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Noda Y, Miyoshi H, Benucci S, Gonzalez A, Bandschapp O, Girard T, Treves S, Zorzato F. Functional characterization of RYR1 variants identified in malignant hyperthermia susceptible individuals. Neuromuscul Disord 2023; 33:951-963. [PMID: 37996280 DOI: 10.1016/j.nmd.2023.10.019] [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: 06/28/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Malignant hyperthermia is a pharmacogenetic disorder triggered by halogenated anesthetic agents in genetically predisposed individuals. Approximately 70 % of these individuals carry mutations in RYR1, the gene encoding the ryanodine receptor calcium channel of skeletal muscle. In this study, we performed functional analysis of 5 RYR1 variants identified in members from 8 families who had been diagnosed by the IVCT. Of the 68 individuals enrolled in the study, 43 were diagnosed as MHS, 23 as MHN, and 2 individuals were not tested. Here we demonstrate that the 5 RyR1 variants cause hypersensitivity to RyR1 agonist-mediated calcium release. According to the EMHG scoring matrix these five genetic variants can be classified as follows: c.8638G>A (p.E2880K) and c.11314C>T (p.R3772W) likely pathogenic, c.11416G>A (p.G3806R), c.14627A>G (p.K4876R) and c.14813T>C (p.I4938T), pathogenic (RefSeq NM_000540.3). We propose that the newly functionally characterized RYR1 variants, be included in the panel of variants to be used for the molecular diagnosis of MHS.
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Affiliation(s)
- Yuko Noda
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland; Department of Anesthesiology, Hiroshima University Hospital, 1-2-3 Kasumi Minami-ku Hiroshima, 734-8551, Japan
| | - Hirotsugu Miyoshi
- Department of Anesthesiology, Hiroshima University Hospital, 1-2-3 Kasumi Minami-ku Hiroshima, 734-8551, Japan
| | - Sofia Benucci
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland
| | | | | | - Thierry Girard
- Anesthesiology, Spitalstrasse 21, Basel 4031, Switzerland
| | - Susan Treves
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland; Department of Life Science and Biotechnology, University of Ferrara, Via Borsari 46, Ferrara 44100, Italy.
| | - Francesco Zorzato
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland; Department of Life Science and Biotechnology, University of Ferrara, Via Borsari 46, Ferrara 44100, Italy.
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Chirasani VR, Pasek DA, Meissner G. Structural and functional interactions between the Ca 2+-, ATP-, and caffeine-binding sites of skeletal muscle ryanodine receptor (RyR1). J Biol Chem 2021; 297:101040. [PMID: 34352272 PMCID: PMC8408527 DOI: 10.1016/j.jbc.2021.101040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/22/2022] Open
Abstract
Ryanodine receptor type 1 (RyR1) releases Ca2+ ions from the sarcoplasmic reticulum of skeletal muscle cells to initiate muscle contraction. Multiple endogenous and exogenous effectors regulate RyR1, such as ATP, Ca2+, caffeine (Caf), and ryanodine. Cryo-EM identified binding sites for the three coactivators Ca2+, ATP, and Caf. However, the mechanism of coregulation and synergy between these activators remains to be determined. Here, we used [3H]ryanodine ligand-binding assays and molecular dynamics simulations to test the hypothesis that both the ATP- and Caf-binding sites communicate with the Ca2+-binding site to sensitize RyR1 to Ca2+. We report that either phosphomethylphosphonic acid adenylate ester (AMPPCP), a nonhydrolyzable ATP analog, or Caf can activate RyR1 in the absence or the presence of Ca2+. However, enhanced RyR1 activation occurred in the presence of Ca2+, AMPPCP, and Caf. In the absence of Ca2+, Na+ inhibited [3H]ryanodine binding without impairing RyR1 activation by AMPPCP and Caf. Computational analysis suggested that Ca2+-, ATP-, and Caf-binding sites modulate RyR1 protein stability through interactions with the carboxyterminal domain and other domains in the activation core. In the presence of ATP and Caf but the absence of Ca2+, Na+ is predicted to inhibit RyR1 by interacting with the Ca2+-binding site. Our data suggested that ATP and Caf binding affected the conformation of the Ca2+-binding site, and conversely, Ca2+ binding affected the conformation of the ATP- and Caf-binding sites. We conclude that Ca2+, ATP, and Caf regulate RyR1 through a network of allosteric interactions involving the Ca2+-, ATP-, and Caf-binding sites.
