1
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Jin X, Huang J, Wang H, Wang K, Yan N. A versatile residue numbering scheme for Na v and Ca v channels. Cell Chem Biol 2024; 31:1394-1404. [PMID: 39151406 DOI: 10.1016/j.chembiol.2024.07.008] [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: 02/18/2024] [Revised: 07/01/2024] [Accepted: 07/18/2024] [Indexed: 08/19/2024]
Abstract
Voltage-gated sodium (Nav) and calcium (Cav) channels are responsible for the initiation of electrical signals. They have long been targeted for the treatment of various diseases. The mounting number of cryoelectron microscopy (cryo-EM) structures for diverse subtypes of Nav and Cav channels from multiple organisms necessitates a generic residue numbering system to establish the structure-function relationship and to aid rational drug design or optimization. Here we suggest a structure-based residue numbering scheme, centering around the most conserved residues on each of the functional segments. We elaborate the generic numbers through illustrative examples, focusing on representative drug-binding sites of eukaryotic Nav and Cav channels. We also extend the numbering scheme to compare common disease mutations among different Nav subtypes. Application of the generic residue numbering scheme affords immediate insights into hotspots for pathogenic mutations and critical loci for drug binding and will facilitate drug discovery targeting Nav and Cav channels.
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Affiliation(s)
- Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Huan Wang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kan Wang
- Department of Anesthesiology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation, Guangming District, Shenzhen, Guangdong Province 518107, China; Shenzhen Bay Laboratory, Guangming District, Shenzhen, Guangdong Province 518132, China.
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2
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Huang J, Pan X, Yan N. Structural biology and molecular pharmacology of voltage-gated ion channels. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00763-7. [PMID: 39103479 DOI: 10.1038/s41580-024-00763-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2024] [Indexed: 08/07/2024]
Abstract
Voltage-gated ion channels (VGICs), including those for Na+, Ca2+ and K+, selectively permeate ions across the cell membrane in response to changes in membrane potential, thus participating in physiological processes involving electrical signalling, such as neurotransmission, muscle contraction and hormone secretion. Aberrant function or dysregulation of VGICs is associated with a diversity of neurological, psychiatric, cardiovascular and muscular disorders, and approximately 10% of FDA-approved drugs directly target VGICs. Understanding the structure-function relationship of VGICs is crucial for our comprehension of their working mechanisms and role in diseases. In this Review, we discuss how advances in single-particle cryo-electron microscopy have afforded unprecedented structural insights into VGICs, especially on their interactions with clinical and investigational drugs. We present a comprehensive overview of the recent advances in the structural biology of VGICs, with a focus on how prototypical drugs and toxins modulate VGIC activities. We explore how these structures elucidate the molecular basis for drug actions, reveal novel pharmacological sites, and provide critical clues to future drug discovery.
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Affiliation(s)
- Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Xiaojing Pan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong, China.
| | - Nieng Yan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.
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3
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Weninger G, Miotto MC, Tchagou C, Reiken S, Dridi H, Brandenburg S, Riedemann GC, Yuan Q, Liu Y, Chang A, Wronska A, Lehnart SE, Marks AR. Structural insights into the regulation of RyR1 by S100A1. Proc Natl Acad Sci U S A 2024; 121:e2400497121. [PMID: 38917010 PMCID: PMC11228480 DOI: 10.1073/pnas.2400497121] [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: 01/09/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
S100A1, a small homodimeric EF-hand Ca2+-binding protein (~21 kDa), plays an important regulatory role in Ca2+ signaling pathways involved in various biological functions including Ca2+ cycling and contractile performance in skeletal and cardiac myocytes. One key target of the S100A1 interactome is the ryanodine receptor (RyR), a huge homotetrameric Ca2+ release channel (~2.3 MDa) of the sarcoplasmic reticulum. Here, we report cryoelectron microscopy structures of S100A1 bound to RyR1, the skeletal muscle isoform, in absence and presence of Ca2+. Ca2+-free apo-S100A1 binds beneath the bridging solenoid (BSol) and forms contacts with the junctional solenoid and the shell-core linker of RyR1. Upon Ca2+-binding, S100A1 undergoes a conformational change resulting in the exposure of the hydrophobic pocket known to serve as a major interaction site of S100A1. Through interactions of the hydrophobic pocket with RyR1, Ca2+-bound S100A1 intrudes deeper into the RyR1 structure beneath BSol than the apo-form and induces sideways motions of the C-terminal BSol region toward the adjacent RyR1 protomer resulting in tighter interprotomer contacts. Interestingly, the second hydrophobic pocket of the S100A1-dimer is largely exposed at the hydrophilic surface making it prone to interactions with the local environment, suggesting that S100A1 could be involved in forming larger heterocomplexes of RyRs with other protein partners. Since S100A1 interactions stabilizing BSol are implicated in the regulation of RyR-mediated Ca2+ release, the characterization of the S100A1 binding site conserved between RyR isoforms may provide the structural basis for the development of therapeutic strategies regarding treatments of RyR-related disorders.
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Affiliation(s)
- Gunnar Weninger
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Marco C Miotto
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Carl Tchagou
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Steven Reiken
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Haikel Dridi
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Sören Brandenburg
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37075 Göttingen, Germany
| | - Gabriel C Riedemann
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Qi Yuan
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Yang Liu
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Alexander Chang
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Anetta Wronska
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37075 Göttingen, Germany
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Center for Molecular Cardiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
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4
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Hu M, Feng X, Liu Q, Liu S, Huang F, Xu H. The ion channels of endomembranes. Physiol Rev 2024; 104:1335-1385. [PMID: 38451235 DOI: 10.1152/physrev.00025.2023] [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: 06/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The endomembrane system consists of organellar membranes in the biosynthetic pathway [endoplasmic reticulum (ER), Golgi apparatus, and secretory vesicles] as well as those in the degradative pathway (early endosomes, macropinosomes, phagosomes, autophagosomes, late endosomes, and lysosomes). These endomembrane organelles/vesicles work together to synthesize, modify, package, transport, and degrade proteins, carbohydrates, and lipids, regulating the balance between cellular anabolism and catabolism. Large ion concentration gradients exist across endomembranes: Ca2+ gradients for most endomembrane organelles and H+ gradients for the acidic compartments. Ion (Na+, K+, H+, Ca2+, and Cl-) channels on the organellar membranes control ion flux in response to cellular cues, allowing rapid informational exchange between the cytosol and organelle lumen. Recent advances in organelle proteomics, organellar electrophysiology, and luminal and juxtaorganellar ion imaging have led to molecular identification and functional characterization of about two dozen endomembrane ion channels. For example, whereas IP3R1-3 channels mediate Ca2+ release from the ER in response to neurotransmitter and hormone stimulation, TRPML1-3 and TMEM175 channels mediate lysosomal Ca2+ and H+ release, respectively, in response to nutritional and trafficking cues. This review aims to summarize the current understanding of these endomembrane channels, with a focus on their subcellular localizations, ion permeation properties, gating mechanisms, cell biological functions, and disease relevance.
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Affiliation(s)
- Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xinghua Feng
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiang Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Siyu Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Fangqian Huang
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States
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5
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Li X, Feng R, Guo Z, Meng Y, Zou Y, Liao W, Peng Q, Zhong H, Zhao W. Direct investigations of the effects of nicardipine on calcium channels of astrocytes by Atomic Force Microscopy. Talanta 2024; 274:125947. [PMID: 38537353 DOI: 10.1016/j.talanta.2024.125947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 05/04/2024]
Abstract
Calcium channel blockers (CCB) of astrocytes can blockade the calcium ions entry through the voltage gated calcium channels (VGCC), and is widely used in the diseases related with VGCC of astrocytes. But many aspects of the interaction mechanisms between the CCB and VGCC of astrocytes still remain unclear due to the limited resolution of the approaches. Herein the effects of the nicardipine (a type of CCB) on VGCC of astrocytes were investigated at very high spatial, force and electrical resolution by multiple modes of Atomic Force Microscopy (AFM) directly. The results reveal that after the addition of nicardipine, the recognition signals of VGCC disappeared; the specific unbinding forces vanished; the conductivity of the astrocytes decreased (the current decreased about 2.9 pA and the capacitance was doubled); the surface potential of the astrocytes reduced about 14.2 mV. The results of electrical properties investigations are consistent with the simulation experiments. The relations between these biophysical and biochemical properties of VGCC have been discussed. All these demonstrate that the interactions between nicardipine and VGCC have been studied at nanometer spatial resolution, at picoNewton force resolution and very high electrical signal resolution (pA in current, pF in capacitance and 0.1 mV in surface potential) level. The approaches are considered to be high resolution and high sensitivity, and will be helpful and useful in the further investigations of the effects of other types of CCB on ion channels, and will also be helpful in the investigations of mechanisms and therapy of ion channelopathies.
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Affiliation(s)
- Xinyu Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Rongrong Feng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Zeling Guo
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Yu Meng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Yulan Zou
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Wenchao Liao
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Qianwei Peng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, People's Republic of China
| | - Haijian Zhong
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China.
| | - Weidong Zhao
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, 341000, People's Republic of China; School of Medical Information Engineering, Gannan Medical University, Ganzhou, 341000, People's Republic of China; Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, People's Republic of China.
