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Greene D, Shiferaw Y. Identifying Key Binding Interactions Between the Cardiac L-Type Calcium Channel and Calmodulin Using Molecular Dynamics Simulations. J Phys Chem B 2024; 128:6097-6111. [PMID: 38870543 PMCID: PMC11215769 DOI: 10.1021/acs.jpcb.4c02251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Defects in the binding of the calcium sensing protein calmodulin (CaM) to the L-type calcium channel (CaV1.2) or to the ryanodine receptor type 2 (RyR2) can lead to dangerous cardiac arrhythmias with distinct phenotypes, such as long-QT syndrome (LQTS) and catecholaminergic ventricular tachycardia (CPVT). Certain CaM mutations lead to LQTS while other mutations lead to CPVT, but the mechanisms by which a specific mutation can lead to each disease phenotype are not well-understood. In this study, we use long, 2 μs molecular dynamics simulations and a multitrajectory approach to identify the key binding interactions between the IQ domain of CaV1.2 and CaM. Five key interactions are found between CaV1.2 and CaM in the C-lobe, 1 in the central linker, and 2 in the N-lobe. In addition, while 5 key interactions appear between residues 120-149 in the C-lobe of CaM when it interacts with CaV1.2, only 1 key interaction is found within this region of CaM when it interacts with the RyR2. We show that this difference in the distribution of key interactions correlates with the known distribution of CaM mutations that lead to LQTS or CPVT. This correlation suggests that a disruption of key binding interactions is a plausible mechanism that can lead to these two different disease phenotypes.
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Affiliation(s)
- D’Artagnan Greene
- Department of Physics and
Astronomy, California State University Northridge, 18111 Nordhoff Street, Northridge, California 91330-8268, United States of
America
| | - Yohannes Shiferaw
- Department of Physics and
Astronomy, California State University Northridge, 18111 Nordhoff Street, Northridge, California 91330-8268, United States of
America
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2
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Denesyuk AI, Permyakov SE, Permyakov EA, Johnson MS, Denessiouk K, Uversky VN. Canonical structural-binding modes in the calmodulin-target protein complexes. J Biomol Struct Dyn 2023; 41:7582-7594. [PMID: 36106955 DOI: 10.1080/07391102.2022.2123391] [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: 05/11/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Intracellular calcium sensor protein calmodulin (CaM) belongs to the large EF-hand protein superfamily. CaM shows a unique and not fully understood ability to bind to multiple targets, allows them to participate in a variety of regulatory processes. The protein has two approximately symmetrical globular domains (the N- and C-lobes). Analysis of the CaM-binding sites of target proteins showed that they have two hydrophobic 'anchor' amino acids separated by 10 to 17 residues. Consequently, several CaM-binding motifs: {1-10}, {1-11}, {1-13}, {1-14}, {1-16}, {1-17}, differing by the distance between the two anchor residues along the amino acid sequence, have been identified. Despite extensive structural information on the role of target-protein amino acid residues in the formation of complexes with CaM, much less is known about the role of amino acids from CaM contributing to these interactions. In this work, a quantitative analysis of the contact surfaces of CaM and target proteins has been carried out for 35 representative three-dimensional structures. It has been shown that, in addition to the two hydrophobic terminal residues of the target fragment, the interaction also involves residues that are 4 residues earlier in the sequence (binding mode {1-5}). It has also been found that the N- and C-lobes of CaM bind the {1-5} motif located at the ends of the target in a structurally identical manner. Methionine residues at positions 51 (corresponding to 124 in the C-lobe), 71 (144), and 72 (145) of the CaM amino acid sequence are key hydrophobic residues for this interaction. They are located at the N- and C-boundaries of the even EF-hand motifs. The hydrophobic core of CaM ('Ф-quatrefoil') consists of 10 amino acids in the N-lobe (and in the C-lobe): Phe16 (Phe89), Phe19 (Phe92), Ile27 (Ile100), Thr29 (Ala102), Leu32 (Leu105), Ile52 (Ile125), Val55 (Ala128), Ile63 (Val136), Phe65 (Tyr138), and Phe68 (Phe141) and do not intersect with the target-binding methionine residues. CaM belongs to the 'dynamic' group of EF-hand proteins, in which calcium and protein ligand binding causes only global conformational changes but does not alter the conservative 'black' and 'grey' clusters described in our earlier works (PLoS One. 2014; 9(10):e109287). The membership of CaM in the 'dynamic' group is determined by the triggering and protective methionine layer: Met51 (Met124), Met71 (Met144) and Met72 (Met145). HIGHLIGHTSInterchain interactions in the unique 35 CaM complex structures were analyzed.Methionine amino acids of the N- and C-lobes of CaM form triggering and protective layers.Interactions of the target terminal residues with these methionine layers are structurally identical.CaM belonging to the 'dynamic' group is determined by the triggering and protective methionine layer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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3
