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Da'as SI, Thanassoulas A, Calver BL, Saleh A, Abdelrahman D, Hasan W, Safieh-Garabedian B, Kontogianni I, Nasrallah GK, Nounesis G, Lai FA, Nomikos M. Divergent Biochemical Properties and Disparate Impact of Arrhythmogenic Calmodulin Mutations on Zebrafish Cardiac Function. J Cell Biochem 2024; 125:e30619. [PMID: 38946237 DOI: 10.1002/jcb.30619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024]
Abstract
Calmodulin (CaM) is a ubiquitous, small cytosolic calcium (Ca2+)-binding sensor that plays a vital role in many cellular processes by binding and regulating the activity of over 300 protein targets. In cardiac muscle, CaM modulates directly or indirectly the activity of several proteins that play a key role in excitation-contraction coupling (ECC), such as ryanodine receptor type 2 (RyR2), l-type Ca2+ (Cav1.2), sodium (NaV1.5) and potassium (KV7.1) channels. Many recent clinical and genetic studies have reported a series of CaM mutations in patients with life-threatening arrhythmogenic syndromes, such as long QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT). We recently showed that four arrhythmogenic CaM mutations (N98I, D132E, D134H, and Q136P) significantly reduce the binding of CaM to RyR2. Herein, we investigate in vivo functional effects of these CaM mutations on the normal zebrafish embryonic heart function by microinjecting complementary RNA corresponding to CaMN98I, CaMD132E, CaMD134H, and CaMQ136P mutants. Expression of CaMD132E and CaMD134H mutants results in significant reduction of the zebrafish heart rate, mimicking a severe form of human bradycardia, whereas expression of CaMQ136P results in an increased heart rate mimicking human ventricular tachycardia. Moreover, analysis of cardiac ventricular rhythm revealed that the CaMD132E and CaMN98I zebrafish groups display an irregular pattern of heart beating and increased amplitude in comparison to the control groups. Furthermore, circular dichroism spectroscopy experiments using recombinant CaM proteins reveals a decreased structural stability of the four mutants compared to the wild-type CaM protein in the presence of Ca2+. Finally, Ca2+-binding studies indicates that all CaM mutations display reduced CaM Ca2+-binding affinities, with CaMD132E exhibiting the most prominent change. Our data suggest that CaM mutations can trigger different arrhythmogenic phenotypes through multiple and complex molecular mechanisms.
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Affiliation(s)
- Sahar I Da'as
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Brian L Calver
- Sir Geraint Evans Wales Heart Research Institute, College of Biomedical and Life Science, Cardiff University, Cardiff, UK
| | - Alaaeldin Saleh
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | | | - Waseem Hasan
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Iris Kontogianni
- National Centre for Scientific Research "Demokritos", Agia Paraskevi, Greece
- National Technical University of Athens, Athens, Greece
| | - Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, Qatar
- Department of Biological Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - George Nounesis
- National Centre for Scientific Research "Demokritos", Agia Paraskevi, Greece
| | - F Anthony Lai
- College of Medicine, QU Health, Qatar University, Doha, Qatar
- Sir Geraint Evans Wales Heart Research Institute, College of Biomedical and Life Science, Cardiff University, Cardiff, UK
| | - Michail Nomikos
- College of Medicine, QU Health, Qatar University, Doha, Qatar
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2
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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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Thanassoulas A, Theodoridou M, Barrak L, Riguene E, Alyaarabi T, Elrayess MA, Lai FA, Nomikos M. Arrhythmia-Associated Calmodulin E105A Mutation Alters the Binding Affinity of CaM to a Ryanodine Receptor 2 CaM-Binding Pocket. Int J Mol Sci 2023; 24:15630. [PMID: 37958614 PMCID: PMC10649572 DOI: 10.3390/ijms242115630] [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: 09/23/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Calmodulin (CaM) is a small, multifunctional calcium (Ca2+)-binding sensor that binds and regulates the open probability of cardiac ryanodine receptor 2 (RyR2) at both low and high cytosolic Ca2+ concentrations. Recent isothermal titration calorimetry (ITC) studies of a number of peptides that correspond to different regions of human RyR2 showed that two regions of human RyR2 (3584-3602aa and 4255-4271aa) bind with high affinity to CaM, suggesting that these two regions might contribute to a putative RyR2 intra-subunit CaM-binding pocket. Moreover, a previously characterized de novo long QT syndrome (LQTS)-associated missense CaM mutation (E105A) which was identified in a 6-year-old boy, who experienced an aborted first episode of cardiac arrest revealed that this mutation dysregulates normal cardiac function in zebrafish by a complex mechanism that involves alterations in both CaM-Ca2+ and CaM-RyR2 interactions. Herein, to gain further insight into how the CaM E105A mutation leads to severe cardiac arrhythmia, we generated large quantities of recombinant CaMWT and CaME105A proteins. We then performed ITC experiments to investigate and compare the interactions of CaMWT and CaME105A mutant protein with two synthetic peptides that correspond to the two aforementioned human RyR2 regions, which we have proposed to contribute to the RyR2 CaM-binding pocket. Our data reveal that the E105A mutation has a significant negative effect on the interaction of CaM with both RyR2 regions in the presence and absence of Ca2+, highlighting the potential contribution of these two human RyR2 regions to an RyR2 CaM-binding pocket, which may be essential for physiological CaM/RyR2 association and thus channel regulation.
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Affiliation(s)
- Angelos Thanassoulas
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
| | - Maria Theodoridou
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Laila Barrak
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
| | - Emna Riguene
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
| | - Tamader Alyaarabi
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
| | - Mohamed A. Elrayess
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar;
| | - F. Anthony Lai
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
| | - Michail Nomikos
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (A.T.); (L.B.); (E.R.); (T.A.); (M.A.E.); (F.A.L.)
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Marino V, Cortivo GD, Dell'Orco D. Ionic displacement of Ca 2+ by Pb 2+ in calmodulin is affected by arrhythmia-associated mutations. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119490. [PMID: 37201768 DOI: 10.1016/j.bbamcr.2023.119490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/14/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Lead is a highly toxic metal that severely perturbs physiological processes even at sub-micromolar levels, often by disrupting the Ca2+ signaling pathways. Recently, Pb2+-associated cardiac toxicity has emerged, with potential involvement of both the ubiquitous Ca2+ sensor protein calmodulin (CaM) and ryanodine receptors. In this work, we explored the hypothesis that Pb2+ contributes to the pathological phenotype of CaM variants associated with congenital arrhythmias. We performed a thorough spectroscopic and computational characterization of CaM conformational switches in the co-presence of Pb2+ and four missense mutations associated with congenital arrhythmias, namely N53I, N97S, E104A and F141L, and analyzed their effects on the recognition of a target peptide of RyR2. When bound to any of the CaM variants, Pb2+ is difficult to displace even under equimolar Ca2+ concentrations, thus locking all CaM variants in a specific conformation, which exhibits characteristics of coiled-coil assemblies. All arrhythmia-associated variants appear to be more susceptible to Pb2+ than WT CaM, as the conformational transition towards the coiled-coil conformation occurs at lower Pb2+, regardless of the presence of Ca2+, with altered cooperativity. The presence of arrhythmia-associated mutations specifically alters the cation coordination of CaM variants, in some cases involving allosteric communication between the EF-hands in the two domains. Finally, while wild type CaM increases the affinity for the RyR2 target in the presence of Pb2+, no specific pattern could be detected for all other variants, ruling out a synergistic effect of Pb2+ and mutations in the recognition process.
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Affiliation(s)
- Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, I-37134 Verona, Italy
| | - Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, I-37134 Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, I-37134 Verona, Italy.
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Life-threatening arrhythmogenic CaM mutations disrupt CaM binding to a distinct RyR2 CaM-binding pocket. Biochim Biophys Acta Gen Subj 2023; 1867:130313. [PMID: 36693454 DOI: 10.1016/j.bbagen.2023.130313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Calmodulin (CaM) modulates the activity of several proteins that play a key role in excitation-contraction coupling (ECC). In cardiac muscle, the major binding partner of CaM is the type-2 ryanodine receptor (RyR2) and altered CaM binding contributes to defects in sarcoplasmic reticulum (SR) calcium (Ca2+) release. Many genetic studies have reported a series of CaM missense mutations in patients with a history of severe arrhythmogenic cardiac disorders. In the present study, we generated four missense CaM mutants (CaMN98I, CaMD132E, CaMD134H and CaMQ136P) and we used a CaM-RyR2 co-immunoprecipitation and a [3H]ryanodine binding assay to directly compare the relative RyR2-binding of wild type and mutant CaM proteins and to investigate the functional effects of these CaM mutations on RyR2 activity. Furthermore, isothermal titration calorimetry (ITC) experiments were performed to investigate and compare the interactions of the wild-type and mutant CaM proteins with various synthetic peptides located in the well-established RyR2 CaM-binding region (3584-3602aa), as well as another CaM-binding region (4255-4271aa) of human RyR2. Our data revealed that all four CaM mutants displayed dramatically reduced RyR2 interaction and defective modulation of [3H]ryanodine binding to RyR2, regardless of LQTS or CPVT association. Moreover, our isothermal titration calorimetry ITC data suggest that RyR2 3584-3602aa and 4255-4271aa regions interact with significant affinity with wild-type CaM, in the presence and absence of Ca2+, two regions that might contribute to a putative intra-subunit CaM-binding pocket. In contrast, screening the interaction of the four arrhythmogenic CaM mutants with two synthetic peptides that correspond to these RyR2 regions, revealed disparate binding properties and signifying differential mechanisms that contribute to reduced RyR2 association.