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6
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Rebbeck RT, Svensson B, Zhang J, Samsó M, Thomas DD, Bers DM, Cornea RL. Kinetics and mapping of Ca-driven calmodulin conformations on skeletal and cardiac muscle ryanodine receptors. Nat Commun 2024; 15:5120. [PMID: 38879623 PMCID: PMC11180167 DOI: 10.1038/s41467-024-48951-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/16/2024] [Indexed: 06/19/2024] Open
Abstract
Calmodulin transduces [Ca2+] information regulating the rhythmic Ca2+ cycling between the sarcoplasmic reticulum and cytoplasm during contraction and relaxation in cardiac and skeletal muscle. However, the structural dynamics by which calmodulin modulates the sarcoplasmic reticulum Ca2+ release channel, the ryanodine receptor, at physiologically relevant [Ca2+] is unknown. Using fluorescence lifetime FRET, we resolve different structural states of calmodulin and Ca2+-driven shifts in the conformation of calmodulin bound to ryanodine receptor. Skeletal and cardiac ryanodine receptor isoforms show different calmodulin-ryanodine receptor conformations, as well as binding and structural kinetics with 0.2-ms resolution, which reflect different functional roles of calmodulin. These FRET methods provide insight into the physiological calmodulin-ryanodine receptor structural states, revealing additional distinct structural states that complement cryo-EM models that are based on less physiological conditions. This technology will drive future studies on pathological calmodulin-ryanodine receptor interactions and dynamics with other important ryanodine receptor bound modulators.
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Affiliation(s)
- Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Bengt Svensson
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jingyan Zhang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Montserrat Samsó
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Donald M Bers
- Department of Pharmacology, University of California at Davis, Davis, CA, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN, USA.
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7
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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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8
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Gao L, Ardiel E, Nurrish S, Kaplan JM. Voltage-induced calcium release in Caenorhabditis elegans body muscles. Proc Natl Acad Sci U S A 2024; 121:e2317753121. [PMID: 38687794 PMCID: PMC11087772 DOI: 10.1073/pnas.2317753121] [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: 10/12/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Type 1 voltage-activated calcium channels (CaV1) in the plasma membrane trigger calcium release from the sarcoplasmic reticulum (SR) by two mechanisms. In voltage-induced calcium release (VICR), CaV1 voltage sensing domains are directly coupled to ryanodine receptors (RYRs), an SR calcium channel. In calcium-induced calcium release (CICR), calcium ions flowing through activated CaV1 channels bind and activate RYR channels. VICR is thought to occur exclusively in vertebrate skeletal muscle while CICR occurs in all other muscles (including all invertebrate muscles). Here, we use calcium-activated SLO-2 potassium channels to analyze CaV1-SR coupling in Caenorhabditis elegans body muscles. SLO-2 channels were activated by both VICR and external calcium. VICR-mediated SLO-2 activation requires two SR calcium channels (RYRs and IP3 Receptors), JPH-1/Junctophilin, a PDZ (PSD95, Dlg1, ZO-1 domain) binding domain (PBD) at EGL-19/CaV1's carboxy-terminus, and SHN-1/Shank (a scaffolding protein that binds EGL-19's PBD). Thus, VICR occurs in invertebrate muscles.
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Affiliation(s)
- Luna Gao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Neurobiology, Harvard Medical School, Boston, MA02115
| | - Evan Ardiel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Neurobiology, Harvard Medical School, Boston, MA02115
| | - Stephen Nurrish
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Neurobiology, Harvard Medical School, Boston, MA02115
| | - Joshua M. Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Neurobiology, Harvard Medical School, Boston, MA02115
- Program in Neuroscience, Harvard Medical School, Boston, MA02115
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9
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Xu J, Liao C, Yin CC, Li G, Zhu Y, Sun F. In situ structural insights into the excitation-contraction coupling mechanism of skeletal muscle. SCIENCE ADVANCES 2024; 10:eadl1126. [PMID: 38507485 PMCID: PMC10954225 DOI: 10.1126/sciadv.adl1126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the architecture of triad junction by cryo-electron tomography, solved the in situ structure of RyR1 in complex with FKBP12 and calmodulin with the resolution of 16.7 Angstrom, and found the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. This unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.
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Affiliation(s)
- Jiashu Xu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chang-Cheng Yin
- Department of Biophysics, The Health Science Center, Peking University, Beijing 100191, China
- Electron Microscopy Analysis Laboratory, The Health Science Center, Peking University, Beijing 100191, China
- Center for Protein Science, Peking University, Beijing 100871, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yun Zhu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China
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10
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Deniaud A, Kabasakal BV, Bufton JC, Schaffitzel C. Sample Preparation for Electron Cryo-Microscopy of Macromolecular Machines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:173-190. [PMID: 38507207 DOI: 10.1007/978-3-031-52193-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
High-resolution structure determination by electron cryo-microscopy underwent a step change in recent years. This now allows study of challenging samples which previously were inaccessible for structure determination, including membrane proteins. These developments shift the focus in the field to the next bottlenecks which are high-quality sample preparations. While the amounts of sample required for cryo-EM are relatively small, sample quality is the key challenge. Sample quality is influenced by the stability of complexes which depends on buffer composition, inherent flexibility of the sample, and the method of solubilization from the membrane for membrane proteins. It further depends on the choice of sample support, grid pre-treatment and cryo-grid freezing protocol. Here, we discuss various widely applicable approaches to improve sample quality for structural analysis by cryo-EM.
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Affiliation(s)
- Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG - Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Burak V Kabasakal
- School of Biochemistry, University of Bristol, Bristol, UK
- Turkish Accelerator and Radiation Laboratory, Gölbaşı, Ankara, Türkiye
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11
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Dulhunty AF. Biophysical reviews top five: voltage-dependent charge movement in nerve and muscle. Biophys Rev 2023; 15:1903-1907. [PMID: 38192339 PMCID: PMC10771356 DOI: 10.1007/s12551-023-01165-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024] Open
Abstract
The discovery of gating currents and asymmetric charge movement in the early 1970s represented a remarkable leap forward in our understanding of the biophysical basis of voltage-dependent events that underlie electrical signalling that is vital for nerve and muscle function. Gating currents and charge movement reflect a fundamental process in which charged amino acid residues in an ion channel protein move in response to a change in the membrane electrical field and therefore activate the specific voltage-dependent response of that protein. The detection of gating currents and asymmetric charge movement over the past 50 years has been pivotal in unraveling the multiple molecular and intra-molecular processes which lead to action potentials in excitable tissues and excitation-contraction (EC) coupling in skeletal muscle. The recording of gating currents and asymmetric charge movement remains an essential component of investigations into the basic molecular mechanisms of neuronal conduction and muscle contraction.
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Affiliation(s)
- Angela F. Dulhunty
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, ACT, Canberra, 2601 Australia
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12
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Yang J, Cheng WX, Wu G, Sheng S, Zhang P. Prediction of folding patterns for intrinsic disordered protein. Sci Rep 2023; 13:20343. [PMID: 37990040 PMCID: PMC10663623 DOI: 10.1038/s41598-023-45969-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
The conformation flexibility of natural protein causes both complexity and difficulty to understand the relationship between structure and function. The prediction of intrinsically disordered protein primarily is focusing on to disclose the regions with structural flexibility involving relevant biological functions and various diseases. The order of amino acids in protein sequence determines possible conformations, folding flexibility and biological function. Although many methods provided the information of intrinsically disordered protein (IDP), but the results are mainly limited to determine the locations of regions without knowledge of possible folding conformations. Here, the developed protein folding fingerprint adopted the protein folding variation matrix (PFVM) to reveal all possible folding patterns for the intrinsically disordered protein along its sequence. The PFVM integrally exhibited the intrinsically disordered protein with disordering regions, degree of disorder as well as folding pattern. The advantage of PFVM will not only provide rich information for IDP, but also may promote the study of protein folding problem.
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Affiliation(s)
- Jiaan Yang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
- Micro Biotech, Ltd., Shanghai, 200123, China.
| | - Wen-Xiang Cheng
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
| | - Gang Wu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Sitong Sheng
- HYK High-throughput Biotechnology Institute, Shenzhen, 518057, Guangdong, China
| | - Peng Zhang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
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13
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Paknejad N, Sapuru V, Hite RK. Structural titration reveals Ca 2+-dependent conformational landscape of the IP 3 receptor. Nat Commun 2023; 14:6897. [PMID: 37898605 PMCID: PMC10613215 DOI: 10.1038/s41467-023-42707-3] [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: 02/16/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are endoplasmic reticulum Ca2+ channels whose biphasic dependence on cytosolic Ca2+ gives rise to Ca2+ oscillations that regulate fertilization, cell division and cell death. Despite the critical roles of IP3R-mediated Ca2+ responses, the structural underpinnings of the biphasic Ca2+ dependence that underlies Ca2+ oscillations are incompletely understood. Here, we collect cryo-EM images of an IP3R with Ca2+ concentrations spanning five orders of magnitude. Unbiased image analysis reveals that Ca2+ binding does not explicitly induce conformational changes but rather biases a complex conformational landscape consisting of resting, preactivated, activated, and inhibited states. Using particle counts as a proxy for relative conformational free energy, we demonstrate that Ca2+ binding at a high-affinity site allows IP3Rs to activate by escaping a low-energy resting state through an ensemble of preactivated states. At high Ca2+ concentrations, IP3Rs preferentially enter an inhibited state stabilized by a second, low-affinity Ca2+ binding site. Together, these studies provide a mechanistic basis for the biphasic Ca2+-dependence of IP3R channel activity.