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Bej A, Ames JB. Chemical shift assignments of calmodulin bound to a cytosolic domain of GluN2A (residues 1004-1024) from the NMDA receptor. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:89-93. [PMID: 37029330 DOI: 10.1007/s12104-023-10125-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023]
Abstract
N-methyl-D-aspartate receptors (NMDARs) consist of glycine-binding GluN1 and glutamate-binding GluN2 subunits that form tetrameric ion channels. NMDARs in the neuronal post-synaptic membrane are important for controlling neuroplasticity and synaptic transmission in the brain. Calmodulin (CaM) binds to the cytosolic C0 domains of both GluN1 (residues 841-865) and GluN2 (residues 1004-1024) that may play a role in the Ca2+-dependent desensitization of NMDAR channels. Mutations that disrupt Ca2+-dependent desensitization of NMDARs are linked to Alzheimer's disease, depression, stroke, epilepsy, and schizophrenia. NMR chemical shift assignments are reported here for Ca2+-saturated CaM bound to the GluN2A C0 domain of NMDAR (BMRB no. 51821).
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Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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4
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Bej A, Ames JB. Chemical shift assignments of calmodulin bound to the GluN1 C0 domain (residues 841-865) of the NMDA receptor. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:61-65. [PMID: 36739573 PMCID: PMC10232624 DOI: 10.1007/s12104-023-10121-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 05/31/2023]
Abstract
Neuroplasticity and synaptic transmission in the brain are regulated by N-methyl-D-aspartate receptors (NMDARs) that consist of hetero-tetrameric combinations of the glycine-binding GluN1 and glutamate-binding GluN2 subunits. Calmodulin (CaM) binds to the cytosolic C0 domain of GluN1 (residues 841-865) that may play a role in the Ca2+-dependent inactivation (CDI) of NMDAR channel activity. Dysregulation of NMDARs are linked to various neurological disorders, including Alzheimer's disease, depression, stroke, epilepsy, and schizophrenia. Here, we report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the GluN1 C0 domain of the human NMDAR (BMRB no. 51715).
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Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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5
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Bartels P, Salveson I, Coleman AM, Anderson DE, Jeng G, Estrada-Tobar ZM, Man KNM, Yu Q, Kuzmenkina E, Nieves-Cintron M, Navedo MF, Horne MC, Hell JW, Ames JB. Half-calcified calmodulin promotes basal activity and inactivation of the L-type calcium channel Ca V1.2. J Biol Chem 2022; 298:102701. [PMID: 36395884 PMCID: PMC9764201 DOI: 10.1016/j.jbc.2022.102701] [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: 07/11/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
The L-type Ca2+ channel CaV1.2 controls gene expression, cardiac contraction, and neuronal activity. Calmodulin (CaM) governs CaV1.2 open probability (Po) and Ca2+-dependent inactivation (CDI) but the mechanisms remain unclear. Here, we present electrophysiological data that identify a half Ca2+-saturated CaM species (Ca2/CaM) with Ca2+ bound solely at the third and fourth EF-hands (EF3 and EF4) under resting Ca2+ concentrations (50-100 nM) that constitutively preassociates with CaV1.2 to promote Po and CDI. We also present an NMR structure of a complex between the CaV1.2 IQ motif (residues 1644-1665) and Ca2/CaM12', a calmodulin mutant in which Ca2+ binding to EF1 and EF2 is completely disabled. We found that the CaM12' N-lobe does not interact with the IQ motif. The CaM12' C-lobe bound two Ca2+ ions and formed close contacts with IQ residues I1654 and Y1657. I1654A and Y1657D mutations impaired CaM binding, CDI, and Po, as did disabling Ca2+ binding to EF3 and EF4 in the CaM34 mutant when compared to WT CaM. Accordingly, a previously unappreciated Ca2/CaM species promotes CaV1.2 Po and CDI, identifying Ca2/CaM as an important mediator of Ca signaling.