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6
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Dal Cortivo G, Marino V, Bianconi S, Dell'Orco D. Calmodulin variants associated with congenital arrhythmia impair selectivity for ryanodine receptors. Front Mol Biosci 2023; 9:1100992. [PMID: 36685279 PMCID: PMC9849693 DOI: 10.3389/fmolb.2022.1100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Among its many molecular targets, the ubiquitous calcium sensor protein calmodulin (CaM) recognizes and regulates the activity of ryanodine receptors type 1 (RyR1) and 2 (RyR2), mainly expressed in skeletal and cardiac muscle, respectively. Such regulation is essential to achieve controlled contraction of muscle cells. To unravel the molecular mechanisms underlying the target recognition process, we conducted a comprehensive biophysical investigation of the interaction between two calmodulin variants associated with congenital arrhythmia, namely N97I and Q135P, and a highly conserved calmodulin-binding region in RyR1 and RyR2. The structural, thermodynamic, and kinetic properties of protein-peptide interactions were assessed together with an in-depth structural and topological investigation based on molecular dynamics simulations. This integrated approach allowed us to identify amino acids that are crucial in mediating allosteric processes, which enable high selectivity in molecular target recognition. Our results suggest that the ability of calmodulin to discriminate between RyR1 an RyR2 targets depends on kinetic discrimination and robust allosteric communication between Ca2+-binding sites (EF1-EF3 and EF3-EF4 pairs), which is perturbed in both N97I and Q135P arrhythmia-associated variants.
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7
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Lin L, Jiang H, Hadiatullah H, Ma R, Korza H, Gu Y, Yuchi Z. Calmodulin Modulation of Insect Ryanodine Receptors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16156-16163. [PMID: 36524829 DOI: 10.1021/acs.jafc.2c07519] [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: 06/17/2023]
Abstract
Ryanodine receptor (RyR) is a giant calcium release channel located on the membrane of the endoplasmic reticulum (ER). Here, we report the regulation of RyRs from two major agricultural pests, diamondback moth and fall armyworm, by insect calmodulin (CaM). The recombinantly expressed full-length insect RyR could be pulled down by insect CaM in the presence of Ca2+, but the efficiency is lower compared to rabbit RyR1 and insect RyR with the CaM-binding domain (CaMBD) replaced by rabbit RyR1 sequence. Interestingly, the enhanced binding of CaM in the mutant insect RyR resulted in an increased sensitivity to the diamide insecticide chlorantraniliprole (CHL), suggesting that this CaM-CaMBD interface could be targeted by potential synergists acting as molecular glue. The thermodynamics of the binding between insect CaM and CaMBD was characterized by isothermal titration calorimetry, and the key residues responsible for the insect-specific regulation were identified through mutagenesis studies.
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Affiliation(s)
- Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, China
| | - Heng Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, China
| | - Hadiatullah Hadiatullah
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, China
| | - Ruifang Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, China
| | - Henryk Korza
- Syngenta Jealott's Hill International Research Centre, Bracknell, BerkshireRG42 6EY, UK
| | - Yucheng Gu
- Syngenta Jealott's Hill International Research Centre, Bracknell, BerkshireRG42 6EY, UK
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin300072, China
- College of Life Sciences, Gannan Normal University, Ganzhou341000, China
- Department of Molecular Pharmacology, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute & Hospital; National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin300072, China
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8
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Dal Cortivo G, Barracchia CG, Marino V, D'Onofrio M, Dell'Orco D. Alterations in calmodulin-cardiac ryanodine receptor molecular recognition in congenital arrhythmias. Cell Mol Life Sci 2022; 79:127. [PMID: 35133504 PMCID: PMC8825638 DOI: 10.1007/s00018-022-04165-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/27/2021] [Accepted: 01/23/2022] [Indexed: 12/03/2022]
Abstract
Calmodulin (CaM), a ubiquitous and highly conserved Ca2+-sensor protein involved in the regulation of over 300 molecular targets, has been recently associated with severe forms of lethal arrhythmia. Here, we investigated how arrhythmia-associated mutations in CaM localized at the C-terminal lobe alter the molecular recognition with Ryanodine receptor 2 (RyR2), specifically expressed in cardiomyocytes. We performed an extensive structural, thermodynamic, and kinetic characterization of the variants D95V/H in the EF3 Ca2+-binding motif and of the D129V and D131H/E variants in the EF4 motif, and probed their interaction with RyR2. Our results show that the specific structural changes observed for individual CaM variants do not extend to the complex with the RyR2 target. Indeed, some common alterations emerge at the protein–protein interaction level, suggesting the existence of general features shared by the arrhythmia-associated variants. All mutants showed a faster rate of dissociation from the target peptide than wild-type CaM. Integration of spectroscopic data with exhaustive molecular dynamics simulations suggests that, in the presence of Ca2+, functional recognition involves allosteric interactions initiated by the N-terminal lobe of CaM, which shows a lower affinity for Ca2+ compared to the C-terminal lobe in the isolated protein.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | | | - Valerio Marino
- Department of Neurosciences Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.
| | - Daniele Dell'Orco
- Department of Neurosciences Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, Italy.
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Prakash O, Held M, McCormick LF, Gupta N, Lian LY, Antonyuk S, Haynes LP, Thomas NL, Helassa N. CPVT-associated calmodulin variants N53I and A102V dysregulate Ca2+ signalling via different mechanisms. J Cell Sci 2022; 135:274029. [PMID: 34888671 PMCID: PMC8917356 DOI: 10.1242/jcs.258796] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited condition that can cause fatal cardiac arrhythmia. Human mutations in the Ca2+ sensor calmodulin (CaM) have been associated with CPVT susceptibility, suggesting that CaM dysfunction is a key driver of the disease. However, the detailed molecular mechanism remains unclear. Focusing on the interaction with the cardiac ryanodine receptor (RyR2), we determined the effect of CPVT-associated variants N53I and A102V on the structural characteristics of CaM and on Ca2+ fluxes in live cells. We provide novel data showing that interaction of both Ca2+/CaM-N53I and Ca2+/CaM-A102V with the RyR2 binding domain is decreased. Ca2+/CaM-RyR23583-3603 high-resolution crystal structures highlight subtle conformational changes for the N53I variant, with A102V being similar to wild type (WT). We show that co-expression of CaM-N53I or CaM-A102V with RyR2 in HEK293 cells significantly increased the duration of Ca2+ events; CaM-A102V exhibited a lower frequency of Ca2+ oscillations. In addition, we show that CaMKIIδ (also known as CAMK2D) phosphorylation activity is increased for A102V, compared to CaM-WT. This paper provides novel insight into the molecular mechanisms of CPVT-associated CaM variants and will facilitate the development of strategies for future therapies.
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Affiliation(s)
- Ohm Prakash
- Liverpool Centre for Cardiovascular Science, Department of Cardiovascular Science and Metabolic Medicine, Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Marie Held
- Liverpool Centre for Cardiovascular Science, Department of Cardiovascular Science and Metabolic Medicine, Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Liam F. McCormick
- Liverpool Centre for Cardiovascular Science, Department of Cardiovascular Science and Metabolic Medicine, Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Nitika Gupta
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Lu-Yun Lian
- Nuclear Magnetic Resonance Centre for Structural Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Svetlana Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Lee P. Haynes
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - N. Lowri Thomas
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, Redwood Building, CF10 3NB, UK
| | - Nordine Helassa
- Liverpool Centre for Cardiovascular Science, Department of Cardiovascular Science and Metabolic Medicine, Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK,Author for correspondence ()
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10
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Young BD, Varney KM, Wilder PT, Costabile BK, Pozharski E, Cook ME, Godoy-Ruiz R, Clarke OB, Mancia F, Weber DJ. Physiologically Relevant Free Ca 2+ Ion Concentrations Regulate STRA6-Calmodulin Complex Formation via the BP2 Region of STRA6. J Mol Biol 2021; 433:167272. [PMID: 34592217 PMCID: PMC8568335 DOI: 10.1016/j.jmb.2021.167272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/13/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022]
Abstract
The interaction of calmodulin (CaM) with the receptor for retinol uptake, STRA6, involves an α-helix termed BP2 that is located on the intracellular side of this homodimeric transporter (Chen et al., 2016 [1]). In the absence of Ca2+, NMR data showed that a peptide derived from BP2 bound to the C-terminal lobe (C-lobe) of Mg2+-bound CaM (MgCaM). Upon titration of Ca2+ into MgCaM-BP2, NMR chemical shift perturbations (CSPs) were observed for residues in the C-lobe, including those in the EF-hand Ca2+-binding domains, EF3 and EF4 (CaKD = 60 ± 7 nM). As higher concentrations of free Ca2+ were achieved, CSPs occurred for residues in the N-terminal lobe (N-lobe) including those in EF1 and EF2 (CaKD = 1000 ± 160 nM). Thermodynamic and kinetic Ca2+ binding studies showed that BP2 addition increased the Ca2+-binding affinity of CaM and slowed its Ca2+ dissociation rates (koff) in both the C- and N-lobe EF-hand domains, respectively. These data are consistent with BP2 binding to the C-lobe of CaM at low free Ca2+ concentrations (<100 nM) like those found at resting intracellular levels. As free Ca2+ levels approach 1000 nM, which is typical inside a cell upon an intracellular Ca2+-signaling event, BP2 is shown here to interact with both the N- and C-lobes of Ca2+-loaded CaM (CaCaM-BP2). Because this structural rearrangement observed for the CaCaM-BP2 complex occurs as intracellular free Ca2+ concentrations approach those typical of a Ca2+-signaling event (CaKD = 1000 ± 160 nM), this conformational change could be relevant to vitamin A transport by full-length CaCaM-STRA6.
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Affiliation(s)
- Brianna D Young
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA
| | - Kristen M Varney
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Paul T Wilder
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edwin Pozharski
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Mary E Cook
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA
| | - Raquel Godoy-Ruiz
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - David J Weber
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA.
