whether the M-channel shares the same mechanism is unclear. Here, we show that KCNQ2 and KCNQ3 feature only a single conductive AO state but with a conserved mechanism for the electro-mechanical (E-M) coupling between voltage sensor activation and pore opening. We identified some epilepsy-linked mutations in KCNQ2 and KCNQ3 that disrupt E-M coupling. The antiepileptic drug retigabine rescued KCNQ3 currents that were abolished by a mutation disrupting E-M coupling, suggesting that modulating the E-M coupling in KCNQ channels presents a potential strategy for antiepileptic therapy.
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Affiliation(s)
- Nien-Du Yang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Richard Kanyo
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Lu Zhao
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Jingru Li
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Po Wei Kang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Alex Kelly Dou
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Kelli McFarland White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
| | - Jeanne M. Nerbonne
- Departments of Developmental Biology and Internal Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harley T. Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St. Louis, MO 63130, USA
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26
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Chi G, Liang Q, Sridhar A, Cowgill JB, Sader K, Radjainia M, Qian P, Castro-Hartmann P, Venkaya S, Singh NK, McKinley G, Fernandez-Cid A, Mukhopadhyay SMM, Burgess-Brown NA, Delemotte L, Covarrubias M, Dürr KL. Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain. Nat Commun 2022; 13:4087. [PMID: 35840580 PMCID: PMC9287412 DOI: 10.1038/s41467-022-29594-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/24/2022] [Indexed: 11/26/2022] Open
Abstract
Kv3 channels have distinctive gating kinetics tailored for rapid repolarization in fast-spiking neurons. Malfunction of this process due to genetic variants in the KCNC1 gene causes severe epileptic disorders, yet the structural determinants for the unusual gating properties remain elusive. Here, we present cryo-electron microscopy structures of the human Kv3.1a channel, revealing a unique arrangement of the cytoplasmic tetramerization domain T1 which facilitates interactions with C-terminal axonal targeting motif and key components of the gating machinery. Additional interactions between S1/S2 linker and turret domain strengthen the interface between voltage sensor and pore domain. Supported by molecular dynamics simulations, electrophysiological and mutational analyses, we identify several residues in the S4/S5 linker which influence the gating kinetics and an electrostatic interaction between acidic residues in α6 of T1 and R449 in the pore-flanking S6T helices. These findings provide insights into gating control and disease mechanisms and may guide strategies for the design of pharmaceutical drugs targeting Kv3 channels.
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Affiliation(s)
- Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Qiansheng Liang
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, UK
| | - Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH, Solna, Sweden
| | - John B Cowgill
- Department of Applied Physics, Science for Life Laboratory, KTH, Solna, Sweden
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Mazdak Radjainia
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, Netherlands
| | - Shayla Venkaya
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exscientia Ltd., The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Nanki Kaur Singh
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Gavin McKinley
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Alejandra Fernandez-Cid
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exact Sciences Ltd., The Sherard Building, Edmund Halley Road, The Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Shubhashish M M Mukhopadhyay
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exscientia Ltd., The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Exact Sciences Ltd., The Sherard Building, Edmund Halley Road, The Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH, Solna, Sweden
| | - Manuel Covarrubias
- Department of Neuroscience and Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
- OMass Therapeutics, Ltd., The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK.
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27
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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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28
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PIP 2-dependent coupling of voltage sensor and pore domains in K v7.2 channel. Commun Biol 2021; 4:1189. [PMID: 34650221 PMCID: PMC8517023 DOI: 10.1038/s42003-021-02729-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/23/2021] [Indexed: 01/10/2023] Open
Abstract
Phosphatidylinositol-4,5-bisphosphate (PIP2) is a signaling lipid which regulates voltage-gated Kv7/KCNQ potassium channels. Altered PIP2 sensitivity of neuronal Kv7.2 channel is involved in KCNQ2 epileptic encephalopathy. However, the molecular action of PIP2 on Kv7.2 gating remains largely elusive. Here, we use molecular dynamics simulations and electrophysiology to characterize PIP2 binding sites in a human Kv7.2 channel. In the closed state, PIP2 localizes to the periphery of the voltage-sensing domain (VSD). In the open state, PIP2 binds to 4 distinct interfaces formed by the cytoplasmic ends of the VSD, the gate, intracellular helices A and B and their linkers. PIP2 binding induces bilayer-interacting conformation of helices A and B and the correlated motion of the VSD and the pore domain, whereas charge-neutralizing mutations block this coupling and reduce PIP2 sensitivity of Kv7.2 channels by disrupting PIP2 binding. These findings reveal the allosteric role of PIP2 in Kv7.2 channel activation. Pant et al. describe the mechanism by which PIP2 might regulate homomeric Kv7.2 channels. They identify sites important in the binding of the PIP2 lipid to Kv7.2 channels and propose that the PIP2 binding to a specific site results in the coupling between the voltage sensor domain (VSD) and pore domain (PD), which stabilizes the open state of the channel.