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Affiliation(s)
- Peter Bartels
- Department of Pharmacology, University of California, Davis, California, USA
| | - Ian Salveson
- Department of Chemistry, University of California, Davis, California, USA
| | - Andrea M Coleman
- Department of Pharmacology, University of California, Davis, California, USA; Department of Chemistry, University of California, Davis, California, USA
| | - David E Anderson
- Department of Chemistry, University of California, Davis, California, USA
| | - Grace Jeng
- Department of Pharmacology, University of California, Davis, California, USA
| | | | - Kwun Nok Mimi Man
- Department of Pharmacology, University of California, Davis, California, USA
| | - Qinhong Yu
- Department of Chemistry, University of California, Davis, California, USA
| | - Elza Kuzmenkina
- Center for Pharmacology, University of Cologne, Cologne, Germany
| | | | - Manuel F Navedo
- Department of Pharmacology, University of California, Davis, California, USA
| | - Mary C Horne
- Department of Pharmacology, University of California, Davis, California, USA.
| | - Johannes W Hell
- Department of Pharmacology, University of California, Davis, California, USA.
| | - James B Ames
- Department of Chemistry, University of California, Davis, California, USA.
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6
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Bej A, Ames JB. Chemical shift assignments of calmodulin under standard conditions at neutral pH. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:213-218. [PMID: 35460468 PMCID: PMC9510097 DOI: 10.1007/s12104-022-10082-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/30/2022] [Indexed: 05/10/2023]
Abstract
The Ca2+ sensor protein, calmodulin (CaM) is ubiquitously expressed in all cells where it binds to hundreds of different target proteins, including dozens of enzymes, receptors, ion channels and numerous Ca2+ transporters. The only published NMR chemical shift assignments for Ca2+-bound CaM (in the absence of a target) have been determined under acidic conditions: at pH 6.5/310 K (BMRB 6541) and pH 6.3/320 K (BMRB 547). However, some CaM/target complexes are not soluble under these conditions. Also, amide chemical shifts are very sensitive to pH and temperature, which can cause large baseline errors when using the existing chemical shift assignments of free CaM to calculate chemical shift perturbations caused by target binding at neutral pH and physiological temperature. We report complete NMR chemical shift assignments of Ca2+-saturated CaM under a set of standard conditions at neutral pH and 308 K that will enable more accurate chemical shift comparison between free CaM and CaM/target complexes (BMRB 51289).
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Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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7
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Bej A, Ames JB. Chemical shift assignments of calmodulin bound to a C-terminal site (residues 1120-1147) in the β-subunit of a retinal cyclic nucleotide-gated channel (CNGB1). BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:337-341. [PMID: 35986879 PMCID: PMC9510104 DOI: 10.1007/s12104-022-10101-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Retinal cyclic nucleotide-gated (CNG) channels consist of two protein subunits (CNGA1 and CNGB1). Calmodulin (CaM) binds to two separate sites within the cytosolic region of CNGB1: CaM binding to an N-terminal site (human CNGB1 residues 565-587, called CaM1) decreases the open probability of CNG channels at elevated Ca2+ levels in dark-adapted photoreceptors, whereas CaM binding to a separate C-terminal site (CNGB1 residues 1120-1147, called CaM2) may increase channel open probability in light activated photoreceptors. We recently reported NMR chemical shift assignments of Ca2+-saturated CaM bound to the CaM1 site of CNGB1 (BMRB no. 51222). Here, we report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the C-terminal CaM2 site of CNGB1 (BMRB no. 51447).