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11
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Woll KA, Van Petegem F. Calcium Release Channels: Structure and Function of IP3 Receptors and Ryanodine Receptors. Physiol Rev 2021; 102:209-268. [PMID: 34280054 DOI: 10.1152/physrev.00033.2020] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ca2+-release channels are giant membrane proteins that control the release of Ca2+ from the endoplasmic and sarcoplasmic reticulum. The two members, ryanodine receptors (RyRs) and inositol-1,4,5-trisphosphate Receptors (IP3Rs), are evolutionarily related and are both activated by cytosolic Ca2+. They share a common architecture, but RyRs have evolved additional modules in the cytosolic region. Their massive size allows for the regulation by tens of proteins and small molecules, which can affect the opening and closing of the channels. In addition to Ca2+, other major triggers include IP3 for the IP3Rs, and depolarization of the plasma membrane for a particular RyR subtype. Their size has made them popular targets for study via electron microscopic methods, with current structures culminating near 3Å. The available structures have provided many new mechanistic insights int the binding of auxiliary proteins and small molecules, how these can regulate channel opening, and the mechanisms of disease-associated mutations. They also help scrutinize previously proposed binding sites, as some of these are now incompatible with the structures. Many questions remain around the structural effects of post-translational modifications, additional binding partners, and the higher-order complexes these channels can make in situ. This review summarizes our current knowledge about the structures of Ca2+-release channels and how this informs on their function.
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Affiliation(s)
- Kellie A Woll
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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12
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Yu Q, Anderson DE, Kaur R, Fisher AJ, Ames JB. The Crystal Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RyR2) at Residues Phe4246-Val4271 Reveals a Fifth Calcium Binding Site. Biochemistry 2021; 60:1088-1096. [PMID: 33754699 PMCID: PMC8211408 DOI: 10.1021/acs.biochem.1c00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Calmodulin (CaM) regulates the activity of a Ca2+ channel known as the cardiac ryanodine receptor (RyR2), which facilitates the release of Ca2+ from the sarcoplasmic reticulum during excitation-contraction coupling in cardiomyocytes. Mutations that disrupt this CaM-dependent channel inactivation result in cardiac arrhythmias. RyR2 contains three different CaM binding sites: CaMBD1 (residues 1940-1965), CaMBD2 (residues 3580-3611), and CaMBD3 (residues 4246-4275). Here, we report a crystal structure of Ca2+-bound CaM bound to RyR2 CaMBD3. The structure reveals Ca2+ bound to the four EF-hands of CaM as well as a fifth Ca2+ bound to CaM in the interdomain linker region involving Asp81 and Glu85. The CaM mutant E85A abolishes the binding of the fifth Ca2+ and weakens the binding of CaMBD3 to Ca2+-bound CaM. Thus, the binding of the fifth Ca2+ is important for stabilizing the complex in solution and is not a crystalline artifact. The CaMBD3 peptide in the complex adopts an α-helix (between Phe4246 and Val4271) that interacts with both lobes of CaM. Hydrophobic residues in the CaMBD3 helix (Leu4255 and Leu4259) form intermolecular contacts with the CaM N-lobe, and the CaMBD3 mutations (L4255A and L4259A) each weaken the binding of CaM to RyR2. Aromatic residues on the opposite side of the CaMBD3 helix (Phe4246 and Tyr4250) interact with the CaM C-lobe, but the mutants (F4246A and Y4250A) have no detectable effect on CaM binding in solution. We suggest that the binding of CaM to CaMBD3 and the binding of a fifth Ca2+ to CaM may contribute to the regulation of RyR2 channel function.
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Affiliation(s)
- Qinhong Yu
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - David E Anderson
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Ramanjeet Kaur
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Andrew J Fisher
- Department of Chemistry, University of California, Davis, California 95616, United States
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, United States
| | - James B Ames
- Department of Chemistry, University of California, Davis, California 95616, United States
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13
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Pathological conformations of disease mutant Ryanodine Receptors revealed by cryo-EM. Nat Commun 2021; 12:807. [PMID: 33547325 PMCID: PMC7864917 DOI: 10.1038/s41467-021-21141-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/14/2021] [Indexed: 12/17/2022] Open
Abstract
Ryanodine Receptors (RyRs) are massive channels that release Ca2+ from the endoplasmic and sarcoplasmic reticulum. Hundreds of mutations are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, we explore the first MH mutation identified in humans by providing cryo-EM snapshots of the pig homolog, R615C, showing that it affects an interface between three solenoid regions. We also show the impact of apo-calmodulin (apoCaM) and how it can induce opening by bending of the bridging solenoid, mediated by its N-terminal lobe. For R615C RyR1, apoCaM binding abolishes a pathological ‘intermediate’ conformation, distributing the population to a mixture of open and closed channels, both different from the structure without apoCaM. Comparisons show that the mutation primarily affects the closed state, inducing partial movements linked to channel activation. This shows that disease mutations can cause distinct pathological conformations of the RyR and facilitate channel opening by disrupting interactions between different solenoid regions. Ryanodine Receptors (RyRs) release Ca2+ from the endoplasmic and sarcoplasmic reticulum. Mutations in RyR are linked to malignant hyperthermia (MH), myopathies, and arrhythmias. Here, a collection of cryoEM structures provides insights into the molecular consequences of MHrelated RyR mutation R615C, and how apoCaM opens RyR1.
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14
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Nelson SED, Weber DK, Rebbeck RT, Cornea RL, Veglia G, Thomas DD. Met125 is essential for maintaining the structural integrity of calmodulin's C-terminal domain. Sci Rep 2020; 10:21320. [PMID: 33288831 PMCID: PMC7721703 DOI: 10.1038/s41598-020-78270-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/17/2020] [Indexed: 11/09/2022] Open
Abstract
We have used NMR and circular dichroism spectroscopy to investigate the structural and dynamic effects of oxidation on calmodulin (CaM), using peroxide and the Met to Gln oximimetic mutations. CaM is a Ca2+-sensitive regulatory protein that interacts with numerous targets. Due to its high methionine content, CaM is highly susceptible to oxidation by reactive oxygen species under conditions of cell stress and age-related muscle degeneration. CaM oxidation alters regulation of a host of CaM's protein targets, emphasizing the importance of understanding the mechanism of CaM oxidation in muscle degeneration and overall physiology. It has been shown that the M125Q CaM mutant can mimic the functional effects of methionine oxidation on CaM's regulation of the calcium release channel, ryanodine receptor (RyR). We report here that the M125Q mutation causes a localized unfolding of the C-terminal lobe of CaM, preventing the formation of a hydrophobic cluster of residues near the EF-hand Ca2+ binding sites. NMR analysis of CaM oxidation by peroxide offers further insights into the susceptibility of CaM's Met residues to oxidation and the resulting structural effects. These results further resolve oxidation-driven structural perturbation of CaM, with implications for RyR regulation and the decay of muscle function in aging.
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Affiliation(s)
- Sarah E D Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
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15
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Genovese I, Giamogante F, Barazzuol L, Battista T, Fiorillo A, Vicario M, D'Alessandro G, Cipriani R, Limatola C, Rossi D, Sorrentino V, Poser E, Mosca L, Squitieri F, Perluigi M, Arena A, van Petegem F, Tito C, Fazi F, Giorgi C, Calì T, Ilari A, Colotti G. Sorcin is an early marker of neurodegeneration, Ca 2+ dysregulation and endoplasmic reticulum stress associated to neurodegenerative diseases. Cell Death Dis 2020; 11:861. [PMID: 33060591 PMCID: PMC7566454 DOI: 10.1038/s41419-020-03063-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022]
Abstract
Dysregulation of calcium signaling is emerging as a key feature in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD), and targeting this process may be therapeutically beneficial. Under this perspective, it is important to study proteins that regulate calcium homeostasis in the cell. Sorcin is one of the most expressed calcium-binding proteins in the human brain; its overexpression increases endoplasmic reticulum (ER) calcium concentration and decreases ER stress in the heart and in other cellular types. Sorcin has been hypothesized to be involved in neurodegenerative diseases, since it may counteract the increased cytosolic calcium levels associated with neurodegeneration. In the present work, we show that Sorcin expression levels are strongly increased in cellular, animal, and human models of AD, PD, and HD, vs. normal cells. Sorcin partially colocalizes with RyRs in neurons and microglia cells; functional experiments with microsomes containing high amounts of RyR2 and RyR3, respectively, show that Sorcin is able to regulate these ER calcium channels. The molecular basis of the interaction of Sorcin with RyR2 and RyR3 is demonstrated by SPR. Sorcin also interacts with other ER proteins as SERCA2 and Sigma-1 receptor in a calcium-dependent fashion. We also show that Sorcin regulates ER calcium transients: Sorcin increases the velocity of ER calcium uptake (increasing SERCA activity). The data presented here demonstrate that Sorcin may represent both a novel early marker of neurodegenerative diseases and a response to cellular stress dependent on neurodegeneration.