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Affiliation(s)
- Navid Paknejad
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY, 10065, USA
| | - Vinay Sapuru
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY, 10065, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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14
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Raisch T, Raunser S. The modes of action of ion-channel-targeting neurotoxic insecticides: lessons from structural biology. Nat Struct Mol Biol 2023; 30:1411-1427. [PMID: 37845413 DOI: 10.1038/s41594-023-01113-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/31/2023] [Indexed: 10/18/2023]
Abstract
Insecticides are indispensable tools for plant protection in modern agriculture. Despite having highly heterogeneous structures, many neurotoxic insecticides use similar principles to inhibit or deregulate neuronal ion channels. Insecticides targeting pentameric ligand-gated channels are structural mimetics of neurotransmitters or manipulate and deregulate the proteins. Those binding to (pseudo-)tetrameric voltage-gated(-like) channels, on the other hand, are natural or synthetic compounds that directly block the ion-conducting pore or prevent conformational changes in the transmembrane domain necessary for opening and closing the pore. The use of a limited number of inhibition mechanisms can be problematic when resistances arise and become more widespread. Therefore, there is a rising interest in the development of insecticides with novel mechanisms that evade resistance and are pest-insect-specific. During the last decade, most known insecticide targets, many with bound compounds, have been structurally characterized, bringing the rational design of novel classes of agrochemicals within closer reach than ever before.
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Affiliation(s)
- Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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15
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Dridi H, Santulli G, Bahlouli L, Miotto MC, Weninger G, Marks AR. Mitochondrial Calcium Overload Plays a Causal Role in Oxidative Stress in the Failing Heart. Biomolecules 2023; 13:1409. [PMID: 37759809 PMCID: PMC10527470 DOI: 10.3390/biom13091409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Heart failure is a serious global health challenge, affecting more than 6.2 million people in the United States and is projected to reach over 8 million by 2030. Independent of etiology, failing hearts share common features, including defective calcium (Ca2+) handling, mitochondrial Ca2+ overload, and oxidative stress. In cardiomyocytes, Ca2+ not only regulates excitation-contraction coupling, but also mitochondrial metabolism and oxidative stress signaling, thereby controlling the function and actual destiny of the cell. Understanding the mechanisms of mitochondrial Ca2+ uptake and the molecular pathways involved in the regulation of increased mitochondrial Ca2+ influx is an ongoing challenge in order to identify novel therapeutic targets to alleviate the burden of heart failure. In this review, we discuss the mechanisms underlying altered mitochondrial Ca2+ handling in heart failure and the potential therapeutic strategies.
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Affiliation(s)
- Haikel Dridi
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY 10032, USA; (L.B.); (M.C.M.); (G.W.); (A.R.M.)
| | - Gaetano Santulli
- Department of Medicine, Division of Cardiology, Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, New York, NY 10461, USA;
| | - Laith Bahlouli
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY 10032, USA; (L.B.); (M.C.M.); (G.W.); (A.R.M.)
| | - Marco C. Miotto
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY 10032, USA; (L.B.); (M.C.M.); (G.W.); (A.R.M.)
| | - Gunnar Weninger
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY 10032, USA; (L.B.); (M.C.M.); (G.W.); (A.R.M.)
| | - Andrew R. Marks
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY 10032, USA; (L.B.); (M.C.M.); (G.W.); (A.R.M.)
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16
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Tian S, Zhong X, Wang H, Wei J, Guo W, Wang R, Paul Estillore J, Napolitano C, Duff HH, Ilhan E, Knight LM, Lloyd MS, Roberts JD, Priori SG, Chen SRW. RyR2 C-terminal truncating variants identified in patients with arrhythmic phenotypes exert a dominant negative effect through formation of wildtype-truncation heteromers. Biochem J 2023; 480:1379-1395. [PMID: 37492947 DOI: 10.1042/bcj20230254] [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: 06/19/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023]
Abstract
Gain-of-function missense variants in the cardiac ryanodine receptor (RyR2) are linked to catecholaminergic polymorphic ventricular tachycardia (CPVT), whereas RyR2 loss-of-function missense variants cause Ca2+ release deficiency syndrome (CRDS). Recently, truncating variants in RyR2 have also been associated with ventricular arrhythmias (VAs) and sudden cardiac death. However, there are limited insights into the potential clinical relevance and in vitro functional impact of RyR2 truncating variants. We performed genetic screening of patients presenting with syncope, VAs, or unexplained sudden death and in vitro characterization of the expression and function of RyR2 truncating variants in HEK293 cells. We identified two previously unknown RyR2 truncating variants (Y4591Ter and R4663Ter) and one splice site variant predicted to result in a frameshift and premature termination (N4717 + 15Ter). These 3 new RyR2 truncating variants and a recently reported RyR2 truncating variant, R4790Ter, were generated and functionally characterized in vitro. Immunoprecipitation and immunoblotting analyses showed that all 4 RyR2 truncating variants formed heteromers with the RyR2-wildtype (WT) protein. Each of these C-terminal RyR2 truncations was non-functional and suppressed [3H]ryanodine binding to RyR2-WT and RyR2-WT mediated store overload induced spontaneous Ca2+ release activity in HEK293 cells. The expression of these RyR2 truncating variants in HEK293 cells was markedly reduced compared with that of the full-length RyR2 WT protein. Our data indicate that C-terminal RyR2 truncating variants are non-functional and can exert a dominant negative impact on the function of the RyR2 WT protein through formation of heteromeric WT/truncation complex.
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Affiliation(s)
- Shanshan Tian
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Xiaowei Zhong
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Hui Wang
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Jinhong Wei
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- School of Medicine, Northwest University, Xi'an 710069, China
| | - Wenting Guo
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ruiwu Wang
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - John Paul Estillore
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Carlo Napolitano
- European Reference Network 'ERN GUARD-Heart', Amsterdam, Netherlands
- Division of Cardiology and Molecular Cardiology, IRCCS Maugeri Foundation-University of Pavia, 27100 Pavia, Italy
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Henry H Duff
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Erkan Ilhan
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Linda M Knight
- Children's Healthcare of Atlanta Cardiology, Atlanta, Georgia, U.S.A
| | - Michael S Lloyd
- Emory University School of Medicine, Atlanta, Georgia, U.S.A
| | - Jason D Roberts
- Population Health Research Institute, McMaster University, and Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Silvia G Priori
- European Reference Network 'ERN GUARD-Heart', Amsterdam, Netherlands
- Division of Cardiology and Molecular Cardiology, IRCCS Maugeri Foundation-University of Pavia, 27100 Pavia, Italy
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Molecular Cardiology Laboratory, Centro de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain
| | - S R Wayne Chen
- Libin Cardiovascular Institute, Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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17
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Magyar ZÉ, Bauer J, Bauerová-Hlinková V, Jóna I, Gaburjakova J, Gaburjakova M, Almássy J. Eu 3+ detects two functionally distinct luminal Ca 2+ binding sites in ryanodine receptors. Biophys J 2023; 122:3516-3531. [PMID: 37533257 PMCID: PMC10502479 DOI: 10.1016/j.bpj.2023.07.029] [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: 02/23/2023] [Revised: 06/26/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023] Open
Abstract
Ryanodine receptors (RyRs) are Ca2+ release channels, gated by Ca2+ in the cytosol and the sarcoplasmic reticulum lumen. Their regulation is impaired in certain cardiac and muscle diseases. Although a lot of data is available on the luminal Ca2+ regulation of RyR, its interpretation is complicated by the possibility that the divalent ions used to probe the luminal binding sites may contaminate the cytoplasmic sites by crossing the channel pore. In this study, we used Eu3+, an impermeable agonist of Ca2+ binding sites, as a probe to avoid this complication and to gain more specific information about the function of the luminal Ca2+ sensor. Single-channel currents were measured from skeletal muscle and cardiac RyRs (RyR1 and RyR2) using the lipid bilayer technique. We show that RyR2 is activated by the luminal addition of Ca2+, whereas RyR1 is inhibited. These results were qualitatively reproducible using Eu3+. The luminal regulation of RyR1 carrying a mutation associated with malignant hyperthermia was not different from that of the wild-type. RyR1 inhibition by Eu3+ was extremely voltage dependent, whereas RyR2 activation did not depend on the membrane potential. These results suggest that the RyR1 inhibition site is in the membrane's electric field (channel pore), whereas the RyR2 activation site is outside. Using in silico analysis and previous results, we predicted putative Ca2+ binding site sequences. We propose that RyR2 bears an activation site, which is missing in RyR1, but both isoforms share the same inhibitory Ca2+ binding site near the channel gate.
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Affiliation(s)
- Zsuzsanna É Magyar
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jacob Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - István Jóna
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jana Gaburjakova
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marta Gaburjakova
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, Slovakia
| | - János Almássy
- Department of Physiology, Semmelweis University, Budapest, Hungary.