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Affiliation(s)
- Venkat R Chirasani
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA.
| | - Daniel A Pasek
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
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Bauerová-Hlinková V, Hajdúchová D, Bauer JA. Structure and Function of the Human Ryanodine Receptors and Their Association with Myopathies-Present State, Challenges, and Perspectives. Molecules 2020; 25:molecules25184040. [PMID: 32899693 PMCID: PMC7570887 DOI: 10.3390/molecules25184040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 01/28/2023] Open
Abstract
Cardiac arrhythmias are serious, life-threatening diseases associated with the dysregulation of Ca2+ influx into the cytoplasm of cardiomyocytes. This dysregulation often arises from dysfunction of ryanodine receptor 2 (RyR2), the principal Ca2+ release channel. Dysfunction of RyR1, the skeletal muscle isoform, also results in less severe, but also potentially life-threatening syndromes. The RYR2 and RYR1 genes have been found to harbor three main mutation “hot spots”, where mutations change the channel structure, its interdomain interface properties, its interactions with its binding partners, or its dynamics. In all cases, the result is a defective release of Ca2+ ions from the sarcoplasmic reticulum into the myocyte cytoplasm. Here, we provide an overview of the most frequent diseases resulting from mutations to RyR1 and RyR2, briefly review some of the recent experimental structural work on these two molecules, detail some of the computational work describing their dynamics, and summarize the known changes to the structure and function of these receptors with particular emphasis on their N-terminal, central, and channel domains.
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Dokholyan NV. Experimentally-driven protein structure modeling. J Proteomics 2020; 220:103777. [PMID: 32268219 PMCID: PMC7214187 DOI: 10.1016/j.jprot.2020.103777] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
Revolutions in natural and exact sciences started at the dawn of last century have led to the explosion of theoretical, experimental, and computational approaches to determine structures of molecules, complexes, as well as their rich conformational dynamics. Since different experimental methods produce information that is attributed to specific time and length scales, corresponding computational methods have to be tailored to these scales and experiments. These methods can be then combined and integrated in scales, hence producing a fuller picture of molecular structure and motion from the "puzzle pieces" offered by various experiments. Here, we describe a number of computational approaches to utilize experimental data to glance into structure of proteins and understand their dynamics. We will also discuss the limitations and the resolution of the constraints-based modeling approaches. SIGNIFICANCE: Experimentally-driven computational structure modeling and determination is a rapidly evolving alternative to traditional approaches for molecular structure determination. These new hybrid experimental-computational approaches are proving to be a powerful microscope to glance into the structural features of intrinsically or partially disordered proteins, dynamics of molecules and complexes. In this review, we describe various approaches in the field of experimentally-driven computational structure modeling.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA.; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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Lawal TA, Wires ES, Terry NL, Dowling JJ, Todd JJ. Preclinical model systems of ryanodine receptor 1-related myopathies and malignant hyperthermia: a comprehensive scoping review of works published 1990-2019. Orphanet J Rare Dis 2020; 15:113. [PMID: 32381029 PMCID: PMC7204063 DOI: 10.1186/s13023-020-01384-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pathogenic variations in the gene encoding the skeletal muscle ryanodine receptor (RyR1) are associated with malignant hyperthermia (MH) susceptibility, a life-threatening hypermetabolic condition and RYR1-related myopathies (RYR1-RM), a spectrum of rare neuromuscular disorders. In RYR1-RM, intracellular calcium dysregulation, post-translational modifications, and decreased protein expression lead to a heterogenous clinical presentation including proximal muscle weakness, contractures, scoliosis, respiratory insufficiency, and ophthalmoplegia. Preclinical model systems of RYR1-RM and MH have been developed to better understand underlying pathomechanisms and test potential therapeutics. METHODS We conducted a comprehensive scoping review of scientific literature pertaining to RYR1-RM and MH preclinical model systems in accordance with the PRISMA Scoping Reviews Checklist and