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Zahradníková A, Pavelková J, Sabo M, Baday S, Zahradník I. Structure-based mechanism of RyR channel operation by calcium and magnesium ions. PLoS Comput Biol 2025; 21:e1012950. [PMID: 40300027 PMCID: PMC12119028 DOI: 10.1371/journal.pcbi.1012950] [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: 12/03/2024] [Revised: 05/28/2025] [Accepted: 03/11/2025] [Indexed: 05/01/2025] Open
Abstract
Ryanodine receptors (RyRs) serve for excitation-contraction coupling in skeletal and cardiac muscle cells in a noticeably different way, not fully understood at the molecular level. We addressed the structure of skeletal (RyR1) and cardiac (RyR2) isoforms relevant to gating by Ca2+ and Mg2+ ions (M2+). Bioinformatics analysis of RyR structures ascertained the EF-hand loops as the M2+ binding inhibition site and revealed its allosteric coupling to the channel gate. The intra-monomeric inactivation pathway interacts with the Ca2+-activation pathway in both RyR isoforms, and the inter-monomeric pathway, stronger in RyR1, couples to the gate through the S23*-loop of the neighbor monomer. These structural findings were implemented in the model of RyR operation based on statistical mechanics and the Monod-Wyman-Changeux theorem. The model, which defines closed, open, and inactivated macrostates allosterically coupled to M2+-binding activation and inhibition sites, approximated the open probability data for both RyR1 and RyR2 channels at a broad range of M2+ concentrations. The proposed mechanism of RyR operation provides a new interpretation of the structural and functional data of mammalian RyR channels on common grounds. This may provide a new platform for designing pharmacological interventions in the relevant diseases of skeletal and cardiac muscles. The synthetic approach developed in this work may find general use in deciphering mechanisms of ion channel functions.
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Affiliation(s)
- Alexandra Zahradníková
- Department of Cellular Cardiology, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Pavelková
- Department of Cellular Cardiology, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Sabo
- Bioinformatics Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Sefer Baday
- Applied Informatics Department, Informatics Institute, Istanbul Technical University, Istanbul, Türkiye
| | - Ivan Zahradník
- Department of Cellular Cardiology, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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Iyer KA, Kobayashi T, Murayama T, Samsó M. Dantrolene inhibition of ryanodine receptor 1 carrying the severe malignant hyperthermia mutation Y522S visualized by cryo-EM. Structure 2025; 33:338-348.e4. [PMID: 39708816 PMCID: PMC11805659 DOI: 10.1016/j.str.2024.11.018] [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: 07/25/2024] [Revised: 10/30/2024] [Accepted: 11/27/2024] [Indexed: 12/23/2024]
Abstract
Mutations in the skeletal isoform of the ryanodine receptor 1 (RyR1) pose grave risks during anesthesia or treatment with succinylcholine muscle relaxants. These can trigger a potentially lethal malignant hyperthermia (MH) episode via intracellular calcium increase mainly from RyR1 channel leakage. Dantrolene is the only known treatment option to prevent death. The main target of dantrolene is RyR1; however, little is known about the mechanism of inhibition. Cryoelectron microscopy (cryo-EM) structures of dantrolene bound to the severe MH Y522S RyR1 mutant in the closed and open states at 2.5-3.3 Å resolution revealed that the drug binds to the channel's cytoplasmic assembly, far from the ion gate, interacting with residues W882, W996, and R1000 in the P1 domain. The finding was validated by Ca2+ imaging and [3H]ryanodine binding in wild-type (WT) and alanine mutants. Dantrolene reduced channel opening probability by restricting the central activation module, "cooling down" the primed conformation caused by the mutation.
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Affiliation(s)
- Kavita A Iyer
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Takuya Kobayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Montserrat Samsó
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA.