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18
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Sun Y, Liu ST, Ling Y, Wang L, Ni H, Guo D, Dong BB, Huang Q, Long LP, Zhang S, Wu SF, Gao CF. Insecticide resistance monitoring of Cnaphalocrocis medinalis (Lepidoptera: Pyralidae) and its mechanism to chlorantraniliprole. PEST MANAGEMENT SCIENCE 2023; 79:3290-3299. [PMID: 37127919 DOI: 10.1002/ps.7512] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/30/2023] [Accepted: 05/02/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The rice leaffolder, Cnaphalocrocis medinalis (Guenée), has become an increasingly occurring pest in Asia in recent years. Chemical control remains the most efficient and primary tool for controlling this pest. In this study, we report the resistance status of C. medinalis in China to multiple insecticides including chlorantraniliprole and the main resistance mechanism. RESULTS Significant variations among field populations of C. medinalis in their resistance to 10 insecticides were observed during 2019-2022. Most of the tested field populations have developed low-to-moderate levels of resistance to abamectin (RR = 2.4-22.2), emamectin benzoate (RR = 1.9-40.3) and spinetoram (RR = 4.2-24.8). Some field populations have developed low resistance to chlorpyrifos (RR = 0.9-6.8). Indoxacarb, metaflumizone, methoxenozide and Bacillus thuringiensis (Bt) potency against all tested populations remained similar. For diamides, significantly higher levels of resistance to chlorantraniliprole (RR = 64.9-113.7) were observed in 2022, whereas all tested field populations in 2019-2021 exhibited susceptible or moderate resistance level to chlorantraniliprole (RR = 1.3-22.1). Cross-resistance between chlorantraniliprole and tetraniliprole was significant. Analysis of ryanodine receptor (RyR) mutations showed that mutation of I4712M was present in resistant populations of C. medinalis with different levels of chlorantraniliprole resistance and was the main mechanism conferring diamide resistance. Mutation of Y4621D also was detected in one tested population. Resistance management strategies for the control of C. medinalis are discussed. CONCLUSION C. medinalis has developed high level of resistance to chlorantraniliprole. RyR mutations were deemed as the mechanism. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yu Sun
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Si-Tong Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Yunnan Agricultural Reclamation Industry Research Institute Co., Ltd., Kunming, China
| | - Yan Ling
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Nanning, China
| | - Li Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Huan Ni
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Di Guo
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Bei-Bei Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qian Huang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Nanning, China
| | - Li-Ping Long
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Nanning, China
| | - Shuai Zhang
- Ministry of Agriculture, National Agro-tech Extension and Service Center, Beijing, China
| | - Shun-Fan Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Cong-Fen Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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19
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Fréchard A, Faux C, Hexnerova R, Crucifix C, Papai G, Smirnova E, McKeon C, Ping FLY, Helmlinger D, Schultz P, Ben-Shem A. The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification. Nat Struct Mol Biol 2023; 30:1337-1345. [PMID: 37550452 DOI: 10.1038/s41594-023-01056-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
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Affiliation(s)
- Alexander Fréchard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Céline Faux
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Rozalie Hexnerova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Corinne Crucifix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Gabor Papai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Ekaterina Smirnova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Conor McKeon
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Florie Lo Ying Ping
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Dominique Helmlinger
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France.
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France.
| | - Adam Ben-Shem
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France.
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20
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Walweel K, Beard N, van Helden DF, Laver DR. Dantrolene inhibition of ryanodine channels (RyR2) in artificial lipid bilayers depends on FKBP12.6. J Gen Physiol 2023; 155:e202213277. [PMID: 37279522 PMCID: PMC10244881 DOI: 10.1085/jgp.202213277] [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: 10/10/2022] [Revised: 03/18/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
Dantrolene is a neutral hydantoin that is clinically used as a skeletal muscle relaxant to prevent overactivation of the skeletal muscle calcium release channel (RyR1) in response to volatile anesthetics. Dantrolene has aroused considerable recent interest as a lead compound for stabilizing calcium release due to overactive cardiac calcium release channels (RyR2) in heart failure. Previously, we found that dantrolene produces up to a 45% inhibition RyR2 with an IC50 of 160 nM, and that this inhibition requires the physiological association between RyR2 and CaM. In this study, we tested the hypothesis that dantrolene inhibition of RyR2 in the presence of CaM is modulated by RyR2 phosphorylation at S2808 and S2814. Phosphorylation was altered by incubations with either exogenous phosphatase (PP1) or kinases; PKA to phosphorylate S2808 or endogenous CaMKII to phosphorylate S2814. We found that PKA caused selective dissociation of FKBP12.6 from the RyR2 complex and a loss of dantrolene inhibition. Rapamycin-induced FKBP12.6 dissociation from RyR2 also resulted in the loss of dantrolene inhibition. Subsequent incubations of RyR2 with exogenous FKBP12.6 reinstated dantrolene inhibition. These findings indicate that the inhibitory action of dantrolene on RyR2 depends on RyR2 association with FKBP12.6 in addition to CaM as previously found.
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Affiliation(s)
- Kafa Walweel
- School of Biomedical Sciences and Pharmacy, University of Newcastle and Hunter Medical Research Institute, Callaghan, Australia
| | - Nicole Beard
- Faculty of Science and Technology, University of Canberra, Bruce, Australia
| | - Dirk F. van Helden
- School of Biomedical Sciences and Pharmacy, University of Newcastle and Hunter Medical Research Institute, Callaghan, Australia
| | - Derek R. Laver
- School of Biomedical Sciences and Pharmacy, University of Newcastle and Hunter Medical Research Institute, Callaghan, Australia
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21
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Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2302471120. [PMID: 37487103 PMCID: PMC10401002 DOI: 10.1073/pnas.2302471120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor templates that enable efficient tagging of endogenous proteins with affinity tags by transient transfection and selection of genome-edited cells in various human cell lines. Combined with technological advancements in single-particle cryogenic electron microscopy, this strategy allows efficient structural studies of endogenous proteins captured in their native cellular environment and during different cellular processes. We demonstrated this strategy by tagging six different human proteins in both HEK293T and Jurkat cells. Moreover, analysis of endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in HEK293T cells allowed us to follow its behavior spatially and temporally in response to prolonged oxidative stress, correlating the increased number of oxidation-induced inactive catalytic sites in GAPDH with its translocation from cytosol to nucleus.
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Affiliation(s)
- Wooyoung Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Klaus Yserentant
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
- HHMI, University of California, San Francisco, CA94143
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22
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Chen GL, Li J, Zhang J, Zeng B. To Be or Not to Be an Ion Channel: Cryo-EM Structures Have a Say. Cells 2023; 12:1870. [PMID: 37508534 PMCID: PMC10378246 DOI: 10.3390/cells12141870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Ion channels are the second largest class of drug targets after G protein-coupled receptors. In addition to well-recognized ones like voltage-gated Na/K/Ca channels in the heart and neurons, novel ion channels are continuously discovered in both excitable and non-excitable cells and demonstrated to play important roles in many physiological processes and diseases such as developmental disorders, neurodegenerative diseases, and cancer. However, in the field of ion channel discovery, there are an unignorable number of published studies that are unsolid and misleading. Despite being the gold standard of a functional assay for ion channels, electrophysiological recordings are often accompanied by electrical noise, leak conductance, and background currents of the membrane system. These unwanted signals, if not treated properly, lead to the mischaracterization of proteins with seemingly unusual ion-conducting properties. In the recent ten years, the technical revolution of cryo-electron microscopy (cryo-EM) has greatly advanced our understanding of the structures and gating mechanisms of various ion channels and also raised concerns about the pore-forming ability of some previously identified channel proteins. In this review, we summarize cryo-EM findings on ion channels with molecular identities recognized or disputed in recent ten years and discuss current knowledge of proposed channel proteins awaiting cryo-EM analyses. We also present a classification of ion channels according to their architectures and evolutionary relationships and discuss the possibility and strategy of identifying more ion channels by analyzing structures of transmembrane proteins of unknown function. We propose that cross-validation by electrophysiological and structural analyses should be essentially required for determining molecular identities of novel ion channels.
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Affiliation(s)
- Gui-Lan Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Bo Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
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23
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Richardson SJ, Thekkedam CG, Casarotto MG, Beard NA, Dulhunty AF. FKBP12 binds to the cardiac ryanodine receptor with negative cooperativity: implications for heart muscle physiology in health and disease. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220169. [PMID: 37122219 PMCID: PMC10150220 DOI: 10.1098/rstb.2022.0169] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Cardiac ryanodine receptors (RyR2) release the Ca2+ from intracellular stores that is essential for cardiac myocyte contraction. The ion channel opening is tightly regulated by intracellular factors, including the FK506 binding proteins, FKBP12 and FKBP12.6. The impact of these proteins on RyR2 activity and cardiac contraction is debated, with often apparently contradictory experimental results, particularly for FKBP12. The isoform that regulates RyR2 has generally been considered to be FKBP12.6, despite the fact that FKBP12 is the major isoform associated with RyR2 in some species and is bound in similar proportions to FKBP12.6 in others, including sheep and humans. Here, we show time- and concentration-dependent effects of adding FKBP12 to RyR2 channels that were partly depleted of FKBP12/12.6 during isolation. The added FKBP12 displaced most remaining endogenous FKBP12/12.6. The results suggest that FKBP12 activates RyR2 with high affinity and inhibits RyR2 with lower affinity, consistent with a model of negative cooperativity in FKBP12 binding to each of the four subunits in the RyR tetramer. The easy dissociation of some FKBP12/12.6 could dynamically alter RyR2 activity in response to changes in in vivo regulatory factors, indicating a significant role for FKBP12/12.6 in Ca2+ signalling and cardiac function in healthy and diseased hearts. This article is part of the theme issue 'The heartbeat: its molecular basis and physiological mechanisms'.
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Affiliation(s)
- S J Richardson
- John Curtin School of Medical Research, Australian National University, Canberra, Australia, Australian Capital Territory 2601, Australia
| | - C G Thekkedam
- John Curtin School of Medical Research, Australian National University, Canberra, Australia, Australian Capital Territory 2601, Australia
| | - M G Casarotto
- John Curtin School of Medical Research, Australian National University, Canberra, Australia, Australian Capital Territory 2601, Australia
| | - N A Beard
- John Curtin School of Medical Research, Australian National University, Canberra, Australia, Australian Capital Territory 2601, Australia
| | - A F Dulhunty
- John Curtin School of Medical Research, Australian National University, Canberra, Australia, Australian Capital Territory 2601, Australia
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24
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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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25
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Dixon RE, Trimmer JS. Endoplasmic Reticulum-Plasma Membrane Junctions as Sites of Depolarization-Induced Ca 2+ Signaling in Excitable Cells. Annu Rev Physiol 2023; 85:217-243. [PMID: 36202100 PMCID: PMC9918718 DOI: 10.1146/annurev-physiol-032122-104610] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane contact sites between endoplasmic reticulum (ER) and plasma membrane (PM), or ER-PM junctions, are found in all eukaryotic cells. In excitable cells they play unique roles in organizing diverse forms of Ca2+ signaling as triggered by membrane depolarization. ER-PM junctions underlie crucial physiological processes such as excitation-contraction coupling, smooth muscle contraction and relaxation, and various forms of activity-dependent signaling and plasticity in neurons. In many cases the structure and molecular composition of ER-PM junctions in excitable cells comprise important regulatory feedback loops linking depolarization-induced Ca2+ signaling at these sites to the regulation of membrane potential. Here, we describe recent findings on physiological roles and molecular composition of native ER-PM junctions in excitable cells. We focus on recent studies that provide new insights into canonical forms of depolarization-induced Ca2+ signaling occurring at junctional triads and dyads of striated muscle, as well as the diversity of ER-PM junctions in these cells and in smooth muscle and neurons.