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Affiliation(s)
- Ilaria Genovese
- Department of Medical Sciences, Laboratory for Technology of Advanced Therapies (LTTA) University of Ferrara, Ferrara, Italy
| | - Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
| | - Theo Battista
- Department of Biochemical Sciences "A. Rossi Fanelli", University Sapienza of Rome, Rome, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", University Sapienza of Rome, Rome, Italy
| | - Mattia Vicario
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Giuseppina D'Alessandro
- Department of Physiology and Pharmacology, University of Rome "Sapienza", Rome, Italy.,IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Raffaela Cipriani
- Department of Physiology and Pharmacology, University of Rome "Sapienza", Rome, Italy
| | - Cristina Limatola
- IRCCS Neuromed, Pozzilli, Isernia, Italy.,Department of Physiology and Pharmacology, Sapienza University, Laboratory Affiliated to Istituto Pasteur Italia - Rome, Rome, Italy
| | - Daniela Rossi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Vincenzo Sorrentino
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Elena Poser
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Luciana Mosca
- Department of Biochemical Sciences "A. Rossi Fanelli", University Sapienza of Rome, Rome, Italy
| | - Ferdinando Squitieri
- Huntington's and Rare Diseases Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, Rome, Italy
| | - Marzia Perluigi
- Department of Biochemical Sciences "A. Rossi Fanelli", University Sapienza of Rome, Rome, Italy
| | - Andrea Arena
- Department of Biochemical Sciences "A. Rossi Fanelli", University Sapienza of Rome, Rome, Italy
| | - Filip van Petegem
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Claudia Tito
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Carlotta Giorgi
- Department of Medical Sciences, Laboratory for Technology of Advanced Therapies (LTTA) University of Ferrara, Ferrara, Italy
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, Italian National Research Council, IBPM-CNR, Rome, Italy.
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, IBPM-CNR, Rome, Italy.
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16
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Zheng W, Wen H. Investigating dual Ca 2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation. Proteins 2020; 88:1528-1539. [PMID: 32557910 DOI: 10.1002/prot.25971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/26/2020] [Accepted: 06/14/2020] [Indexed: 11/09/2022]
Abstract
The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+ -activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (eg, with Ca2+ bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR isoform 1 (RyR1) were solved by cryo-electron microscopy, revealing the location of a Ca2+ binding site for activation. Toward elucidating the Ca2+ -modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of activating and solvent Ca2+ (total simulation time is >5 μs). In the presence of solvent Ca2+ , Ca2+ binding to the activating site enhanced dynamics of RyR1 with higher inter-subunit flexibility, asymmetric inter-subunit motions, outward domain motions and partial pore dilation, which may prime RyR1 for subsequent channel opening. In contrast, the solvent Ca2+ alone reduced dynamics of RyR1 and led to inward domain motions and pore contraction, which may cause inhibition. Combining our simulation with the map of disease mutation sites in RyR1, we constructed a wiring diagram of key domains coupled via specific hydrogen bonds involving the mutation sites, some of which were modulated by Ca2+ binding. The structural and dynamic information gained from this study will inform future mutational and functional studies of RyR1 activation and inhibition by Ca2+ .
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, USA
| | - Han Wen
- Department of Physics, University at Buffalo, Buffalo, New York, USA
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17
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Holt C, Hamborg L, Lau K, Brohus M, Sørensen AB, Larsen KT, Sommer C, Van Petegem F, Overgaard MT, Wimmer R. The arrhythmogenic N53I variant subtly changes the structure and dynamics in the calmodulin N-terminal domain, altering its interaction with the cardiac ryanodine receptor. J Biol Chem 2020; 295:7620-7634. [PMID: 32317284 DOI: 10.1074/jbc.ra120.013430] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/18/2020] [Indexed: 12/11/2022] Open
Abstract
Mutations in the genes encoding the highly conserved Ca2+-sensing protein calmodulin (CaM) cause severe cardiac arrhythmias, including catecholaminergic polymorphic ventricular tachycardia or long QT syndrome and sudden cardiac death. Most of the identified arrhythmogenic mutations reside in the C-terminal domain of CaM and mostly affect Ca2+-coordinating residues. One exception is the catecholaminergic polymorphic ventricular tachycardia-causing N53I substitution, which resides in the N-terminal domain (N-domain). It does not affect Ca2+ coordination and has only a minor impact on binding affinity toward Ca2+ and on other biophysical properties. Nevertheless, the N53I substitution dramatically affects CaM's ability to reduce the open probability of the cardiac ryanodine receptor (RyR2) while having no effect on the regulation of the plasmalemmal voltage-gated Ca2+ channel, Cav1.2. To gain more insight into the molecular disease mechanism of this mutant, we used NMR to investigate the structures and dynamics of both apo- and Ca2+-bound CaM-N53I in solution. We also solved the crystal structures of WT and N53I CaM in complex with the primary calmodulin-binding domain (CaMBD2) from RyR2 at 1.84-2.13 Å resolutions. We found that all structures of the arrhythmogenic CaM-N53I variant are highly similar to those of WT CaM. However, we noted that the N53I substitution exposes an additional hydrophobic surface and that the intramolecular dynamics of the protein are significantly altered such that they destabilize the CaM N-domain. We conclude that the N53I-induced changes alter the interaction of the CaM N-domain with RyR2 and thereby likely cause the arrhythmogenic phenotype of this mutation.
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Affiliation(s)
- Christian Holt
- Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark
| | - Louise Hamborg
- Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark
| | - Kelvin Lau
- University of British Columbia, Department of Biochemistry and Molecular Biology, V6T 1Z3 Vancouver, British Columbia, Canada
| | - Malene Brohus
- Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark
| | | | | | - Cordula Sommer
- Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark
| | - Filip Van Petegem
- University of British Columbia, Department of Biochemistry and Molecular Biology, V6T 1Z3 Vancouver, British Columbia, Canada
| | | | - Reinhard Wimmer
- Aalborg University, Department of Chemistry and Bioscience, 9220 Aalborg, Denmark
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18
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Wang K, Brohus M, Holt C, Overgaard MT, Wimmer R, Van Petegem F. Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca 2+ binding and cause misfolding. J Physiol 2020; 598:1169-1186. [PMID: 32012279 DOI: 10.1113/jp279307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/28/2020] [Indexed: 01/09/2023] Open
Abstract
KEY POINTS Mutations in the calmodulin protein (CaM) are associated with arrhythmia syndromes. This study focuses on understanding the structural characteristics of CaM disease mutants and their interactions with the voltage-gated calcium channel CaV 1.2. Arrhythmia mutations in CaM can lead to loss of Ca2+ binding, uncoupling of Ca2+ binding cooperativity, misfolding of the EF-hands and altered affinity for the calcium channel. These results help us to understand how different CaM mutants have distinct effects on structure and interactions with protein targets to cause disease. ABSTRACT Calmodulinopathies are life-threatening arrhythmia syndromes that arise from mutations in calmodulin (CaM), a calcium sensing protein whose sequence is completely conserved across all vertebrates. These mutations have been shown to interfere with the function of cardiac ion channels, including the voltage-gated Ca2+ channel CaV 1.2 and the ryanodine receptor (RyR2), in a mutation-specific manner. The ability of different CaM disease mutations to discriminate between these channels has been enigmatic. We present crystal structures of several C-terminal lobe mutants and an N-terminal lobe mutant in complex with the CaV 1.2 IQ domain, in conjunction with binding assays and complementary structural biology techniques. One mutation (D130G) causes a pathological conformation, with complete separation of EF-hands within the C-lobe and loss of Ca2+ binding in EF-hand 4. Another variant (Q136P) has severely reduced affinity for the IQ domain, and shows changes in the CD spectra under Ca2+ -saturating conditions when unbound to the IQ domain. Ca2+ binding to a pair of EF-hands normally proceeds with very high cooperativity, but we found that N98S CaM can adopt different conformations with either one or two Ca2+ ions bound to the C-lobe, possibly disrupting the cooperativity. An N-lobe variant (N54I), which causes severe stress-induced arrhythmia, does not show any major changes in complex with the IQ domain, providing a structural basis for why this mutant does not affect function of CaV 1.2. These findings show that different CaM mutants have distinct effects on both the CaM structure and interactions with protein targets, and act via distinct pathological mechanisms to cause disease.
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Affiliation(s)
- Kaiqian Wang
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, V6T 1Z3 Vancouver, BC, Canada
| | - Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Christian Holt
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, V6T 1Z3 Vancouver, BC, Canada
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19
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McCarthy MR, Savich Y, Cornea RL, Thomas DD. Resolved Structural States of Calmodulin in Regulation of Skeletal Muscle Calcium Release. Biophys J 2020; 118:1090-1100. [PMID: 32049056 DOI: 10.1016/j.bpj.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/20/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
Calmodulin (CaM) is proposed to modulate activity of the skeletal muscle sarcoplasmic reticulum (SR) calcium release channel (ryanodine receptor, RyR1 isoform) via a mechanism dependent on the conformation of RyR1-bound CaM. However, the correlation between CaM structure and functional regulation of RyR in physiologically relevant conditions is largely unknown. Here, we have used time-resolved fluorescence resonance energy transfer (TR-FRET) to study structural changes in CaM that may play a role in the regulation of RyR1. We covalently labeled each lobe of CaM (N and C) with fluorescent probes and used intramolecular TR-FRET to assess interlobe distances when CaM is bound to RyR1 in SR membranes, purified RyR1, or a peptide corresponding to the CaM-binding domain of RyR (RyRp). TR-FRET resolved an equilibrium between two distinct structural states (conformations) of CaM, each characterized by an interlobe distance and Gaussian distribution width (disorder). In isolated CaM, at low Ca2+, the two conformations of CaM are resolved, centered at 5 nm (closed) and 7 nm (open). At high Ca2+, the equilibrium shifts to favor the open conformation. In the presence of RyRp at high Ca2+, the closed conformation shifts to a more compact conformation and is the major component. When CaM is bound to full-length RyR1, either purified or in SR membranes, strikingly different results were obtained: 1) the two conformations are resolved and more ordered, 2) the open state is the major component, and 3) Ca2+ stabilized the closed conformation by a factor of two. We conclude that the Ca2+-dependent structural distribution of CaM bound to RyR1 is distinct from that of CaM bound to RyRp. We propose that the function of RyR1 is tuned to the Ca2+-dependent structural dynamics of bound CaM.
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Affiliation(s)
- Megan R McCarthy
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota
| | - Yahor Savich
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota; School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, Minnesota.