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Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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8
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Sosa-Peinado A, León-Cruz E, Velázquez-López I, Matuz-Mares D, Cano-Sánchez P, González-Andrade M. Theoretical-experimental studies of calmodulin-peptide interactions at different calcium equivalents. J Biomol Struct Dyn 2022; 40:2689-2700. [DOI: 10.1080/07391102.2020.1841679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Erika León-Cruz
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Deyamira Matuz-Mares
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Patricia Cano-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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9
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Bej A, Ames JB. Chemical shift assignments of calmodulin bound to the β-subunit of a retinal cyclic nucleotide-gated channel (CNGB1). BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:147-151. [PMID: 35107779 PMCID: PMC9068646 DOI: 10.1007/s12104-022-10072-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/24/2022] [Indexed: 05/25/2023]
Abstract
Rod cyclic nucleotide-gated (CNG) channels are formed by two protein subunits (CNGA1 and CNGB1). Calmodulin (CaM) binds to the cytosolic regulatory domain of CNGB1 and decreases the open probability of CNGA1/CNGB1 channels. The CaM binding site within bovine CNGB1 (residues 679-702) binds tightly to Ca2+-bound CaM, which promotes Ca2+-induced inactivation of CNGA1/CNGB1 channels in retinal rods. We report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the CaM-binding domain of CNGB1 (BMRB no. 51222).
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Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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10
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Yaduvanshi S, Ero R, Kumar V. The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics. PLoS One 2021; 16:e0258112. [PMID: 34610038 PMCID: PMC8491939 DOI: 10.1371/journal.pone.0258112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/18/2021] [Indexed: 11/18/2022] Open
Abstract
Calmodulin, a ubiquitous eukaryotic calcium sensor responsible for the regulation of many fundamental cellular processes, is a highly flexible protein and exhibits an unusually wide range of conformations. Furthermore, CaM is known to interact with more than 300 cellular targets. Molecular dynamics (MD) simulation trajectories suggest that EF-hand loops show different magnitudes of flexibility. Therefore, the four EF-hand motifs have different affinities for Ca2+ ions, which enables CaM to function on wide range of Ca2+ ion concentrations. EF-hand loops are 2-3 times more flexible in apo CaM whereas least flexible in Ca2+/CaM-IQ motif complexes. We report a unique intermediate conformation of Ca2+/CaM while transitioning from extended to compact form. We also report the complex formation process between Ca2+/CaM and IQ CaM-binding motifs. Our results showed how IQ motif recognise its binding site on the CaM and how CaM transforms from extended to compact form upon binding to IQ motif.
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Affiliation(s)
- Shivani Yaduvanshi
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Noida, Noida, Uttar Pradesh, India
| | - Rya Ero
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veerendra Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Noida, Noida, Uttar Pradesh, India
- * E-mail:
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11
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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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12
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Crystal structures of Ca 2+-calmodulin bound to Na V C-terminal regions suggest role for EF-hand domain in binding and inactivation. Proc Natl Acad Sci U S A 2019; 116:10763-10772. [PMID: 31072926 DOI: 10.1073/pnas.1818618116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.