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Ogasawara M, Nishino I. Update on RYR1-related myopathies. Curr Opin Neurol 2024; 37:504-508. [PMID: 38994695 DOI: 10.1097/wco.0000000000001296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
PURPOSE OF REVIEW RYR1-related myopathy (RYR1-RM) is a group of myopathies caused by mutations in the RYR1 gene, which encodes the ryanodine receptor 1 (RYR1). This review discusses recent advances in the clinical features, pathology, pathogenesis, and therapeutics of RYR1-RM. RECENT FINDINGS Although treatments such as salbutamol, pyridostigmine, and N-acetylcysteine have been explored as potential therapies for RYR1-RM, none have been conclusively proven to be effective. However, recent clinical trials of Rycal ARM210 in patients with RYR1-RM have shown promising results, including reduced fatigue and improved proximal muscle strength.Recent advances in three-dimensional structural analysis of RYR1 channels, facilitated by cryo-electron microscopy (cryo-EM), have elucidated the distinct molecular mechanisms underlying RYR1 functionality. Additionally, high-throughput screening methods, including FRET-based and endoplasmic reticulum Ca 2+ -based assays, have been successful in identifying potential candidates for the treatment of RYR1-RM. SUMMARY Recent advances in clinical and pathological understanding have provided new insights into RYR1-RM. Novel pathomechanisms elucidated by cryo-EM and rapid screening methods have led to the identification of several promising drug candidates. We are hopeful about the potential of Rycal, other new drugs, and gene therapy, offering a promising outlook for the future.
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Affiliation(s)
- Masashi Ogasawara
- Department of Pediatrics, Showa General Hospital, Hanakoganei
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Ogawahigashi-cho, Kodaira, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Ogawahigashi-cho, Kodaira, Tokyo, Japan
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Taweechat P, Boonamnaj P, Samsó M, Sompornpisut P. Significance of Zn 2+ in RyR1 for Structural Integrity and Ligand Binding: Insight from Molecular Dynamics. J Phys Chem B 2024; 128:4670-4684. [PMID: 38717304 PMCID: PMC11103704 DOI: 10.1021/acs.jpcb.4c01189] [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: 02/23/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
Ryanodine receptor type 1 (RyR1) is a Ca2+-release channel central to skeletal muscle excitation-contraction (EC) coupling. RyR1's cryo-EM structures reveal a zinc-finger motif positioned within the cytoplasmic C-terminal domain (CTD). Yet, owing to limitations in cryo-EM resolution, RyR1 structures lack precision in detailing the metal coordination structure, prompting the need for an accurate model. In this study, we employed molecular dynamics (MD) simulations and the density functional theory (DFT) method to refine the binding characteristics of Zn2+ in the zinc-finger site of the RyR1 channel. Our findings also highlight substantial conformational changes in simulations conducted in the absence of Zn2+. Notably, we observed a loss of contact at the interface between protein domains proximal to the zinc-finger site, indicating a crucial role of Zn2+ in maintaining structural integrity and interdomain interactions within RyR1. Furthermore, this study provides valuable insights into the modulation of ATP, Ca2+, and caffeine binding, shedding light on the intricate relationship between Zn2+ coordination and the dynamic behavior of RyR1. Our integrative approach combining MD simulations and DFT calculations enhances our understanding of the molecular mechanisms governing ligand binding in RyR1.