the framework proposed by Arksey and O'Malley. Two major electronic databases (PubMed and EMBASE) were searched without language restriction for articles and abstracts published between January 1, 1990 and July 3, 2019. RESULTS Our search yielded 5049 publications from which 262 were included in this review. A majority of variants tested in RYR1 preclinical models were localized to established MH/central core disease (MH/CCD) hot spots. A total of 250 unique RYR1 variations were reported in human/rodent/porcine models with 95% being missense substitutions. The most frequently reported RYR1 variant was R614C/R615C (human/porcine total n = 39), followed by Y523S/Y524S (rabbit/mouse total n = 30), I4898T/I4897T/I4895T (human/rabbit/mouse total n = 20), and R163C/R165C (human/mouse total n = 18). The dyspedic mouse was utilized by 47% of publications in the rodent category and its RyR1-null (1B5) myotubes were transfected in 23% of publications in the cellular model category. In studies of transfected HEK-293 cells, 57% of RYR1 variations affected the RyR1 channel and activation core domain. A total of 15 RYR1 mutant mouse strains were identified of which ten were heterozygous, three were compound heterozygous, and a further two were knockout. Porcine, avian, zebrafish, C. elegans, canine, equine, and drosophila model systems were also reported. CONCLUSIONS Over the past 30 years, there were 262 publications on MH and RYR1-RM preclinical model systems featuring more than 200 unique RYR1 variations tested in a broad range of species. Findings from these studies have set the foundation for therapeutic development for MH and RYR1-RM.
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Affiliation(s)
- Tokunbor A Lawal
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emily S Wires
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - Nancy L Terry
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD, USA
| | - James J Dowling
- Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joshua J Todd
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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Xu L, Harms FL, Chirasani VR, Pasek DA, Kortüm F, Meinecke P, Dokholyan NV, Kutsche K, Meissner G. Single-channel properties of skeletal muscle ryanodine receptor pore Δ 4923FF 4924 in two brothers with a lethal form of fetal akinesia. Cell Calcium 2020; 87:102182. [PMID: 32097819 DOI: 10.1016/j.ceca.2020.102182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 11/26/2022]
Abstract
Ryanodine receptor ion channels (RyR1s) release Ca2+ ions from the sarcoplasmic reticulum to regulate skeletal muscle contraction. By whole-exome sequencing, we identified the heterozygous RYR1 variant c.14767_14772del resulting in the in-frame deletion p.(Phe4923_Phe4924del) in two brothers with a lethal form of the fetal akinesia deformation syndrome (FADS). The two deleted phenylalanines (RyR1-Δ4923FF4924) are located in the S6 pore-lining helix of RyR1. Clinical features in one of the two siblings included severe hypotonia, thin ribs, swallowing inability, and respiratory insufficiency that caused early death. Functional consequences of the RyR1-Δ4923FF4924 variant were determined using recombinant 2,200-kDa homotetrameric and heterotetrameric RyR1 channel complexes that were expressed in HEK293 cells and characterized by cellular, electrophysiological, and computational methods. Cellular Ca2+ release in response to caffeine indicated that the homotetrameric variant formed caffeine-sensitive Ca2+ conducting channels in HEK293 cells. In contrast, the homotetrameric channel complex was not activated by Ca2+ and did not conduct Ca2+ based on single-channel measurements. The computational analysis suggested decreased protein stability and loss of salt bridge interactions between RyR1-R4944 and RyR1-D4938, increasing the electrostatic interaction energy of Ca2+ in a region 20 Å from the mutant site. Co-expression of wild-type and mutant RyR1s resulted in Ca2+-dependent channel activities that displayed intermediate Ca2+ conductances and suggested maintenance of a reduced Ca2+ release in the two patients. Our findings reveal that the RYR1 pore variant p.(Phe4923_Phe4924del) attenuates the flow of Ca2+ through heterotetrameric channels, but alone was not sufficient to cause FADS, indicating additional genetic factors to be involved.
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Affiliation(s)
- Le Xu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Venkat R Chirasani
- Departments of Pharmacology, and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, United States
| | - Daniel A Pasek
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nikolay V Dokholyan
- Departments of Pharmacology, and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, United States
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States.