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Affiliation(s)
- Rose E Dixon
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, California, USA;
| | - James S Trimmer
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, California, USA;
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26
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Abstract
This Review provides an update on ryanodine receptors (RyRs) and their role in human diseases of heart, muscle, and brain. Calcium (Ca2+) is a requisite second messenger in all living organisms. From C. elegans to mammals, Ca2+ is necessary for locomotion, bodily functions, and neural activity. However, too much of a good thing can be bad. Intracellular Ca2+ overload can result in loss of function and death. Intracellular Ca2+ release channels evolved to safely provide large, rapid Ca2+ signals without exposure to toxic extracellular Ca2+. RyRs are intracellular Ca2+ release channels present throughout the zoosphere. Over the past 35 years, our knowledge of RyRs has advanced to the level of atomic-resolution structures revealing their role in the mechanisms underlying the pathogenesis of human disorders of heart, muscle, and brain. Stress-induced RyR-mediated intracellular Ca2+ leak in the heart can promote heart failure and cardiac arrhythmias. In skeletal muscle, RyR1 leak contributes to muscle weakness in inherited myopathies, to age-related loss of muscle function and cancer-associated muscle weakness, and to impaired muscle function in muscular dystrophies, including Duchenne. In the brain, leaky RyR channels contribute to cognitive dysfunction in Alzheimer's disease, posttraumatic stress disorder, and Huntington's disease. Novel therapeutics targeting dysfunctional RyRs are showing promise.
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27
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Campiglio M, Dyrda A, Tuinte WE, Török E. Ca V1.1 Calcium Channel Signaling Complexes in Excitation-Contraction Coupling: Insights from Channelopathies. Handb Exp Pharmacol 2023; 279:3-39. [PMID: 36592225 DOI: 10.1007/164_2022_627] [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] [Indexed: 01/03/2023]
Abstract
In skeletal muscle, excitation-contraction (EC) coupling relies on the mechanical coupling between two ion channels: the L-type voltage-gated calcium channel (CaV1.1), located in the sarcolemma and functioning as the voltage sensor of EC coupling, and the ryanodine receptor 1 (RyR1), located on the sarcoplasmic reticulum serving as the calcium release channel. To this day, the molecular mechanism by which these two ion channels are linked remains elusive. However, recently, skeletal muscle EC coupling could be reconstituted in heterologous cells, revealing that only four proteins are essential for this process: CaV1.1, RyR1, and the cytosolic proteins CaVβ1a and STAC3. Due to the crucial role of these proteins in skeletal muscle EC coupling, any mutation that affects any one of these proteins can have devastating consequences, resulting in congenital myopathies and other pathologies.Here, we summarize the current knowledge concerning these four essential proteins and discuss the pathophysiology of the CaV1.1, RyR1, and STAC3-related skeletal muscle diseases with an emphasis on the molecular mechanisms. Being part of the same signalosome, mutations in different proteins often result in congenital myopathies with similar symptoms or even in the same disease.
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Affiliation(s)
- Marta Campiglio
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria.
| | - Agnieszka Dyrda
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
| | - Wietske E Tuinte
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
| | - Enikő Török
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
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28
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Wang ZW, Riaz S, Niu L. Roles and Sources of Calcium in Synaptic Exocytosis. ADVANCES IN NEUROBIOLOGY 2023; 33:139-170. [PMID: 37615866 DOI: 10.1007/978-3-031-34229-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Calcium ions (Ca2+) play a critical role in triggering neurotransmitter release. The rate of release is directly related to the concentration of Ca2+ at the presynaptic site, with a supralinear relationship. There are two main sources of Ca2+ that trigger synaptic vesicle fusion: influx through voltage-gated Ca2+ channels in the plasma membrane and release from the endoplasmic reticulum via ryanodine receptors. This chapter will cover the sources of Ca2+ at the presynaptic nerve terminal, the relationship between neurotransmitter release rate and Ca2+ concentration, and the mechanisms that achieve the necessary Ca2+ concentrations for triggering synaptic exocytosis at the presynaptic site.
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Affiliation(s)
- Zhao-Wen Wang
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA.
| | - Sadaf Riaz
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Longgang Niu
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
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29
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Greene D, Barton M, Luchko T, Shiferaw Y. Molecular Dynamics Simulations of the Cardiac Ryanodine Receptor Type 2 (RyR2) Gating Mechanism. J Phys Chem B 2022; 126:9790-9809. [PMID: 36384028 PMCID: PMC9720719 DOI: 10.1021/acs.jpcb.2c03031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to fatal cardiac arrhythmias such as catecholaminergic polymorphic ventricular tachycardia (CPVT). While many CPVT mutations are associated with an increase in Ca2+ leak from the sarcoplasmic reticulum, the mechanistic details of RyR2 channel gating are not well understood, and this poses a barrier in the development of new pharmacological treatments. To address this, we explore the gating mechanism of the RyR2 using molecular dynamics (MD) simulations. We test the effect of changing the conformation of certain structural elements by constructing chimera RyR2 structures that are derived from the currently available closed and open cryo-electron microscopy (cryo-EM) structures, and we then use MD simulations to relax the system. Our key finding is that the position of the S4-S5 linker (S4S5L) on a single subunit can determine whether the channel as a whole is open or closed. Our analysis reveals that the position of the S4S5L is regulated by interactions with the U-motif on the same subunit and with the S6 helix on an adjacent subunit. We find that, in general, channel gating is crucially dependent on high percent occupancy interactions between adjacent subunits. We compare our interaction analysis to 49 CPVT1 mutations in the literature and find that 73% appear near a high percent occupancy interaction between adjacent subunits. This suggests that disruption of cooperative, high percent occupancy interactions between adjacent subunits is a primary cause of channel leak and CPVT in mutant RyR2 channels.
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30
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Yan X, Pei K, Guan Z, Liu F, Yan J, Jin X, Wang Q, Hou M, Tang C, Yin P. AI-empowered integrative structural characterization of m 6A methyltransferase complex. Cell Res 2022; 32:1124-1127. [PMID: 36357785 PMCID: PMC9715571 DOI: 10.1038/s41422-022-00741-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/12/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xuhui Yan
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Kai Pei
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Peking University, Beijing, China
| | - Zeyuan Guan
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Feiqing Liu
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Junjun Yan
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Xiaohuan Jin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Qiang Wang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Mengjun Hou
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
| | - Chun Tang
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Peking University, Beijing, China
| | - Ping Yin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei China
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31
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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32
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Tsuboi Y, Oyama K, Kobirumaki-Shimozawa F, Murayama T, Kurebayashi N, Tachibana T, Manome Y, Kikuchi E, Noguchi S, Inoue T, Inoue YU, Nishino I, Mori S, Ishida R, Kagechika H, Suzuki M, Fukuda N, Yamazawa T. Mice with R2509C-RYR1 mutation exhibit dysfunctional Ca2+ dynamics in primary skeletal myocytes. J Gen Physiol 2022; 154:213526. [PMID: 36200983 PMCID: PMC9546722 DOI: 10.1085/jgp.202213136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/22/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Type 1 ryanodine receptor (RYR1) is a Ca2+ release channel in the sarcoplasmic reticulum (SR) of the skeletal muscle and plays a critical role in excitation-contraction coupling. Mutations in RYR1 cause severe muscle diseases, such as malignant hyperthermia, a disorder of Ca2+-induced Ca2+ release (CICR) through RYR1 from the SR. We recently reported that volatile anesthetics induce malignant hyperthermia (MH)-like episodes through enhanced CICR in heterozygous R2509C-RYR1 mice. However, the characterization of Ca2+ dynamics has yet to be investigated in skeletal muscle cells from homozygous mice because these animals die in utero. In the present study, we generated primary cultured skeletal myocytes from R2509C-RYR1 mice. No differences in cellular morphology were detected between wild type (WT) and mutant myocytes. Spontaneous Ca2+ transients and cellular contractions occurred in WT and heterozygous myocytes, but not in homozygous myocytes. Electron microscopic observation revealed that the sarcomere length was shortened to ∼1.7 µm in homozygous myocytes, as compared to ∼2.2 and ∼2.3 µm in WT and heterozygous myocytes, respectively. Consistently, the resting intracellular Ca2+ concentration was higher in homozygous myocytes than in WT or heterozygous myocytes, which may be coupled with a reduced Ca2+ concentration in the SR. Finally, using infrared laser-based microheating, we found that heterozygous myocytes showed larger heat-induced Ca2+ transients than WT myocytes. Our findings suggest that the R2509C mutation in RYR1 causes dysfunctional Ca2+ dynamics in a mutant-gene dose-dependent manner in the skeletal muscles, in turn provoking MH-like episodes and embryonic lethality in heterozygous and homozygous mice, respectively.