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20
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Søndergaard MT, Liu Y, Guo W, Wei J, Wang R, Brohus M, Overgaard MT, Chen SRW. Role of cardiac ryanodine receptor calmodulin-binding domains in mediating the action of arrhythmogenic calmodulin N-domain mutation N54I. FEBS J 2019; 287:2256-2280. [PMID: 31763755 DOI: 10.1111/febs.15147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 09/12/2019] [Accepted: 11/19/2019] [Indexed: 11/27/2022]
Abstract
The Ca2+ -sensing protein calmodulin (CaM) inhibits cardiac ryanodine receptor (RyR2)-mediated Ca2+ release. CaM mutations associated with arrhythmias and sudden cardiac death have been shown to diminish CaM-dependent inhibition of RyR2, but the underlying mechanisms are not well understood. Nearly all arrhythmogenic CaM mutations identified are located in the C-domain of CaM and exert marked effects on Ca2+ binding to CaM and on the CaM C-domain interaction with the CaM-binding domain 2 (CaMBD2) in RyR2. Interestingly, the arrhythmogenic N-domain mutation CaM-N54I has little or no effect on Ca2+ binding to CaM or the CaM C-domain-RyR2 CaMBD2 interaction, unlike all CaM C-domain mutations. This suggests that CaM-N54I may diminish CaM-dependent RyR2 inhibition by affecting CaM N-domain interactions with RyR2 CaMBDs other than CaMBD2. To explore this possibility, we assessed the effects of deleting each of the four known CaMBDs in RyR2 (CaMBD1a, -1b, -2, or -3) on the CaM-dependent inhibition of RyR2-mediated Ca2+ release in HEK293 cells. We found that removing CaMBD1a, CaMBD1b, or CaMBD3 did not alter the effects of CaM-N54I or CaM-WT on RyR2 inhibition. On the other hand, deleting RyR2-CaMBD2 abolished the effects of both CaM-N54I and CaM-WT. Our results support that CaM-N54I causes aberrant RyR2 regulation via an uncharacterized CaMBD or less likely CaMBD2, and that RyR2 CaMBD2 is required for the actions of both N- and C-domain CaM mutations. Moreover, our results show that CaMBD1a is central to RyR2 regulation, but CaMBD1a, CaMBD1b, and CaMBD3 are not required for CaM-dependent inhibition of RyR2 in HEK293 cells.
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Affiliation(s)
- Mads T Søndergaard
- Department of Chemistry and Bioscience, Aalborg University, Denmark.,Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, AB, Canada
| | - Yingjie Liu
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, AB, Canada
| | - Wenting Guo
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, AB, Canada
| | - Jinhong Wei
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, AB, Canada
| | - Ruiwu Wang
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, AB, Canada
| | - Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Denmark
| | | | - S R Wayne Chen
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, AB, Canada
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21
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Yamaguchi N. Molecular Insights into Calcium Dependent Regulation of Ryanodine Receptor Calcium Release Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1131:321-336. [DOI: 10.1007/978-3-030-12457-1_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Søndergaard MT, Liu Y, Brohus M, Guo W, Nani A, Carvajal C, Fill M, Overgaard MT, Chen SRW. Diminished inhibition and facilitated activation of RyR2-mediated Ca 2+ release is a common defect of arrhythmogenic calmodulin mutations. FEBS J 2019; 286:4554-4578. [PMID: 31230402 DOI: 10.1111/febs.14969] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/23/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
Abstract
A number of calmodulin (CaM) mutations cause severe cardiac arrhythmias, but their arrhythmogenic mechanisms are unclear. While some of the arrhythmogenic CaM mutations have been shown to impair CaM-dependent inhibition of intracellular Ca2+ release through the ryanodine receptor type 2 (RyR2), the impact of a majority of these mutations on RyR2 function is unknown. Here, we investigated the effect of 14 arrhythmogenic CaM mutations on the CaM-dependent RyR2 inhibition. We found that all the arrhythmogenic CaM mutations tested diminished CaM-dependent inhibition of RyR2-mediated Ca2+ release and increased store-overload induced Ca2+ release (SOICR) in HEK293 cells. Moreover, all the arrhythmogenic CaM mutations tested either failed to inhibit or even promoted RyR2-mediated Ca2+ release in permeabilized HEK293 cells with elevated cytosolic Ca2+ , which was markedly different from the inhibitory action of CaM wild-type. The CaM mutations also altered the Ca2+ -dependency of CaM binding to the RyR2 CaM-binding domain. These results demonstrate that diminished inhibition, and even facilitated activation, of RyR2-mediated Ca2+ release is a common defect of arrhythmogenic CaM mutations.
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Affiliation(s)
- Mads T Søndergaard
- Department of Chemistry and Bioscience, Aalborg University, Denmark.,Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
| | - Yingjie Liu
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
| | - Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Denmark
| | - Wenting Guo
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada
| | - Alma Nani
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL, USA
| | - Catherine Carvajal
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL, USA
| | - Michael Fill
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL, USA
| | | | - S R Wayne Chen
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada.,Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL, USA
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23
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Ca 2+-dependent calmodulin binding to cardiac ryanodine receptor (RyR2) calmodulin-binding domains. Biochem J 2019; 476:193-209. [PMID: 30530841 PMCID: PMC6340113 DOI: 10.1042/bcj20180545] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/17/2022]
Abstract
The Ca2+ sensor calmodulin (CaM) regulates cardiac ryanodine receptor (RyR2)-mediated Ca2+ release from the sarcoplasmic reticulum. CaM inhibits RyR2 in a Ca2+-dependent manner and aberrant CaM-dependent inhibition results in life-threatening cardiac arrhythmias. However, the molecular details of the CaM–RyR2 interaction remain unclear. Four CaM-binding domains (CaMBD1a, -1b, -2, and -3) in RyR2 have been proposed. Here, we investigated the Ca2+-dependent interactions between CaM and these CaMBDs by monitoring changes in the fluorescence anisotropy of carboxytetramethylrhodamine (TAMRA)-labeled CaMBD peptides during titration with CaM at a wide range of Ca2+ concentrations. We showed that CaM bound to all four CaMBDs with affinities that increased with Ca2+ concentration. CaM bound to CaMBD2 and -3 with high affinities across all Ca2+ concentrations tested, but bound to CaMBD1a and -1b only at Ca2+ concentrations above 0.2 µM. Binding experiments using individual CaM domains revealed that the CaM C-domain preferentially bound to CaMBD2, and the N-domain to CaMBD3. Moreover, the Ca2+ affinity of the CaM C-domain in complex with CaMBD2 or -3 was so high that these complexes are essentially Ca2+ saturated under resting Ca2+ conditions. Conversely, the N-domain senses Ca2+ exactly in the transition from resting to activating Ca2+ when complexed to either CaMBD2 or -3. Altogether, our results support a binding model where the CaM C-domain is anchored to RyR2 CaMBD2 and saturated with Ca2+ during Ca2+ oscillations, while the CaM N-domain functions as a dynamic Ca2+ sensor that can bridge noncontiguous regions of RyR2 or clamp down onto CaMBD2.
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24
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Arrhythmia mutations in calmodulin cause conformational changes that affect interactions with the cardiac voltage-gated calcium channel. Proc Natl Acad Sci U S A 2018; 115:E10556-E10565. [PMID: 30348784 DOI: 10.1073/pnas.1808733115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Calmodulin (CaM) represents one of the most conserved proteins among eukaryotes and is known to bind and modulate more than a 100 targets. Recently, several disease-associated mutations have been identified in the CALM genes that are causative of severe cardiac arrhythmia syndromes. Although several mutations have been shown to affect the function of various cardiac ion channels, direct structural insights into any CaM disease mutation have been lacking. Here we report a crystallographic and NMR investigation of several disease mutant CaMs, linked to long-QT syndrome, in complex with the IQ domain of the cardiac voltage-gated calcium channel (CaV1.2). Surprisingly, two mutants (D95V, N97I) cause a major distortion of the C-terminal lobe, resulting in a pathological conformation not reported before. These structural changes result in altered interactions with the CaV1.2 IQ domain. Another mutation (N97S) reduces the affinity for Ca2+ by introducing strain in EF hand 3. A fourth mutant (F141L) shows structural changes in the Ca2+-free state that increase the affinity for the IQ domain. These results thus show that different mechanisms underlie the ability of CaM disease mutations to affect Ca2+-dependent inactivation of the voltage-gated calcium channel.
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25
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Hernández‐Ochoa EO, Melville Z, Vanegas C, Varney KM, Wilder PT, Melzer W, Weber DJ, Schneider MF. Loss of S100A1 expression leads to Ca 2+ release potentiation in mutant mice with disrupted CaM and S100A1 binding to CaMBD2 of RyR1. Physiol Rep 2018; 6:e13822. [PMID: 30101473 PMCID: PMC6087734 DOI: 10.14814/phy2.13822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/24/2022] Open
Abstract
Calmodulin (CaM) and S100A1 fine-tune skeletal muscle Ca2+ release via opposite modulation of the ryanodine receptor type 1 (RyR1). Binding to and modulation of RyR1 by CaM and S100A1 occurs predominantly at the region ranging from amino acid residue 3614-3640 of RyR1 (here referred to as CaMBD2). Using synthetic peptides, it has been shown that CaM binds to two additional regions within the RyR1, specifically residues 1975-1999 and 4295-4325 (CaMBD1 and CaMBD3, respectively). Because S100A1 typically binds to similar motifs as CaM, we hypothesized that S100A1 could also bind to CaMBD1 and CaMBD3. Our goals were: (1) to establish whether S100A1 binds to synthetic peptides containing CaMBD1 and CaMBD3 using isothermal calorimetry (ITC), and (2) to identify whether S100A1 and CaM modulate RyR1 Ca2+ release activation via sites other than CaMBD2 in RyR1 in its native cellular context. We developed the mouse model (RyR1D-S100A1KO), which expresses point mutation RyR1-L3625D (RyR1D) that disrupts the modulation of RyR1 by CaM and S100A1 at CaMBD2 and also lacks S100A1 (S100A1KO). ITC assays revealed that S100A1 binds with different affinities to CaMBD1 and CaMBD3. Using high-speed Ca2+ imaging and a model for Ca2+ binding and transport, we show that the RyR1D-S100A1KO muscle fibers exhibit a modest but significant increase in myoplasmic Ca2+ transients and enhanced Ca2+ release flux following field stimulation when compared to fibers from RyR1D mice, which were used as controls to eliminate any effect of binding at CaMBD2, but with preserved S100A1 expression. Our results suggest that S100A1, similar to CaM, binds to CaMBD1 and CaMBD3 within the RyR1, but that CaMBD2 appears to be the primary site of RyR1 regulation by CaM and S100A1.