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Affiliation(s)
- Panyakorn Taweechat
- Center
of Excellence in Computational Chemistry, Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panisak Boonamnaj
- Center
of Excellence in Computational Chemistry, Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Montserrat Samsó
- Department
of Physiology and Biophysics, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
| | - Pornthep Sompornpisut
- Center
of Excellence in Computational Chemistry, Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Li HB, Ji XL, Nie PH, Sun NH, Li RH. Perioperative management of bronchoscopy in a child patient with central core disease: A case report and literature review. Int J Surg Case Rep 2024; 118:109629. [PMID: 38657516 PMCID: PMC11063512 DOI: 10.1016/j.ijscr.2024.109629] [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: 01/23/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
INTRODUCTION We described the perioperative management of a child patient with central core disease for bronchoscopy with bronchoalveolar lavage. It is safe to avoid triggering agents (volatile anesthetics and succinylcholine) probably in preventing this appearance of malignant hyperthermia (MH). It is important to recognize potential complications and know how to prevent and manage them in patients with this condition. PRESENTATION OF CASE A 5-year-old boy (weight: 8.8 kg; height: 63 cm) presented to the pediatric department after five days of intermittent fever (highest body temperature is 39.3 °C) and cough, and aggravation 1 day, meanwhile he had phlegm in throat but he couldn't cough out. The child was found to have motor retardation at his one-month-old physical examination, then genetic analysis showed central core disease. Bronchoscopy with bronchoalveolar lavage was performed for better treatment under the premise of symptomatic treatment. DISCUSSION The patients with central core disease are particularly to develop malignant hyperthermia, so adequate precautions are in place to prevent and treat MH before anesthetic induction. The anesthesiologists need to make adequate preoperative anesthesia management strategies to ensure the safety of the child with central core disease for bronchoscopy with bronchoalveolar lavage. The child was discharged from the hospital one week after anti-inflammatory and anti-asthmatic treatment. CONCLUSION We summarized the anesthetic precautions and management in patients with central core disease, meanwhile we offered some suggestions about anesthetic focus on bronchoscopy with bronchoalveolar lavage.
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Affiliation(s)
- Hong-Bo Li
- Department of Anesthesiology, WeiFang People's Hospital, 151th, Guangwen Road, Weifang 261041, China
| | - Xiang-Lin Ji
- Department of Anesthesiology, WeiFang People's Hospital, 151th, Guangwen Road, Weifang 261041, China
| | - Pei-He Nie
- Department of Anesthesiology, WeiFang People's Hospital, 151th, Guangwen Road, Weifang 261041, China
| | - Neng-Hong Sun
- Department of Anesthesiology, WeiFang People's Hospital, 151th, Guangwen Road, Weifang 261041, China
| | - Rui-Hua Li
- Department of Anesthesiology, WeiFang People's Hospital, 151th, Guangwen Road, Weifang 261041, China.
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Šeflová J, Schwarz JA, Smith AN, Svensson B, Blackwell DJ, Phillips TA, Nikolaienko R, Bovo E, Rebbeck RT, Zima AV, Thomas DD, Van Petegem F, Knollmann BC, Johnston JN, Robia SL, Cornea RL. RyR2 Binding of an Antiarrhythmic Cyclic Depsipeptide Mapped Using Confocal Fluorescence Lifetime Detection of FRET. ACS Chem Biol 2023; 18:2290-2299. [PMID: 37769131 PMCID: PMC11648969 DOI: 10.1021/acschembio.3c00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Hyperactivity of cardiac sarcoplasmic reticulum (SR) ryanodine receptor (RyR2) Ca2+-release channels contributes to heart failure and arrhythmias. Reducing the RyR2 activity, particularly during cardiac relaxation (diastole), is a desirable therapeutic goal. We previously reported that the unnatural enantiomer (ent) of an insect-RyR activator, verticilide, inhibits porcine and mouse RyR2 at diastolic (nanomolar) Ca2+ and has in vivo efficacy against atrial and ventricular arrhythmia. To determine the ent-verticilide structural mode of action on RyR2 and guide its further development via medicinal chemistry structure-activity relationship studies, here, we used fluorescence lifetime (FLT)-measurements of Förster resonance energy transfer (FRET) in HEK293 cells expressing human RyR2. For these studies, we used an RyR-specific FRET molecular-toolkit and computational methods for trilateration (i.e., using distances to locate a point of interest). Multiexponential analysis of FLT-FRET measurements between four donor-labeled FKBP12.6 variants and acceptor-labeled ent-verticilide yielded distance relationships placing the acceptor probe at two candidate loci within the RyR2 cryo-EM map. One locus is within the Ry12 domain (at the corner periphery of the RyR2 tetrameric complex). The other locus is sandwiched at the interface between helical domain 1 and the SPRY3 domain. These findings document RyR2-target engagement by ent-verticilide, reveal new insight into the mechanism of action of this new class of RyR2-targeting drug candidate, and can serve as input in future computational determinations of the ent-verticilide binding site on RyR2 that will inform structure-activity studies for lead optimization.