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Laugel-Haushalter V, Morkmued S, Stoetzel C, Geoffroy V, Muller J, Boland A, Deleuze JF, Chennen K, Pitiphat W, Dollfus H, Niederreither K, Bloch-Zupan A, Pungchanchaikul P. Genetic Evidence Supporting the Role of the Calcium Channel, CACNA1S, in Tooth Cusp and Root Patterning. Front Physiol 2018; 9:1329. [PMID: 30319441 PMCID: PMC6170876 DOI: 10.3389/fphys.2018.01329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/03/2018] [Indexed: 01/08/2023] Open
Abstract
In this study, we report a unique dominantly inherited disorganized supernumerary cusp and single root phenotype presented by 11 affected individuals belonging to 5 north-eastern Thai families. Using whole exome sequencing (WES) we identified a common single missense mutation that segregates with the phenotype in exon 6 of CACNA1S (Cav1.1) (NM_000069.2: c.[865A > G];[=] p.[Ile289Val];[=]), the Calcium Channel, Voltage-Dependent, L Type, Alpha-1s Subunit, OMIM ∗ 114208), affecting a highly conserved amino-acid isoleucine residue within the pore forming subdomain of CACNA1S protein. This is a strong genetic evidence that a voltage-dependent calcium ion channel is likely to play a role in influencing tooth morphogenesis and patterning.
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Affiliation(s)
- Virginie Laugel-Haushalter
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine, FMTS, Université de Strasbourg, Strasbourg, France
| | - Supawich Morkmued
- Biofilm Research Group, Department of Pediatric Dentistry, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CERBM, INSERM U 1258, CNRS- UMR 7104, Université de Strasbourg, Strasbourg, France
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine, FMTS, Université de Strasbourg, Strasbourg, France
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine, FMTS, Université de Strasbourg, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine, FMTS, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, Commissariat à l'Energie Atomique et aux Energies Alternatives, Paris, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, Commissariat à l'Energie Atomique et aux Energies Alternatives, Paris, France
| | - Kirsley Chennen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CERBM, INSERM U 1258, CNRS- UMR 7104, Université de Strasbourg, Strasbourg, France.,Department of Computer Science, ICube, CNRS - UMR 7357, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Strasbourg, France
| | - Waranuch Pitiphat
- Department of Community Dentistry, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine, FMTS, Université de Strasbourg, Strasbourg, France.,Centre de Référence pour les Affections Rares en Génétique Ophtalmologique, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Niederreither
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CERBM, INSERM U 1258, CNRS- UMR 7104, Université de Strasbourg, Strasbourg, France.,Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France
| | - Agnès Bloch-Zupan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CERBM, INSERM U 1258, CNRS- UMR 7104, Université de Strasbourg, Strasbourg, France.,Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Hôpitaux Universitaires de Strasbourg (HUS), Pôle de Médecine et Chirurgie Bucco-Dentaires Hôpital Civil, Centre de Référence des Maladies Rares Orales et Dentaires, O-Rares, Filière Santé Maladies Rares TETE COU, European Reference Network ERN CRANIO, Strasbourg, France
| | - Patimaporn Pungchanchaikul
- Biofilm Research Group, Department of Pediatric Dentistry, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
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14
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Thomas CM, Timson DJ. Calmodulins from Schistosoma mansoni: Biochemical analysis and interaction with IQ-motifs from voltage-gated calcium channels. Cell Calcium 2018; 74:1-13. [DOI: 10.1016/j.ceca.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 01/27/2023]
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15
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Niu J, Yang W, Yue DT, Inoue T, Ben-Johny M. Duplex signaling by CaM and Stac3 enhances Ca V1.1 function and provides insights into congenital myopathy. J Gen Physiol 2018; 150:1145-1161. [PMID: 29950399 PMCID: PMC6080896 DOI: 10.1085/jgp.201812005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/23/2018] [Accepted: 05/11/2018] [Indexed: 01/24/2023] Open
Abstract
CaV1.1 is essential for skeletal muscle excitation-contraction coupling. Its functional expression is tuned by numerous regulatory proteins, yet underlying modulatory mechanisms remain ambiguous as CaV1.1 fails to function in heterologous systems. In this study, by dissecting channel trafficking versus gating, we evaluated the requirements for functional CaV1.1 in heterologous systems. Although coexpression of the auxiliary β subunit is sufficient for surface-membrane localization, this baseline trafficking is weak, and channels elicit a diminished open probability. The regulatory proteins calmodulin and stac3 independently enhance channel trafficking and gating via their interaction with the CaV1.1 carboxy terminus. Myopathic stac3 mutations weaken channel binding and diminish trafficking. Our findings demonstrate that multiple regulatory proteins orchestrate CaV1.1 function via duplex mechanisms. Our work also furnishes insights into the pathophysiology of stac3-associated congenital myopathy and reveals novel avenues for pharmacological intervention.