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Affiliation(s)
- Erick O. Hernández‐Ochoa
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
| | - Zephan Melville
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
| | - Camilo Vanegas
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
| | - Kristen M. Varney
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
- Center for Biomolecular Therapeutics (CBT)University of Maryland School of MedicineMaryland
| | - Paul T. Wilder
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
- Center for Biomolecular Therapeutics (CBT)University of Maryland School of MedicineMaryland
| | - Werner Melzer
- Institute of Applied PhysiologyUlm UniversityUlmGermany
| | - David J. Weber
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
- Center for Biomolecular Therapeutics (CBT)University of Maryland School of MedicineMaryland
| | - Martin F. Schneider
- Department of Biochemistry and Molecular BiologyUniversity of Maryland School of MedicineBaltimoreMaryland
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26
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Structural dynamics of calmodulin-ryanodine receptor interactions: electron paramagnetic resonance using stereospecific spin labels. Sci Rep 2018; 8:10681. [PMID: 30013092 PMCID: PMC6048129 DOI: 10.1038/s41598-018-29064-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
We have used electron paramagnetic resonance, with rigid and stereospecific spin labels, to resolve structural states in calmodulin (CaM), as affected by binding of Ca and a CaM-binding peptide (RyRp) derived from the ryanodine receptor (RyR), the Ca channel that triggers muscle contraction. CaM mutants containing a pair of cysteines in the N-lobe and/or C-lobe were engineered and labeled with a stereospecifically bound bifunctional spin label (BSL). RyRp was synthesized with and without TOAC (a stereospecifically attached spin-labeled amino acid) substituted for a single amino acid near the N-terminus. Intramolecular DEER distance measurements of doubly-labeled BSL-CaM revealed that CaM exists in dynamic equilibrium among multiple states, consistent with open, closed, and compact structural models. Addition of RyRp shifted the equilibrium partially toward the compact state in the absence of Ca, and completely toward the compact state in the presence of Ca, supporting a conformational selection model. Inter-protein distance measurements show that Ca stabilizes the compact state primarily by inducing ordered binding of the CaM N-lobe to RyRp, while only slightly affecting the C-lobe. The results provide insight into the structural mechanism of CaM-mediated RyR regulation, while demonstrating the power of using two types of rigidly and stereospecifically bound spin labels.
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27
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Lin L, Liu C, Nayak BC, He W, You M, Yuchi Z. A two-step purification strategy using calmodulin as an affinity tag. J Chromatogr A 2018; 1544:16-22. [PMID: 29499842 DOI: 10.1016/j.chroma.2018.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/01/2018] [Accepted: 02/21/2018] [Indexed: 11/19/2022]
Abstract
Calmodulin (CaM) is a Ca2+-binding protein that plays an important role in cellular Ca2+-signaling. CaM interacts with diverse downstream target proteins and regulates their functions in a Ca2+-dependent manner. CaM changes its conformation and hydrophobicity upon [Ca2+] change and consequently changes its interaction with CaM-binding domains from the targets. Based on these special properties of CaM, it was used as an affinity tag to develop a novel purification strategy by using it for two sequential orthogonal purification steps: 1) an affinity purification step, in which CaM-tag interacts with an immobilized CaM-binding domain; and 2) a hydrophobic interaction chromatography step, during which CaM binds to a phenyl sepharose column. In both steps, the CaM-tagged protein binds in the presence of Ca2+ and unbinds in the presence of ethylenediaminetetraacetic acid (EDTA). An optional third step can be added to remove the CaM-tag if necessary. We used green fluorescent protein (GFP) as a test protein to demonstrate the effectiveness of the method. High yield and high purity of GFP with proper function was obtained using this novel strategy. We believe that this method can be applied to a wide range of protein targets for structural and functional studies.
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Affiliation(s)
- Lianyun Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Bidhan Chandra Nayak
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhiguang Yuchi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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28
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Meissner G. The structural basis of ryanodine receptor ion channel function. J Gen Physiol 2017; 149:1065-1089. [PMID: 29122978 PMCID: PMC5715910 DOI: 10.1085/jgp.201711878] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/12/2017] [Indexed: 01/25/2023] Open
Abstract
Large-conductance Ca2+ release channels known as ryanodine receptors (RyRs) mediate the release of Ca2+ from an intracellular membrane compartment, the endo/sarcoplasmic reticulum. There are three mammalian RyR isoforms: RyR1 is present in skeletal muscle; RyR2 is in heart muscle; and RyR3 is expressed at low levels in many tissues including brain, smooth muscle, and slow-twitch skeletal muscle. RyRs form large protein complexes comprising four 560-kD RyR subunits, four ∼12-kD FK506-binding proteins, and various accessory proteins including calmodulin, protein kinases, and protein phosphatases. RyRs share ∼70% sequence identity, with the greatest sequence similarity in the C-terminal region that forms the transmembrane, ion-conducting domain comprising ∼500 amino acids. The remaining ∼4,500 amino acids form the large regulatory cytoplasmic "foot" structure. Experimental evidence for Ca2+, ATP, phosphorylation, and redox-sensitive sites in the cytoplasmic structure have been described. Exogenous effectors include the two Ca2+ releasing agents caffeine and ryanodine. Recent work describing the near atomic structures of mammalian skeletal and cardiac muscle RyRs provides a structural basis for the regulation of the RyRs by their multiple effectors.
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Affiliation(s)
- Gerhard Meissner
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC
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29
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Her C, McCaffrey JE, Thomas DD, Karim CB. Calcium-Dependent Structural Dynamics of a Spin-Labeled RyR Peptide Bound to Calmodulin. Biophys J 2017; 111:2387-2394. [PMID: 27926840 DOI: 10.1016/j.bpj.2016.10.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/21/2016] [Accepted: 10/11/2016] [Indexed: 12/19/2022] Open
Abstract
We have used chemical synthesis, electron paramagnetic resonance (EPR), and circular dichroism to detect and analyze the structural dynamics of a ryanodine receptor (RyR) peptide bound to calmodulin (CaM). The skeletal muscle calcium release channel RyR1 is activated by Ca2+-free CaM and inhibited by Ca2+-bound CaM. To probe the structural mechanism for this regulation, wild-type RyRp and four spin-labeled derivatives were synthesized, each containing the nitroxide probe 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxylic acid substituted for a single amino acid. In 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxylic acid, the probe is rigidly and stereospecifically coupled to the α-carbon, enabling direct detection by EPR of peptide backbone structural dynamics. In the absence of CaM, circular dichroism indicates a complete lack of secondary structure, while 40% trifluoroethanol (TFE) induces >90% helicity and is unperturbed by the spin label. The EPR spectrum of each spin-labeled peptide indicates nanosecond dynamic disorder that is substantially reduced by TFE, but a significant gradient in dynamics is observed, decreasing from N- to C-terminus, both in the presence and absence of TFE. When bound to CaM, the probe nearest RyRp's N-terminus shows rapid rotational motion consistent with peptide backbone dynamics of a locally unfolded peptide, while the other three sites show substantial restriction of dynamics, consistent with helical folding. The two N-terminal sites, which bind to the C-lobe of CaM, do not show a significant Ca2+-dependence in mobility, while both C-terminal sites, which bind to the N-lobe of CaM, are significantly less mobile in the presence of bound Ca2+. These results support a model in which the interaction of RyR with CaM is nonuniform along the peptide, and the primary effect of Ca2+ is to increase the interaction of the C-terminal portion of the peptide with the N-terminal lobe of CaM. These results provide, to our knowledge, new insight into the Ca2+-dependent regulation of RyR by CaM.
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Affiliation(s)
- Cheng Her
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Jesse E McCaffrey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota.
| | - Christine B Karim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota.
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30
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Xu L, Gomez AC, Pasek DA, Meissner G, Yamaguchi N. Two EF-hand motifs in ryanodine receptor calcium release channels contribute to isoform-specific regulation by calmodulin. Cell Calcium 2017; 66:62-70. [PMID: 28807150 DOI: 10.1016/j.ceca.2017.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/08/2017] [Accepted: 05/24/2017] [Indexed: 01/03/2023]
Abstract
The mammalian ryanodine receptor Ca2+ release channel (RyR) has a single conserved high affinity calmodulin (CaM) binding domain. However, the skeletal muscle RyR1 is activated and cardiac muscle RyR2 is inhibited by CaM at submicromolar Ca2+. This suggests isoform-specific domains are involved in RyR regulation by CaM. To gain insight into the differential regulation of cardiac and skeletal muscle RyRs by CaM, RyR1/RyR2 chimeras and mutants were expressed in HEK293 cells, and their single channel activities were measured using a lipid bilayer method. All RyR1/RyR2 chimeras and mutants were inhibited by CaM at 2μM Ca2+, consistent with CaM inhibition of RyR1 and RyR2 at micromolar Ca2+ concentrations. An RyR1/RyR2 chimera with RyR1 N-terminal amino acid residues (aa) 1-3725 and RyR2 C-terminal aa 3692-4968 were inhibited by CaM at <1μM Ca2+ similar to RyR2. In contrast, RyR1/RyR2 chimera with RyR1 aa 1-4301 and RyR2 4254-4968 was activated at <1μM Ca2+ similar to RyR1. Replacement of RyR1 aa 3726-4298 with corresponding residues from RyR2 conferred CaM inhibition at <1μM Ca2+, which suggests RyR1 aa 3726-4298 are required for activation by CaM. Characterization of additional RyR1/RyR2 chimeras and mutants in two predicted Ca2+ binding motifs in RyR1 aa 4081-4092 (EF1) and aa 4116-4127 (EF2) suggests that both EF-hand motifs and additional sequences in the large N-terminal regions are required for isoform-specific RyR1 and RyR2 regulation by CaM at submicromolar Ca2+ concentrations.