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Affiliation(s)
- Yoshitaka Tsuboi
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, Japan.,Department of Molecular Physiology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kotaro Oyama
- Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Gunma, Japan.,Department of Cell Physiology, The Jikei University School of Medicine, Tokyo, Japan
| | | | - Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nagomi Kurebayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshiaki Tachibana
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshinobu Manome
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, Japan
| | - Emi Kikuchi
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Shuichi Mori
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryosuke Ishida
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Norio Fukuda
- Department of Cell Physiology, The Jikei University School of Medicine, Tokyo, Japan
| | - Toshiko Yamazawa
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, Japan.,Department of Molecular Physiology, The Jikei University School of Medicine, Tokyo, Japan
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33
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Zhang Y, Rabesahala de Meritens C, Beckmann A, Lai FA, Zissimopoulos S. Defective ryanodine receptor N-terminus inter-subunit interaction is a common mechanism in neuromuscular and cardiac disorders. Front Physiol 2022; 13:1032132. [PMID: 36311249 PMCID: PMC9597452 DOI: 10.3389/fphys.2022.1032132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/28/2022] [Indexed: 07/28/2023] Open
Abstract
The ryanodine receptor (RyR) is a homotetrameric channel mediating sarcoplasmic reticulum Ca2+ release required for skeletal and cardiac muscle contraction. Mutations in RyR1 and RyR2 lead to life-threatening malignant hyperthermia episodes and ventricular tachycardia, respectively. In this brief report, we use chemical cross-linking to demonstrate that pathogenic RyR1 R163C and RyR2 R169Q mutations reduce N-terminus domain (NTD) tetramerization. Introduction of positively-charged residues (Q168R, M399R) in the NTD-NTD inter-subunit interface normalizes RyR2-R169Q NTD tetramerization. These results indicate that perturbation of NTD-NTD inter-subunit interactions is an underlying molecular mechanism in both RyR1 and RyR2 pathophysiology. Importantly, our data provide proof of concept that stabilization of this critical RyR1/2 structure-function parameter offers clear therapeutic potential.
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Affiliation(s)
- Yadan Zhang
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | | | - Astrid Beckmann
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - F. Anthony Lai
- College of Medicine and Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Spyros Zissimopoulos
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
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Rossi D, Catallo MR, Pierantozzi E, Sorrentino V. Mutations in proteins involved in E-C coupling and SOCE and congenital myopathies. J Gen Physiol 2022; 154:213407. [PMID: 35980353 PMCID: PMC9391951 DOI: 10.1085/jgp.202213115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
In skeletal muscle, Ca2+ necessary for muscle contraction is stored and released from the sarcoplasmic reticulum (SR), a specialized form of endoplasmic reticulum through the mechanism known as excitation–contraction (E-C) coupling. Following activation of skeletal muscle contraction by the E-C coupling mechanism, replenishment of intracellular stores requires reuptake of cytosolic Ca2+ into the SR by the activity of SR Ca2+-ATPases, but also Ca2+ entry from the extracellular space, through a mechanism called store-operated calcium entry (SOCE). The fine orchestration of these processes requires several proteins, including Ca2+ channels, Ca2+ sensors, and Ca2+ buffers, as well as the active involvement of mitochondria. Mutations in genes coding for proteins participating in E-C coupling and SOCE are causative of several myopathies characterized by a wide spectrum of clinical phenotypes, a variety of histological features, and alterations in intracellular Ca2+ balance. This review summarizes current knowledge on these myopathies and discusses available knowledge on the pathogenic mechanisms of disease.
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Affiliation(s)
- Daniela Rossi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy.,Interdepartmental Program of Molecular Diagnosis and Pathogenetic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliero Universitaria Senese, Siena, Italy
| | - Maria Rosaria Catallo
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Enrico Pierantozzi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Vincenzo Sorrentino
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy.,Interdepartmental Program of Molecular Diagnosis and Pathogenetic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliero Universitaria Senese, Siena, Italy
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Bolaños P, Calderón JC. Excitation-contraction coupling in mammalian skeletal muscle: Blending old and last-decade research. Front Physiol 2022; 13:989796. [PMID: 36117698 PMCID: PMC9478590 DOI: 10.3389/fphys.2022.989796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The excitation–contraction coupling (ECC) in skeletal muscle refers to the Ca2+-mediated link between the membrane excitation and the mechanical contraction. The initiation and propagation of an action potential through the membranous system of the sarcolemma and the tubular network lead to the activation of the Ca2+-release units (CRU): tightly coupled dihydropyridine and ryanodine (RyR) receptors. The RyR gating allows a rapid, massive, and highly regulated release of Ca2+ from the sarcoplasmic reticulum (SR). The release from triadic places generates a sarcomeric gradient of Ca2+ concentrations ([Ca2+]) depending on the distance of a subcellular region from the CRU. Upon release, the diffusing Ca2+ has multiple fates: binds to troponin C thus activating the contractile machinery, binds to classical sarcoplasmic Ca2+ buffers such as parvalbumin, adenosine triphosphate and, experimentally, fluorescent dyes, enters the mitochondria and the SR, or is recycled through the Na+/Ca2+ exchanger and store-operated Ca2+ entry (SOCE) mechanisms. To commemorate the 7th decade after being coined, we comprehensively and critically reviewed “old”, historical landmarks and well-established concepts, and blended them with recent advances to have a complete, quantitative-focused landscape of the ECC. We discuss the: 1) elucidation of the CRU structures at near-atomic resolution and its implications for functional coupling; 2) reliable quantification of peak sarcoplasmic [Ca2+] using fast, low affinity Ca2+ dyes and the relative contributions of the Ca2+-binding mechanisms to the whole concert of Ca2+ fluxes inside the fibre; 3) articulation of this novel quantitative information with the unveiled structural details of the molecular machinery involved in mitochondrial Ca2+ handing to understand how and how much Ca2+ enters the mitochondria; 4) presence of the SOCE machinery and its different modes of activation, which awaits understanding of its magnitude and relevance in situ; 5) pharmacology of the ECC, and 6) emerging topics such as the use and potential applications of super-resolution and induced pluripotent stem cells (iPSC) in ECC. Blending the old with the new works better!
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Affiliation(s)
- Pura Bolaños
- Laboratory of Cellular Physiology, Centre of Biophysics and Biochemistry, Venezuelan Institute for Scientific Research (IVIC), Caracas, Venezuela
| | - Juan C. Calderón
- Physiology and Biochemistry Research Group-PHYSIS, Faculty of Medicine, University of Antioquia, Medellín, Colombia
- *Correspondence: Juan C. Calderón,
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Ishida R, Mori S, Murayama T, Nakamichi A, Chai X, Kurebayashi N, Iinuma H, Kagechika H. Development of a water-soluble ryanodine receptor 1 inhibitor. Bioorg Med Chem 2022; 74:117027. [DOI: 10.1016/j.bmc.2022.117027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022]
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Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Proc Natl Acad Sci U S A 2022; 119:e2207200119. [PMID: 35858375 PMCID: PMC9388094 DOI: 10.1073/pnas.2207200119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.
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Molecular, Subcellular, and Arrhythmogenic Mechanisms in Genetic RyR2 Disease. Biomolecules 2022; 12:biom12081030. [PMID: 35892340 PMCID: PMC9394283 DOI: 10.3390/biom12081030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
The ryanodine receptor (RyR2) has a critical role in controlling Ca2+ release from the sarcoplasmic reticulum (SR) throughout the cardiac cycle. RyR2 protein has multiple functional domains with specific roles, and four of these RyR2 protomers are required to form the quaternary structure that comprises the functional channel. Numerous mutations in the gene encoding RyR2 protein have been identified and many are linked to a wide spectrum of arrhythmic heart disease. Gain of function mutations (GoF) result in a hyperactive channel that causes excessive spontaneous SR Ca2+ release. This is the predominant cause of the inherited syndrome catecholaminergic polymorphic ventricular tachycardia (CPVT). Recently, rare hypoactive loss of function (LoF) mutations have been identified that produce atypical effects on cardiac Ca2+ handling that has been termed calcium release deficiency syndrome (CRDS). Aberrant Ca2+ release resulting from both GoF and LoF mutations can result in arrhythmias through the Na+/Ca2+ exchange mechanism. This mini-review discusses recent findings regarding the role of RyR2 domains and endogenous regulators that influence RyR2 gating normally and with GoF/LoF mutations. The arrhythmogenic consequences of GoF/LoF mutations will then be discussed at the macromolecular and cellular level.
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Miotto MC, Weninger G, Dridi H, Yuan Q, Liu Y, Wronska A, Melville Z, Sittenfeld L, Reiken S, Marks AR. Structural analyses of human ryanodine receptor type 2 channels reveal the mechanisms for sudden cardiac death and treatment. SCIENCE ADVANCES 2022; 8:eabo1272. [PMID: 35857850 PMCID: PMC9299551 DOI: 10.1126/sciadv.abo1272] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/03/2022] [Indexed: 05/29/2023]
Abstract
Ryanodine receptor type 2 (RyR2) mutations have been linked to an inherited form of exercise-induced sudden cardiac death called catecholaminergic polymorphic ventricular tachycardia (CPVT). CPVT results from stress-induced sarcoplasmic reticular Ca2+ leak via the mutant RyR2 channels during diastole. We present atomic models of human wild-type (WT) RyR2 and the CPVT mutant RyR2-R2474S determined by cryo-electron microscopy with overall resolutions in the range of 2.6 to 3.6 Å, and reaching local resolutions of 2.25 Å, unprecedented for RyR2 channels. Under nonactivating conditions, the RyR2-R2474S channel is in a "primed" state between the closed and open states of WT RyR2, rendering it more sensitive to activation that results in stress-induced Ca2+ leak. The Rycal drug ARM210 binds to RyR2-R2474S, reverting the primed state toward the closed state. Together, these studies provide a mechanism for CPVT and for the therapeutic actions of ARM210.