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Affiliation(s)
- Jacqueline Niu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
| | - Wanjun Yang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
| | | | - Takanari Inoue
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD
- Center for Cell Dynamics, Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, MD
| | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY
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16
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Direct visualization of interaction between calmodulin and connexin45. Biochem J 2017; 474:4035-4051. [PMID: 28963343 DOI: 10.1042/bcj20170426] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/12/2017] [Accepted: 09/25/2017] [Indexed: 01/21/2023]
Abstract
Calmodulin (CaM) is an intracellular Ca2+ transducer involved in numerous activities in a broad Ca2+ signaling network. Previous studies have suggested that the Ca2+/CaM complex may participate in gap junction regulation via interaction with putative CaM-binding motifs in connexins; however, evidence of direct interactions between CaM and connexins has remained elusive to date due to challenges related to the study of membrane proteins. Here, we report the first direct interaction of CaM with Cx45 (connexin45) of γ-family in living cells under physiological conditions by monitoring bioluminescence resonance energy transfer. The interaction between CaM and Cx45 in cells is strongly dependent on intracellular Ca2+ concentration and can be blocked by the CaM inhibitor, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide hydrochloride (W7). We further reveal a CaM-binding site at the cytosolic loop (residues 164-186) of Cx45 using a peptide model. The strong binding (Kd ∼ 5 nM) observed between CaM and Cx45 peptide, monitored by fluorescence-labeled CaM, is found to be Ca2+-dependent. Furthermore, high-resolution nuclear magnetic resonance spectroscopy reveals that CaM and Cx45 peptide binding leads to global chemical shift changes of 15N-labeled CaM, but does not alter the size of the structure. Observations involving both N- and C-domains of CaM to interact with the Cx45 peptide differ from the embraced interaction with Cx50 from another connexin family. Such interaction further increases Ca2+ sensitivity of CaM, especially at the N-terminal domain. Results of the present study suggest that both helicity and the interaction mode of the cytosolic loop are likely to contribute to CaM's modulation of connexins.
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17
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Zhang P, Tripathi S, Trinh H, Cheung MS. Opposing Intermolecular Tuning of Ca 2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides. Biophys J 2017; 112:1105-1119. [PMID: 28355539 PMCID: PMC5374985 DOI: 10.1016/j.bpj.2017.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/27/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+ signaling pathways in neurons. It was shown experimentally that Ca2+/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca2+-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca2+ affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng13–49), which binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. Unlike the holoCaM-CaMKII peptide, whose structure can be determined by crystallography, the structural description of the apoCaM-Ng13–49 is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng13–49 structures by matching the changes in the chemical shifts of CaM upon Ng13–49 binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca2+ affinity for CaM with and without binding targets in atomistic models using Jarzynski’s equality. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng13–49 by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM, enabling Ca2+ release. In contrast, CaMKII peptide increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng13–49 and holoCaM-CaMKII delineates the importance of CaM’s progressive mechanism of target binding on its Ca2+ binding affinities.