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Affiliation(s)
- Jaroslava Šeflová
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Jacob A Schwarz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Abigail N Smith
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Bengt Svensson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Taylor A Phillips
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Roman Nikolaienko
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Elisa Bovo
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Aleksey V Zima
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Björn C Knollmann
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey N Johnston
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Chicago, Illinois 60153, United States
| | - Răzvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Dhureja M, Arthur R, Soni D, Upadhayay S, Temgire P, Kumar P. Calcium channelopathies in neurodegenerative disorder: an untold story of RyR and SERCA. Expert Opin Ther Targets 2023; 27:1159-1172. [PMID: 37971192 DOI: 10.1080/14728222.2023.2277863] [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: 08/26/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION Recent neuroscience breakthroughs have shed light on the sophisticated relationship between calcium channelopathies and movement disorders, exposing a previously undiscovered tale focusing on the Ryanodine Receptor (RyR) and the Sarco/Endoplasmic Reticulum Calcium ATPase (SERCA). Calcium signaling mainly orchestrates neural communication, which regulates synaptic transmission and total network activity. It has been determined that RyR play a significant role in managing neuronal functions, most notably in releasing intracellular calcium from the endoplasmic reticulum. AREAS COVERED It highlights the involvement of calcium channels such as RyR and SERCA in physiological and pathophysiological conditions. EXPERT OPINION Links between RyR and SERCA activity dysregulation, aberrant calcium levels, motor and cognitive dysfunction have brought attention to the importance of RyR and SERCA modulation in neurodegenerative disorders. Understanding the obscure function of these proteins will open up new therapeutic possibilities to address the underlying causes of neurodegenerative diseases. The unreported RyR and SERCA narrative broadens the understanding of calcium channelopathies in movement disorders and calls for more research into cutting-edge therapeutic approaches.
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Affiliation(s)
- Maanvi Dhureja
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | - Divya Soni
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | - Shubham Upadhayay
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | - Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Bathinda, India
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Molecular Aspects Implicated in Dantrolene Selectivity with Respect to Ryanodine Receptor Isoforms. Int J Mol Sci 2023; 24:ijms24065409. [PMID: 36982484 PMCID: PMC10049336 DOI: 10.3390/ijms24065409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/24/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Dantrolene is an intra-cellularly acting skeletal muscle relaxant used for the treatment of the rare genetic disorder, malignant hyperthermia (MH). In most cases, MH susceptibility is caused by dysfunction of the skeletal ryanodine receptor (RyR1) harboring one of nearly 230 single-point MH mutations. The therapeutic effect of dantrolene is the result of a direct inhibitory action on the RyR1 channel, thus suppressing aberrant Ca2+ release from the sarcoplasmic reticulum. Despite the almost identical dantrolene-binding sequence exits in all three mammalian RyR isoforms, dantrolene appears to be an isoform-selective inhibitor. Whereas RyR1 and RyR3 channels are competent to bind dantrolene, the RyR2 channel, predominantly expressed in the heart, is unresponsive. However, a large body of evidence suggests that the RyR2 channel becomes sensitive to dantrolene-mediated inhibition under certain pathological conditions. Although a consistent picture of the dantrolene effect emerges from in vivo studies, in vitro results are often contradictory. Hence, our goal in this perspective is to provide the best possible clues to the molecular mechanism of dantrolene’s action on RyR isoforms by identifying and discussing potential sources of conflicting results, mainly coming from cell-free experiments. Moreover, we propose that, specifically in the case of the RyR2 channel, its phosphorylation could be implicated in acquiring the channel responsiveness to dantrolene inhibition, interpreting functional findings in the structural context.
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