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Affiliation(s)
- Marco C. Miotto
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Gunnar Weninger
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Haikel Dridi
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Qi Yuan
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Yang Liu
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Anetta Wronska
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Zephan Melville
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Leah Sittenfeld
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Steven Reiken
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
| | - Andrew R. Marks
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA
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40
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Hadiatullah H, He Z, Yuchi Z. Structural Insight Into Ryanodine Receptor Channelopathies. Front Pharmacol 2022; 13:897494. [PMID: 35677449 PMCID: PMC9168041 DOI: 10.3389/fphar.2022.897494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
The ryanodine receptors (RyRs) are large cation-selective ligand-gated channels that are expressed in the sarcoplasmic reticulum (SR) membrane. They mediate the controlled release of Ca2+ from SR and play an important role in many cellular processes. The mutations in RyRs are associated with several skeletal muscle and cardiac conditions, including malignant hyperthermia (MH), central core disease (CCD), catecholaminergic polymorphic ventricular tachycardia (CPVT), and arrhythmogenic right ventricular dysplasia (ARVD). Recent breakthroughs in structural biology including cryo-electron microscopy (EM) and X-ray crystallography allowed the determination of a number of near-atomic structures of RyRs, including wildtype and mutant structures as well as the structures in complex with different modulating molecules. This allows us to comprehend the physiological gating and regulatory mechanisms of RyRs and the underlying pathological mechanisms of the disease-causing mutations. In this review, based on the insights gained from the available high-resolution structures of RyRs, we address several questions: 1) what are the gating mechanisms of different RyR isoforms; 2) how RyRs are regulated by multiple channel modulators, including ions, small molecules, and regulatory proteins; 3) how do disease-causing mutations affect the structure and function of RyRs; 4) how can these structural information aid in the diagnosis of the related diseases and the development of pharmacological therapies.
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Affiliation(s)
- Hadiatullah Hadiatullah
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Molecular Pharmacology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhao He
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Molecular Pharmacology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Molecular Pharmacology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- *Correspondence: Zhiguang Yuchi,
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Kobayashi T, Tsutsumi A, Kurebayashi N, Saito K, Kodama M, Sakurai T, Kikkawa M, Murayama T, Ogawa H. Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations. Nat Commun 2022; 13:2821. [PMID: 35595836 PMCID: PMC9123176 DOI: 10.1038/s41467-022-30429-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Cardiac ryanodine receptor (RyR2) is a large Ca2+ release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca2+ and RyR2 mutations are implicated in severe arrhythmogenic diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remains unknown. Here, we address the gating mechanism of RyR2 by combining high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated two fundamental mechanisms for channel gating: interactions close to the channel pore stabilize the channel to prevent hyperactivity and a series of interactions in the surrounding regions is necessary for channel opening upon Ca2+ binding. Mutations at the residues involved in the former and the latter mechanisms cause gain-of-function and loss-of-function, respectively. Our results reveal gating mechanisms of the RyR2 channel and alterations by pathogenic mutations at the atomic level. Ryanodine receptor 2 (RyR2) is a Ca2+ release channel essential for cardiac excitation-contraction coupling. Here, the authors use structural and functional analysis to reveal RyR2 gating mechanism and its alterations by pathogenic mutations.
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Affiliation(s)
- Takuya Kobayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nagomi Kurebayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kei Saito
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Masami Kodama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Sakurai
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Haruo Ogawa
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
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Yan W, Cao M, Ruan X, Jiang L, Lee S, Lemanek A, Ghassemian M, Pizzo DP, Wan Y, Qiao Y, Chin AR, Duggan E, Wang D, Nolan JP, Esko JD, Schenk S, Wang SE. Cancer-cell-secreted miR-122 suppresses O-GlcNAcylation to promote skeletal muscle proteolysis. Nat Cell Biol 2022; 24:793-804. [PMID: 35469018 PMCID: PMC9107513 DOI: 10.1038/s41556-022-00893-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/10/2022] [Indexed: 01/18/2023]
Abstract
A decline in skeletal muscle mass and low muscular strength are prognostic factors in advanced human cancers. Here we found that breast cancer suppressed O-linked N-acetylglucosamine (O-GlcNAc) protein modification in muscle through extracellular-vesicle-encapsulated miR-122, which targets O-GlcNAc transferase (OGT). Mechanistically, O-GlcNAcylation of ryanodine receptor 1 (RYR1) competed with NEK10-mediated phosphorylation and increased K48-linked ubiquitination and proteasomal degradation; the miR-122-mediated decrease in OGT resulted in increased RYR1 abundance. We further found that muscular protein O-GlcNAcylation was regulated by hypoxia and lactate through HIF1A-dependent OGT promoter activation and was elevated after exercise. Suppressed O-GlcNAcylation in the setting of cancer, through increasing RYR1, led to higher cytosolic Ca2+ and calpain protease activation, which triggered cleavage of desmin filaments and myofibrillar destruction. This was associated with reduced skeletal muscle mass and contractility in tumour-bearing mice. Our findings link O-GlcNAcylation to muscular protein homoeostasis and contractility and reveal a mechanism of cancer-associated muscle dysregulation.
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Affiliation(s)
- Wei Yan
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
| | - Minghui Cao
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Xianhui Ruan
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Li Jiang
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Sylvia Lee
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Adriana Lemanek
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California, San Diego, La Jolla, CA, USA
| | - Donald P Pizzo
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Yuhao Wan
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Yueqing Qiao
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Andrew R Chin
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | | | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, CA, USA.
| | - Shizhen Emily Wang
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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Fusto A, Cassandrini D, Fiorillo C, Codemo V, Astrea G, D’Amico A, Maggi L, Magri F, Pane M, Tasca G, Sabbatini D, Bello L, Battini R, Bernasconi P, Fattori F, Bertini ES, Comi G, Messina S, Mongini T, Moroni I, Panicucci C, Berardinelli A, Donati A, Nigro V, Pini A, Giannotta M, Dosi C, Ricci E, Mercuri E, Minervini G, Tosatto S, Santorelli F, Bruno C, Pegoraro E. Expanding the clinical-pathological and genetic spectrum of RYR1-related congenital myopathies with cores and minicores: an Italian population study. Acta Neuropathol Commun 2022; 10:54. [PMID: 35428369 PMCID: PMC9013059 DOI: 10.1186/s40478-022-01357-0] [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: 02/03/2022] [Accepted: 03/25/2022] [Indexed: 11/10/2022] Open
Abstract
Mutations in the RYR1 gene, encoding ryanodine receptor 1 (RyR1), are a well-known cause of Central Core Disease (CCD) and Multi-minicore Disease (MmD). We screened a cohort of 153 patients carrying an histopathological diagnosis of core myopathy (cores and minicores) for RYR1 mutation. At least one RYR1 mutation was identified in 69 of them and these patients were further studied. Clinical and histopathological features were collected. Clinical phenotype was highly heterogeneous ranging from asymptomatic or paucisymptomatic hyperCKemia to severe muscle weakness and skeletal deformity with loss of ambulation. Sixty-eight RYR1 mutations, generally missense, were identified, of which 16 were novel. The combined analysis of the clinical presentation, disease progression and the structural bioinformatic analyses of RYR1 allowed to associate some phenotypes to mutations in specific domains. In addition, this study highlighted the structural bioinformatics potential in the prediction of the pathogenicity of RYR1 mutations. Further improvement in the comprehension of genotype-phenotype relationship of core myopathies can be expected in the next future: the actual lack of the human RyR1 crystal structure paired with the presence of large intrinsically disordered regions in RyR1, and the frequent presence of more than one RYR1 mutation in core myopathy patients, require designing novel investigation strategies to completely address RyR1 mutation effect.
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Molza AE, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Front Mol Biosci 2022; 9:826136. [PMID: 35480882 PMCID: PMC9035671 DOI: 10.3389/fmolb.2022.826136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.
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Affiliation(s)
- Anne-Elisabeth Molza
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Yvonne Westermaier
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | - Pierre Ducrot
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA, United States
| | - Charles H. Robert
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Chantal Prévost
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
- *Correspondence: Chantal Prévost ,
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Abstract
NALCN regulates the resting membrane potential by mediating the Na+ leak current in neurons, and it functions as a channelosome in complex with FAM155A, UNC79, and UNC80. Dysfunction of the NALCN channelosome causes a broad range of neurological and developmental diseases called NALCN channelopathies in humans. How the auxiliary subunits, especially the two large components UNC79 and UNC80, assemble with NALCN and regulate its function remains unclear. Here we report an overall architecture of the human NALCN channelosome. UNC79 and UNC80 each adopt an S-shape super-helical structure consisting of HEAT and armadillo repeats, forming a super-coiled heterodimeric assembly in the cytoplasmic side, which may provide a scaffold for the binding of other potential modulators of the channelosome. The UNC79-UNC80 assembly specifically associates with the NALCN-FAM155A subcomplex through the intracellular II-III linker of NALCN. Disruptions of the interaction interfaces between UNC79 and UNC80, and between the II-III linker of NALCN and the UNC79-UNC80 assembly, significantly reduce the NALCN-mediated currents in HEK293T system, suggesting the importance of the UNC79-UNC80 assembly in regulating channelosome function. Cross-linking mass spectrometry analysis identified an additional calmodulin (CaM) bound in the carboxyl-terminal domain of NALCN. Our study thus provides a structural basis for understanding the unique assembly mechanism and functional regulation of the NALCN channelosome, and also provides an opportunity for the interpretation of many disease-related mutations in UNC80.