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29
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Pipatpolkai T, Quetschlich D, Stansfeld PJ. From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels. J Mol Biol 2021; 433:167105. [PMID: 34139216 PMCID: PMC8361781 DOI: 10.1016/j.jmb.2021.167105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/05/2022]
Abstract
Potassium (K+) ion channels are crucial in numerous cellular processes as they hyperpolarise a cell through K+ conductance, returning a cell to its resting potential. K+ channel mutations result in multiple clinical complications such as arrhythmia, neonatal diabetes and migraines. Since 1995, the regulation of K+ channels by phospholipids has been heavily studied using a range of interdisciplinary methods such as cellular electrophysiology, structural biology and computational modelling. As a result, K+ channels are model proteins for the analysis of protein-lipid interactions. In this review, we will focus on the roles of lipids in the regulation of K+ channels, and how atomic-level structures, along with experimental techniques and molecular simulations, have helped guide our understanding of the importance of phospholipid interactions.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Physiology Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, UK
| | - Daniel Quetschlich
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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30
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Elbahnsi A, Delemotte L. Structure and Sequence-based Computational Approaches to Allosteric Signal Transduction: Application to Electromechanical Coupling in Voltage-gated Ion Channels. J Mol Biol 2021; 433:167095. [PMID: 34107281 DOI: 10.1016/j.jmb.2021.167095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/17/2022]
Abstract
Allosteric signaling underlies the function of many biomolecules, including membrane proteins such as ion channels. Experimental methods have enabled specific quantitative insights into the coupling between the voltage sensing domain (VSD) and the pore gate of voltage-gated ion channels, located tens of Ångström apart from one another, as well as pinpointed specific residues and domains that participate in electromechanical signal transmission. Nevertheless, an overall atomic-level resolution picture is difficult to obtain from these methods alone. Today, thanks to the cryo-EM resolution revolution, we have access to high resolution structures of many different voltage-gated ion channels in various conformational states, putting a quantitative description of the processes at the basis of these changes within our close reach. Here, we review computational methods that build on structures to detect and characterize allosteric signaling and pathways. We then examine what has been learned so far about electromechanical coupling between VSD and pore using such methods. While no general theory of electromechanical coupling in voltage-gated ion channels integrating results from all these methods is available yet, we outline the types of insights that could be achieved in the near future using the methods that have not yet been put to use in this field of application.
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Affiliation(s)
- Ahmad Elbahnsi
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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Kang PW, Chakouri N, Diaz J, Tomaselli GF, Yue DT, Ben-Johny M. Elementary mechanisms of calmodulin regulation of Na V1.5 producing divergent arrhythmogenic phenotypes. Proc Natl Acad Sci U S A 2021; 118:e2025085118. [PMID: 34021086 PMCID: PMC8166197 DOI: 10.1073/pnas.2025085118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In cardiomyocytes, NaV1.5 channels mediate initiation and fast propagation of action potentials. The Ca2+-binding protein calmodulin (CaM) serves as a de facto subunit of NaV1.5. Genetic studies and atomic structures suggest that this interaction is pathophysiologically critical, as human mutations within the NaV1.5 carboxy-terminus that disrupt CaM binding are linked to distinct forms of life-threatening arrhythmias, including long QT syndrome 3, a "gain-of-function" defect, and Brugada syndrome, a "loss-of-function" phenotype. Yet, how a common disruption in CaM binding engenders divergent effects on NaV1.5 gating is not fully understood, though vital for elucidating arrhythmogenic mechanisms and for developing new therapies. Here, using extensive single-channel analysis, we find that the disruption of Ca2+-free CaM preassociation with NaV1.5 exerts two disparate effects: 1) a decrease in the peak open probability and 2) an increase in persistent NaV openings. Mechanistically, these effects arise from a CaM-dependent switch in the NaV inactivation mechanism. Specifically, CaM-bound channels preferentially inactivate from the open state, while those devoid of CaM exhibit enhanced closed-state inactivation. Further enriching this scheme, for certain mutant NaV1.5, local Ca2+ fluctuations elicit a rapid recruitment of CaM that reverses the increase in persistent Na current, a factor that may promote beat-to-beat variability in late Na current. In all, these findings identify the elementary mechanism of CaM regulation of NaV1.5 and, in so doing, unravel a noncanonical role for CaM in tuning ion channel gating. Furthermore, our results furnish an in-depth molecular framework for understanding complex arrhythmogenic phenotypes of NaV1.5 channelopathies.
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Affiliation(s)
- Po Wei Kang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218;
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Nourdine Chakouri
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
| | - Johanna Diaz
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
| | - Gordon F Tomaselli
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David T Yue
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Manu Ben-Johny
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218;
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
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