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Affiliation(s)
- Pengzhi Zhang
- Department of Physics, University of Houston, Houston, Texas
| | | | - Hoa Trinh
- Department of Physics, University of Houston, Houston, Texas
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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18
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Keller JP. Solution of the structure of a calmodulin–peptide complex in a novel configuration from a variably twinned data set. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:22-31. [DOI: 10.1107/s2059798316019318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 12/02/2016] [Indexed: 12/12/2022]
Abstract
Structure determination of conformationally variable proteins can prove challenging even when many possible molecular-replacement (MR) search models of high sequence similarity are available. Calmodulin (CaM) is perhaps the best-studied archetype of these flexible proteins: while there are currently ∼450 structures of significant sequence similarity available in the Protein Data Bank (PDB), novel conformations of CaM and complexes thereof continue to be reported. Here, the details of the solution of a novel peptide–CaM complex structure by MR are presented, in which only one MR solution of marginal quality was found despite the use of 120 different search models, an exclusivity enhanced by the presence of a high degree of hemihedral twinning (overall refined twin fraction = 0.43). Ambiguities in the initial MR electron-density maps were overcome by using MR-SAD: phases from the MR partial model were used to identify weak anomalous scatterers (calcium, sulfur and chloride), which were in turn used to improve the phases, automatically rebuild the structure and resolve sequence ambiguities. Retrospective analysis of consecutive wedges of the original data sets showed twin fractions ranging from 0.32 to 0.55, suggesting that the data sets were variably twinned. Despite these idiosyncrasies and obstacles, the data themselves and the final model were of high quality and indeed showed a novel, nearly right-angled conformation of the bound peptide.
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19
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Briot J, Tétreault MP, Bourdin B, Parent L. Inherited Ventricular Arrhythmias: The Role of the Multi-Subunit Structure of the L-Type Calcium Channel Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 966:55-64. [PMID: 28315127 DOI: 10.1007/5584_2016_186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The normal heartbeat is conditioned by transient increases in the intracellular free Ca2+ concentration. Ca2+ influx in cardiomyocytes is regulated by the activity of the heteromeric L-type voltage-activated CaV1.2 channel. A complex network of interactions between the different proteins forming the ion channel supports the kinetics and the activation gating of the Ca2+ influx. Alterations in the biophysical and biochemical properties or in the biogenesis in any of these proteins can lead to serious disturbances in the cardiac rhythm. The multi-subunit nature of the channel complex is better comprehended by examining the high-resolution three-dimensional structure of the closely related CaV1.1 channel. The architectural map identifies precise interaction loci between the different subunits and paves the way for elucidating the mechanistic basis for the regulation of Ca2+ balance in cardiac myocytes under physiological and pathological conditions.
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Affiliation(s)
- Julie Briot
- Département de Pharmacologie et Physiologie, Faculté de Médecine, Institut Cardiologie de Montréal, Université de Montréal, 5000 Bélanger, Montréal, QC, H1T 1C8, Canada
| | - Marie-Philippe Tétreault
- Département de Pharmacologie et Physiologie, Faculté de Médecine, Institut Cardiologie de Montréal, Université de Montréal, 5000 Bélanger, Montréal, QC, H1T 1C8, Canada
| | - Benoîte Bourdin
- Département de Pharmacologie et Physiologie, Faculté de Médecine, Institut Cardiologie de Montréal, Université de Montréal, 5000 Bélanger, Montréal, QC, H1T 1C8, Canada
| | - Lucie Parent
- Département de Pharmacologie et Physiologie, Faculté de Médecine, Institut Cardiologie de Montréal, Université de Montréal, 5000 Bélanger, Montréal, QC, H1T 1C8, Canada.