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Engel MA, Wörmann YR, Kaestner H, Schüler C. An Optogenetic Arrhythmia Model—Insertion of Several Catecholaminergic Polymorphic Ventricular Tachycardia Mutations Into Caenorhabditis elegans UNC-68 Disturbs Calstabin-Mediated Stabilization of the Ryanodine Receptor Homolog. Front Physiol 2022; 13:691829. [PMID: 35399287 PMCID: PMC8990320 DOI: 10.3389/fphys.2022.691829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/15/2022] [Indexed: 11/14/2022] Open
Abstract
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited disturbance of the heart rhythm (arrhythmia) that is induced by stress or that occurs during exercise. Most mutations that have been linked to CPVT are found in two genes, i.e., ryanodine receptor 2 (RyR2) and calsequestrin 2 (CASQ2), two proteins fundamentally involved in the regulation of intracellular Ca2+ in cardiac myocytes. We inserted six CPVT-causing mutations via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 into unc-68 and csq-1, the Caenorhabditis elegans homologs of RyR and CASQ, respectively. We characterized those mutations via video-microscopy, electrophysiology, and calcium imaging in our previously established optogenetic arrhythmia model. In this study, we additionally enabled high(er) throughput recordings of intact animals by combining optogenetic stimulation with a microfluidic chip system. Whereas only minor/no pump deficiency of the pharynx was observed at baseline, three mutations of UNC-68 (S2378L, P2460S, Q4623R; RyR2-S2246L, -P2328S, -Q4201R) reduced the ability of the organ to follow 4 Hz optogenetic stimulation. One mutation (Q4623R) was accompanied by a strong reduction of maximal pump rate. In addition, S2378L and Q4623R evoked an altered calcium handling during optogenetic stimulation. The 1,4-benzothiazepine S107, which is suggested to stabilize RyR2 channels by enhancing the binding of calstabin2, reversed the reduction of pumping ability in a mutation-specific fashion. However, this depends on the presence of FKB-2, a C. elegans calstabin2 homolog, indicating the involvement of calstabin2 in the disease-causing mechanisms of the respective mutations. In conclusion, we showed for three CPVT-like mutations in C. elegans RyR a reduced pumping ability upon light stimulation, i.e., an arrhythmia-like phenotype, that can be reversed in two cases by the benzothiazepine S107 and that depends on stabilization via FKB-2. The genetically amenable nematode in combination with optogenetics and high(er) throughput recordings is a promising straightforward system for the investigation of RyR mutations and the selection of mutation-specific drugs.
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Affiliation(s)
- Marcial Alexander Engel
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Yves René Wörmann
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Hanna Kaestner
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Christina Schüler
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- *Correspondence: Christina Schüler,
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Qiu K, Wang Y, Xu D, He L, Zhang X, Yan E, Wang L, Yin J. Ryanodine receptor RyR1-mediated elevation of Ca 2+ concentration is required for the late stage of myogenic differentiation and fusion. J Anim Sci Biotechnol 2022; 13:9. [PMID: 35144690 PMCID: PMC8832842 DOI: 10.1186/s40104-021-00668-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background Cytosolic Ca2+ plays vital roles in myogenesis and muscle development. As a major Ca2+ release channel of endoplasmic reticulum (ER), ryanodine receptor 1 (RyR1) key mutations are main causes of severe congenital myopathies. The role of RyR1 in myogenic differentiation has attracted intense research interest but remains unclear. Results In the present study, both RyR1-knockdown myoblasts and CRISPR/Cas9-based RyR1-knockout myoblasts were employed to explore the role of RyR1 in myogenic differentiation, myotube formation as well as the potential mechanism of RyR1-related myopathies. We observed that RyR1 expression was dramatically increased during the late stage of myogenic differentiation, accompanied by significantly elevated cytoplasmic Ca2+ concentration. Inhibition of RyR1 by siRNA-mediated knockdown or chemical inhibitor, dantrolene, significantly reduced cytosolic Ca2+ and blocked multinucleated myotube formation. The elevation of cytoplasmic Ca2+ concentration can effectively relieve myogenic differentiation stagnation by RyR1 inhibition, demonstrating that RyR1 modulates myogenic differentiation via regulation of Ca2+ release channel. However, RyR1-knockout-induced Ca2+ leakage led to the severe ER stress and excessive unfolded protein response, and drove myoblasts into apoptosis. Conclusions Therefore, we concluded that Ca2+ release mediated by dramatic increase in RyR1 expression is required for the late stage of myogenic differentiation and fusion. This study contributes to a novel understanding of the role of RyR1 in myogenic differentiation and related congenital myopathies, and provides a potential target for regulation of muscle characteristics and meat quality. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00668-x.
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Affiliation(s)
- Kai Qiu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,Risk Assessment Laboratory of Feed Derived Factors to Animal Product Quality Safety of Ministry of Agriculture & Rural Affairs & National Engineering Research Center of Biological Feed, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yubo Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Doudou Xu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Linjuan He
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Enfa Yan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lu Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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48
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Borges RJ, Salvador GHM, Pimenta DC, Dos Santos LD, Fontes MRM, Usón I. SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural sources. Nucleic Acids Res 2022; 50:e50. [PMID: 35104880 PMCID: PMC9122596 DOI: 10.1093/nar/gkac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/05/2022] [Accepted: 01/30/2022] [Indexed: 12/28/2022] Open
Abstract
Proteins isolated from natural sources can be composed of a mixture of isoforms with similar physicochemical properties that coexist in the final steps of purification. Yet, even where unverified, the assumed sequence is enforced throughout the structural studies. Herein, we propose a novel perspective to address the usually neglected sequence heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER. The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data, and the genetic information relating sequence conservation is integrated into this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MS de novo sequencing with genomic-based algorithms to detect point mutations. We calibrated SLIDER with Gallus gallus lysozyme, whose sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterize a metalloproteinase and a phospholipase A2-like protein from the venom of Bothrops moojeni and a crotoxin from Crotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural sources.
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Affiliation(s)
- Rafael J Borges
- Departament of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil.,Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Guilherme H M Salvador
- Departament of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Daniel C Pimenta
- Biochemistry and Biophysics Laboratory, Butantan Institute, São Paulo, São Paulo 05503-900, Brazil
| | - Lucilene D Dos Santos
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP), Botucatu, São Paulo 18618-687, Brazil.,Biotechnology Institute (IBTEC), São Paulo State University (UNESP), Botucatu, São Paulo 18607-440, Brazil
| | - Marcos R M Fontes
- Departament of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona 08028, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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49
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Chirasani VR, Popov KI, Meissner G, Dokholyan NV. Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1. Proteins 2022; 90:385-394. [PMID: 34455637 PMCID: PMC8738105 DOI: 10.1002/prot.26228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/05/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023]
Abstract
Ryanodine receptor 1 (RyR1) is an intracellular calcium ion (Ca2+ ) release channel required for skeletal muscle contraction. Although cryo-electron microscopy identified binding sites of three coactivators Ca2+ , ATP, and caffeine (CFF), the mechanism of co-regulation and synergy of these activators is unknown. Here, we report allosteric connections among the three ligand-binding sites and pore region in (i) Ca2+ bound-closed, (ii) ATP/CFF bound-closed, (iii) Ca2+ /ATP/CFF bound-closed, and (iv) Ca2+ /ATP/CFF bound-open RyR1 states. We identified two dominant networks of interactions that mediate communication between the Ca2+ -binding site and pore region in Ca2+ bound-closed state, which partially overlapped with the pore communications in ATP/CFF bound-closed RyR1 state. In Ca2+ /ATP/CFF bound-closed and -open RyR1 states, co-regulatory interactions were analogous to communications in the Ca2+ bound-closed and ATP/CFF bound-closed states. Both ATP- and CFF-binding sites mediate communication between the Ca2+ -binding site and the pore region in Ca2+ /ATP/CFF bound-open RyR1 structure. We conclude that Ca2+ , ATP, and CFF propagate their effects to the pore region through a network of overlapping interactions that mediate allosteric control and molecular synergy in channel regulation.
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Affiliation(s)
- Venkat R Chirasani
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Konstantin I Popov
- 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
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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50
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Yamazawa T, Kobayashi T, Kurebayashi N, Murayama T. [Therapeutic effects of novel type1 ryanodine receptor inhibitor on skeletal muscle diseases]. Nihon Yakurigaku Zasshi 2022; 157:15-22. [PMID: 34980804 DOI: 10.1254/fpj.21068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Type 1 ryanodine receptor (RyR1) plays a key role in Ca2+ release from the sarcoplasmic reticulum (SR) during excitation-contraction coupling of skeletal muscle. Mutations in RyR1 hyperactivate the channel to cause malignant hyperthermia (MH). MH is a serious complication characterized by skeletal muscle rigidity and elevated body temperature in response to commonly used inhalational anesthetics. Thus far, more than 300 mutations in RyR1 gene have been reported in patients with MH. Some heat stroke triggered by exercise or environmental heat stress is also related to MH mutations in the RyR1 gene. The only drug approved for ameliorating the symptoms of MH is dantrolene, which has been first developed in 1960s as a muscle relaxant. However, dantrolene has several disadvantages for clinical use: poor water solubility which makes rapid preparation difficult in emergency situations and long plasma half-life, which causes long-lasting side effects such as muscle weakness. Here we show that a novel RyR1-selective inhibitor, 6,7-(methylenedioxy)-1-octyl-4-quinolone-3-carboxylic acid (Compound 1, Cpd1), effectively rescues MH and heat stroke in new mouse model relevant to MH. Cpd1 has great advantages of higher water solubility and shorter plasma half-life compared to dantrolene. Our data suggest that Cpd1 has the potential to be a promising new candidate for effective treatment of patients carrying RyR1 mutations.
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Affiliation(s)
- Toshiko Yamazawa
- Department of Molecular Physiology, The Jikei University School of Medicine
| | - Takuya Kobayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine
| | - Nagomi Kurebayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine
| | - Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine
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