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Affiliation(s)
- Le Xu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States
| | - Angela C Gomez
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Cardiac Signaling Center, University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, SC 29425, United States
| | - Daniel A Pasek
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States
| | - Naohiro Yamaguchi
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Cardiac Signaling Center, University of South Carolina, Medical University of South Carolina and Clemson University, Charleston, SC 29425, United States.
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31
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Zheng W, Liu Z. Investigating the inter-subunit/subdomain interactions and motions relevant to disease mutations in the N-terminal domain of ryanodine receptors by molecular dynamics simulation. Proteins 2017; 85:1633-1644. [PMID: 28508509 DOI: 10.1002/prot.25318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/28/2017] [Accepted: 05/08/2017] [Indexed: 11/12/2022]
Abstract
The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles, and numerous disease mutations have been identified in two RyR isoforms, RyR1 in skeletal muscle and RyR2 in cardiac muscle. A deep understanding of the activation/regulation mechanisms of RyRs has been hampered by the shortage of high-resolution structures and dynamic information for this giant tetrameric complex in different functional states. Toward elucidating the molecular mechanisms of disease mutations in RyRs, we performed molecular dynamics simulation of the N-terminal domain (NTD) which is not only the best-resolved structural component of RyRs, but also a hotspot of disease mutations. First, we simulated the tetrameric NTD of wild-type RyR1 and three disease mutants (K155E, R157Q, and R164Q) that perturb the inter-subunit interfaces. Our simulations identified a dynamic network of salt bridges involving charged residues at the inter-subunit/subdomain interfaces and disease-mutation sites. By perturbing this key network, the above three mutations result in greater flexibility with the highest inter-subunit opening probability for R157Q. Next, we simulated the monomeric NTD of RyR2 in the presence or absence of a central Cl- anion which is known to stabilize the interfaces between the three NTD subdomains (A, B, and C). We found that the loss of Cl- restructures the salt-bridge network near the Cl- -binding site, leading to rotations of subdomain A/B relative to subdomain C and enhanced mobility between the subdomains. This finding supports a mechanism for disease mutations in the NTD of RyR2 via perturbation of the Cl- binding. The rich structural and dynamic information gained from this study will guide future mutational and functional studies of the NTD of RyRs. Proteins 2017; 85:1633-1644. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, 14260
| | - Zheng Liu
- Department of Cardiology, Shanghai Tenth People's Hospital and Pan-Vascular Research Institute, Heart, Lung, and Blood Center, Tongji University School of Medicine, Shanghai, China
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Søndergaard MT, Liu Y, Larsen KT, Nani A, Tian X, Holt C, Wang R, Wimmer R, Van Petegem F, Fill M, Chen SRW, Overgaard MT. The Arrhythmogenic Calmodulin p.Phe142Leu Mutation Impairs C-domain Ca2+ Binding but Not Calmodulin-dependent Inhibition of the Cardiac Ryanodine Receptor. J Biol Chem 2017; 292:1385-1395. [PMID: 27927985 PMCID: PMC5270481 DOI: 10.1074/jbc.m116.766253] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/30/2016] [Indexed: 11/29/2022] Open
Abstract
A number of point mutations in the intracellular Ca2+-sensing protein calmodulin (CaM) are arrhythmogenic, yet their underlying mechanisms are not clear. These mutations generally decrease Ca2+ binding to CaM and impair inhibition of CaM-regulated Ca2+ channels like the cardiac Ca2+ release channel (ryanodine receptor, RyR2), and it appears that attenuated CaM Ca2+ binding correlates with impaired CaM-dependent RyR2 inhibition. Here, we investigated the RyR2 inhibitory action of the CaM p.Phe142Leu mutation (F142L; numbered including the start-Met), which markedly reduces CaM Ca2+ binding. Surprisingly, CaM-F142L had little to no aberrant effect on RyR2-mediated store overload-induced Ca2+ release in HEK293 cells compared with CaM-WT. Furthermore, CaM-F142L enhanced CaM-dependent RyR2 inhibition at the single channel level compared with CaM-WT. This is in stark contrast to the actions of arrhythmogenic CaM mutations N54I, D96V, N98S, and D130G, which all diminish CaM-dependent RyR2 inhibition. Thermodynamic analysis showed that apoCaM-F142L converts an endothermal interaction between CaM and the CaM-binding domain (CaMBD) of RyR2 into an exothermal one. Moreover, NMR spectra revealed that the CaM-F142L-CaMBD interaction is structurally different from that of CaM-WT at low Ca2+ These data indicate a distinct interaction between CaM-F142L and the RyR2 CaMBD, which may explain the stronger CaM-dependent RyR2 inhibition by CaM-F142L, despite its reduced Ca2+ binding. Collectively, these results add to our understanding of CaM-dependent regulation of RyR2 as well as the mechanistic effects of arrhythmogenic CaM mutations. The unique properties of the CaM-F142L mutation may provide novel clues on how to suppress excessive RyR2 Ca2+ release by manipulating the CaM-RyR2 interaction.
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Affiliation(s)
- Mads Toft Søndergaard
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
- the Libin Cardiovascular Institute of Alberta, the Department of Physiology and Pharmacology and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Yingjie Liu
- the Libin Cardiovascular Institute of Alberta, the Department of Physiology and Pharmacology and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Kamilla Taunsig Larsen
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Alma Nani
- the Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois 60612
| | - Xixi Tian
- the Libin Cardiovascular Institute of Alberta, the Department of Physiology and Pharmacology and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Christian Holt
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ruiwu Wang
- the Libin Cardiovascular Institute of Alberta, the Department of Physiology and Pharmacology and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Reinhard Wimmer
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Filip Van Petegem
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, and
| | - Michael Fill
- the Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois 60612
| | - S R Wayne Chen
- the Libin Cardiovascular Institute of Alberta, the Department of Physiology and Pharmacology and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
- the Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois 60612
| | - Michael Toft Overgaard
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark,
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Dulhunty AF, Board PG, Beard NA, Casarotto MG. Physiology and Pharmacology of Ryanodine Receptor Calcium Release Channels. ADVANCES IN PHARMACOLOGY 2017; 79:287-324. [DOI: 10.1016/bs.apha.2016.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Yuchi Z, Van Petegem F. Ryanodine receptors under the magnifying lens: Insights and limitations of cryo-electron microscopy and X-ray crystallography studies. Cell Calcium 2016; 59:209-27. [DOI: 10.1016/j.ceca.2016.04.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/08/2016] [Accepted: 04/09/2016] [Indexed: 10/21/2022]
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Zheng W. Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling. Proteins 2015; 83:2307-18. [DOI: 10.1002/prot.24951] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Wenjun Zheng
- Department of Physics; State University of New York at Buffalo; Buffalo New York 14260
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Brath U, Swamy SI, Veiga AX, Tung CC, Van Petegem F, Erdélyi M. Paramagnetic Ligand Tagging To Identify Protein Binding Sites. J Am Chem Soc 2015; 137:11391-8. [PMID: 26289584 PMCID: PMC4583072 DOI: 10.1021/jacs.5b06220] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Transient
biomolecular interactions are the cornerstones of the
cellular machinery. The identification of the binding sites for low
affinity molecular encounters is essential for the development of
high affinity pharmaceuticals from weakly binding leads but is hindered
by the lack of robust methodologies for characterization of weakly
binding complexes. We introduce a paramagnetic ligand tagging approach
that enables localization of low affinity protein–ligand binding
clefts by detection and analysis of intermolecular protein NMR pseudocontact
shifts, which are invoked by the covalent attachment of a paramagnetic
lanthanoid chelating tag to the ligand of interest. The methodology
is corroborated by identification of the low millimolar volatile anesthetic
interaction site of the calcium sensor protein calmodulin. It presents
an efficient route to binding site localization for low affinity complexes
and is applicable to rapid screening of protein–ligand systems
with varying binding affinity.