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King MM, Kayastha BB, Franklin MJ, Patrauchan MA. Calcium Regulation of Bacterial Virulence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:827-855. [PMID: 31646536 DOI: 10.1007/978-3-030-12457-1_33] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcium (Ca2+) is a universal signaling ion, whose major informational role shaped the evolution of signaling pathways, enabling cellular communications and responsiveness to both the intracellular and extracellular environments. Elaborate Ca2+ regulatory networks have been well characterized in eukaryotic cells, where Ca2+ regulates a number of essential cellular processes, ranging from cell division, transport and motility, to apoptosis and pathogenesis. However, in bacteria, the knowledge on Ca2+ signaling is still fragmentary. This is complicated by the large variability of environments that bacteria inhabit with diverse levels of Ca2+. Yet another complication arises when bacterial pathogens invade a host and become exposed to different levels of Ca2+ that (1) are tightly regulated by the host, (2) control host defenses including immune responses to bacterial infections, and (3) become impaired during diseases. The invading pathogens evolved to recognize and respond to the host Ca2+, triggering the molecular mechanisms of adhesion, biofilm formation, host cellular damage, and host-defense resistance, processes enabling the development of persistent infections. In this review, we discuss: (1) Ca2+ as a determinant of a host environment for invading bacterial pathogens, (2) the role of Ca2+ in regulating main events of host colonization and bacterial virulence, and (3) the molecular mechanisms of Ca2+ signaling in bacterial pathogens.
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Affiliation(s)
- Michelle M King
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Biraj B Kayastha
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Michael J Franklin
- Department of Microbiology and Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Xu L, Chirasani VR, Carter JS, Pasek DA, Dokholyan NV, Yamaguchi N, Meissner G. Ca 2+-mediated activation of the skeletal-muscle ryanodine receptor ion channel. J Biol Chem 2018; 293:19501-19509. [PMID: 30341173 DOI: 10.1074/jbc.ra118.004453] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/14/2018] [Indexed: 02/05/2023] Open
Abstract
Cryo-electron micrograph studies recently have identified a Ca2+-binding site in the 2,200-kDa ryanodine receptor ion channel (RyR1) in skeletal muscle. To clarify the role of this site in regulating RyR1 activity, here we applied mutational, electrophysiological, and computational methods. Three amino acid residues that interact directly with Ca2+ were replaced, and these RyR1 variants were expressed in HEK293 cells. Single-site RyR1-E3893Q, -E3893V, -E3967Q, -E3967V, and -T5001A variants and double-site RyR1-E3893Q/E3967Q and -E3893V/E3967V variants displayed cellular Ca2+ release in response to caffeine, which indicated that they retained functionality as caffeine-sensitive, Ca2+-conducting channels in the HEK293 cell system. Using [3H]ryanodine binding and single-channel measurements of membrane isolates, we found that single- and double-site RyR1-E3893 and -E3967 variants are not activated by Ca2+ We also noted that RyR1-E3893Q/E3967Q and -E3893V/E3967V variants maintain caffeine- and ATP-induced activation and that RyR1-E3893Q/E3967Q is inhibited by Mg2+ and elevated Ca2+ RyR1-T5001A exhibited decreased Ca2+ sensitivity compared with WT-RyR1 in single-channel measurements. Computational methods suggested that electrostatic interactions between Ca2+ and negatively charged glutamate residues have a critical role in transducing the functional effects of Ca2+ on RyR1. We conclude that the removal of negative charges in the recently identified RyR1 Ca2+-binding site impairs RyR1 activation by physiological Ca2+ concentrations and results in loss of binding to Ca2+ or reduced Ca2+ affinity of the binding site.
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Affiliation(s)
- Le Xu
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Venkat R Chirasani
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260.,the Departments of Pharmacology and Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850
| | - Jordan S Carter
- the Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425, and.,the Cardiac Signaling Center, Clemson University, Charleston, South Carolina 29425
| | - Daniel A Pasek
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Nikolay V Dokholyan
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260.,the Departments of Pharmacology and Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850
| | - Naohiro Yamaguchi
- the Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina 29425, and.,the Cardiac Signaling Center, Clemson University, Charleston, South Carolina 29425
| | - Gerhard Meissner
- From the Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260,
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