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Affiliation(s)
- Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Shashikala I Swamy
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Alberte X Veiga
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
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Søndergaard MT, Tian X, Liu Y, Wang R, Chazin WJ, Chen SRW, Overgaard MT. Arrhythmogenic Calmodulin Mutations Affect the Activation and Termination of Cardiac Ryanodine Receptor-mediated Ca2+ Release. J Biol Chem 2015; 290:26151-62. [PMID: 26309258 DOI: 10.1074/jbc.m115.676627] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 11/06/2022] Open
Abstract
The intracellular Ca(2+) sensor calmodulin (CaM) regulates the cardiac Ca(2+) release channel/ryanodine receptor 2 (RyR2), and mutations in CaM cause arrhythmias such as catecholaminergic polymorphic ventricular tachycardia (CPVT) and long QT syndrome. Here, we investigated the effect of CaM mutations causing CPVT (N53I), long QT syndrome (D95V and D129G), or both (CaM N97S) on RyR2-mediated Ca(2+) release. All mutations increased Ca(2+) release and rendered RyR2 more susceptible to store overload-induced Ca(2+) release (SOICR) by lowering the threshold of store Ca(2+) content at which SOICR occurred and the threshold at which SOICR terminated. To obtain mechanistic insights, we investigated the Ca(2+) binding of the N- and C-terminal domains (N- and C-domain) of CaM in the presence of a peptide corresponding to the CaM-binding domain of RyR2. The N53I mutation decreased the affinity of Ca(2+) binding to the N-domain of CaM, relative to CaM WT, but did not affect the C-domain. Conversely, mutations N97S, D95V, and D129G had little or no effect on Ca(2+) binding to the N-domain but markedly decreased the affinity of the C-domain for Ca(2+). These results suggest that mutations D95V, N97S, and D129G alter the interaction between CaM and the CaMBD and thus RyR2 regulation. Because the N53I mutation minimally affected Ca(2+) binding to the C-domain, it must cause aberrant regulation via a different mechanism. These results support aberrant RyR2 regulation as the disease mechanism for CPVT associated with CaM mutations and shows that CaM mutations not associated with CPVT can also affect RyR2. A model for the CaM-RyR2 interaction, where the Ca(2+)-saturated C-domain is constitutively bound to RyR2 and the N-domain senses increases in Ca(2+) concentration, is proposed.
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Affiliation(s)
- Mads T Søndergaard
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark, the Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology and Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Xixi Tian
- the Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology and Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Yingjie Liu
- the Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology and Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Ruiwu Wang
- the Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology and Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Walter J Chazin
- the Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235
| | - S R Wayne Chen
- the Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology and Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Michael T Overgaard
- From the Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark,
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Marshall CB, Nishikawa T, Osawa M, Stathopulos PB, Ikura M. Calmodulin and STIM proteins: Two major calcium sensors in the cytoplasm and endoplasmic reticulum. Biochem Biophys Res Commun 2015; 460:5-21. [PMID: 25998729 DOI: 10.1016/j.bbrc.2015.01.106] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/22/2023]
Abstract
The calcium (Ca(2+)) ion is a universal signalling messenger which plays vital physiological roles in all eukaryotes. To decode highly regulated intracellular Ca(2+) signals, cells have evolved a number of sensor proteins that are ideally adapted to respond to a specific range of Ca(2+) levels. Among many such proteins, calmodulin (CaM) is a multi-functional cytoplasmic Ca(2+) sensor with a remarkable ability to interact with and regulate a plethora of structurally diverse target proteins. CaM achieves this 'multi-talented' functionality through two EF-hand domains, each with an independent capacity to bind targets, and an adaptable flexible linker. By contrast, stromal interaction molecule-1 and -2 (STIMs) have evolved for a specific role in endoplasmic reticulum (ER) Ca(2+) sensing using EF-hand machinery analogous to CaM; however, whereas CaM structurally adjusts to dissimilar binding partners, STIMs use the EF-hand machinery to self-regulate the stability of the Ca(2+) sensing domain. The molecular mechanisms underlying the Ca(2+)-dependent signal transduction by CaM and STIMs have revealed a remarkable repertoire of actions and underscore the flexibility of nature in molecular evolution and adaption to discrete Ca(2+) levels. Recent genomic sequencing efforts have uncovered a number of disease-associated mutations in both CaM and STIM1. This article aims to highlight the most recent key structural and functional findings in the CaM and STIM fields, and discusses how these two Ca(2+) sensor proteins execute their biological functions.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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Distinctive malfunctions of calmodulin mutations associated with heart RyR2-mediated arrhythmic disease. Biochim Biophys Acta Gen Subj 2015; 1850:2168-76. [PMID: 26164367 DOI: 10.1016/j.bbagen.2015.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/22/2015] [Accepted: 07/02/2015] [Indexed: 01/11/2023]
Abstract
Calmodulin (CaM) is a cytoplasmic calcium sensor that interacts with the cardiac ryanodine receptor (RyR2), a large Ca(2+) channel complex that mediates Ca(2+) efflux from the sarcoplasmic reticulum (SR) to activate cardiac muscle contraction. Direct CaM association with RyR2 is an important physiological regulator of cardiac muscle excitation-contraction coupling and defective CaM-RyR2 protein interaction has been reported in cases of heart failure. Recent genetic studies have identified CaM missense mutations in patients with a history of severe cardiac arrhythmogenic disorders that present divergent clinical features, including catecholaminergic polymorphic ventricular tachycardia (CPVT), long QT syndrome (LQTS) and idiopathic ventricular fibrillation (IVF). Herein, we describe how two CPVT- (N54I & N98S) and three LQTS-associated (D96V, D130G & F142L) CaM mutations result in alteration of their biochemical and biophysical properties. Ca(2+)-binding studies indicate that the CPVT-associated CaM mutations, N54I & N98S, exhibit the same or a 3-fold reduced Ca(2+)-binding affinity, respectively, versus wild-type CaM, whereas the LQTS-associated CaM mutants, D96V, D130G & F142L, display more profoundly reduced Ca(2+)-binding affinity. In contrast, all five CaM mutations confer a disparate RyR2 interaction and modulation of [(3)H]ryanodine binding to RyR2, regardless of CPVT or LQTS association. Our findings suggest that the clinical presentation of CPVT or LQTS associated with these five CaM mutations may involve both altered intrinsic Ca(2+)-binding as well as defective interaction with RyR2.
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40
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Van Petegem F. Ryanodine Receptors: Allosteric Ion Channel Giants. J Mol Biol 2015; 427:31-53. [DOI: 10.1016/j.jmb.2014.08.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/02/2014] [Accepted: 08/05/2014] [Indexed: 01/27/2023]
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Seo MD, Enomoto M, Ishiyama N, Stathopulos PB, Ikura M. Structural insights into endoplasmic reticulum stored calcium regulation by inositol 1,4,5-trisphosphate and ryanodine receptors. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1980-91. [PMID: 25461839 DOI: 10.1016/j.bbamcr.2014.11.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
The two major calcium (Ca²⁺) release channels on the sarco/endoplasmic reticulum (SR/ER) are inositol 1,4,5-trisphosphate and ryanodine receptors (IP3Rs and RyRs). They play versatile roles in essential cell signaling processes, and abnormalities of these channels are associated with a variety of diseases. Structural information on IP3Rs and RyRs determined using multiple techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (EM), has significantly advanced our understanding of the mechanisms by which these Ca²⁺ release channels function under normal and pathophysiological circumstances. In this review, structural advances on the understanding of the mechanisms of IP3R and RyR function and dysfunction are summarized. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.
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Affiliation(s)
- Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 443-749, Republic of Korea; College of Pharmacy, Ajou University, Suwon, Gyeonggi 443-749, Republic of Korea
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Noboru Ishiyama
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada.
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Troczka BJ, Williams AJ, Bass C, Williamson MS, Field LM, Davies TGE. Molecular cloning, characterisation and mRNA expression of the ryanodine receptor from the peach-potato aphid, Myzus persicae. Gene 2014; 556:106-12. [PMID: 25447916 PMCID: PMC4309888 DOI: 10.1016/j.gene.2014.11.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/03/2014] [Accepted: 11/14/2014] [Indexed: 02/04/2023]
Abstract
The peach potato aphid, Myzus persicae, is one of the most important agricultural pests of temperate climates. It is mainly controlled through the judicious application of insecticides; however, over time, aphids have developed resistance to many insecticidal classes. The recent introduction of synthetic diamide insecticides, with a novel mode of action, potentially offers new tools to control aphid populations. These diamides act on the ryanodine receptor (RyR), a large endoplasmic calcium release channel. In this study we have cloned cDNAs encoding the complete open reading frame of the RyR from M. persicae. The open reading frame is 15,306 base pairs long and encodes a protein of 5101 amino acids. The aphid RyR shares many of the features of other insect and vertebrate RyRs, including a highly conserved transmembrane region. However, unlike the other RyRs characterised to date, the M. persicae channel does not display alternative splicing at any stage of its developmental cycle, so it cannot generate functional variants of the channel.
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Affiliation(s)
- B J Troczka
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - A J Williams
- Institute of Molecular & Experimental Medicine, Cardiff University School of Medicine, Wales Heart Research Institute, Heath Park, Cardiff CF14 4XN, UK
| | - C Bass
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - M S Williamson
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - L M Field
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - T G E Davies
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
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Calcium-dependent energetics of calmodulin domain interactions with regulatory regions of the Ryanodine Receptor Type 1 (RyR1). Biophys Chem 2014; 193-194:35-49. [PMID: 25145833 DOI: 10.1016/j.bpc.2014.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
Abstract
Calmodulin (CaM) allosterically regulates the homo-tetrameric human Ryanodine Receptor Type 1 (hRyR1): apo CaM activates the channel, while (Ca(2+))4-CaM inhibits it. CaM-binding RyR1 residues 1975-1999 and 3614-3643 were proposed to allow CaM to bridge adjacent RyR1 subunits. Fluorescence anisotropy titrations monitored the binding of CaM and its domains to peptides encompassing hRyR(11975-1999) or hRyR1(3614-3643). Both CaM and its C-domain associated in a calcium-independent manner with hRyR1(3614-3643) while N-domain required calcium and bound ~250-fold more weakly. Association with hRyR1(11975-1999) was weak. Both hRyR1 peptides increased the calcium-binding affinity of both CaM domains, while maintaining differences between them. These energetics support the CaM C-domain association with hRyR1(3614-3643) at low calcium, positioning CaM to respond to calcium efflux. However, the CaM N-domain affinity for hRyR(11975-1999) alone was insufficient to support CaM bridging adjacent RyR1 subunits. Other proteins or elements of the hRyR1 structure must contribute to the energetics of CaM-mediated regulation.
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