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20
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TRPM4-dependent post-synaptic depolarization is essential for the induction of NMDA receptor-dependent LTP in CA1 hippocampal neurons. Pflugers Arch 2015; 468:593-607. [PMID: 26631168 PMCID: PMC4792339 DOI: 10.1007/s00424-015-1764-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022]
Abstract
TRPM4 is a calcium-activated but calcium-impermeable non-selective cation (CAN) channel. Previous studies have shown that TRPM4 is an important regulator of Ca(2+)-dependent changes in membrane potential in excitable and non-excitable cell types. However, its physiological significance in neurons of the central nervous system remained unclear. Here, we report that TRPM4 proteins form a CAN channel in CA1 neurons of the hippocampus and we show that TRPM4 is an essential co-activator of N-methyl-D-aspartate (NMDA) receptors (NMDAR) during the induction of long-term potentiation (LTP). Disrupting the Trpm4 gene in mice specifically eliminates NMDAR-dependent LTP, while basal synaptic transmission, short-term plasticity, and NMDAR-dependent long-term depression are unchanged. The induction of LTP in Trpm4 (-/-) neurons was rescued by facilitating NMDA receptor activation or post-synaptic membrane depolarization. Accordingly, we obtained normal LTP in Trpm4 (-/-) neurons in a pairing protocol, where post-synaptic depolarization was applied in parallel to pre-synaptic stimulation. Taken together, our data are consistent with a novel model of LTP induction in CA1 hippocampal neurons, in which TRPM4 is an essential player in a feed-forward loop that generates the post-synaptic membrane depolarization which is necessary to fully activate NMDA receptors during the induction of LTP but which is dispensable for the induction of long-term depression (LTD). These results have important implications for the understanding of the induction process of LTP and the development of nootropic medication.
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21
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Abstract
The structures of the cytosolic portion of voltage activated sodium channels (CTNav) in complexes with calmodulin and other effectors in the presence and the absence of calcium provide information about the mechanisms by which these effectors regulate channel activity. The most studied of these complexes, those of Nav1.2 and Nav1.5, show details of the conformations and the specific contacts that are involved in channel regulation. Another voltage activated sodium channel, Nav1.4, shows significant calcium dependent inactivation, while its homolog Nav1.5 does not. The available structures shed light on the possible localization of the elements responsible for this effect. Mutations in the genes of these 3 Nav channels are associated with several disease conditions: Nav1.2, neurological conditions; Nav1.4, syndromes involving skeletal muscle; and Nav1.5, cardiac arrhythmias. Many of these disease-specific mutations are located at the interfaces involving CTNav and its effectors.
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Affiliation(s)
- Sandra B Gabelli
- a Structural Enzymology and Thermodynamics Group; Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD USA.,b Division of Cardiology; Department of Medicine, Johns Hopkins University School of Medicine ; Baltimore , MD USA.,c Department of Oncology ; Johns Hopkins University School of Medicine ; Baltimore , MD USA
| | - Jesse B Yoder
- a Structural Enzymology and Thermodynamics Group; Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD USA
| | - Gordon F Tomaselli
- b Division of Cardiology; Department of Medicine, Johns Hopkins University School of Medicine ; Baltimore , MD USA
| | - L Mario Amzel
- a Structural Enzymology and Thermodynamics Group; Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD USA
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22
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The Ever Changing Moods of Calmodulin: How Structural Plasticity Entails Transductional Adaptability. J Mol Biol 2014; 426:2717-35. [DOI: 10.1016/j.jmb.2014.05.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 11/20/2022]
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23
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Halling DB, Kenrick SA, Riggs AF, Aldrich RW. Calcium-dependent stoichiometries of the KCa2.2 (SK) intracellular domain/calmodulin complex in solution. ACTA ACUST UNITED AC 2014; 143:231-52. [PMID: 24420768 PMCID: PMC4001768 DOI: 10.1085/jgp.201311007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biophysical analyses indicate that the Ca2+-activated K+ channel SK2 binds calmodulin with multiple stoichiometries, distinct from the two SK2-two calmodulin stoichiometry identified by crystallography. Ca2+ activates SK Ca2+-activated K+ channels through the protein Ca2+ sensor, calmodulin (CaM). To understand how SK channels operate, it is necessary to determine how Ca2+ regulates CaM binding to its target on SK. Tagless, recombinant SK peptide (SKp), was purified for binding studies with CaM at low and high Ca2+ concentrations. Composition gradient multi-angle light scattering accurately measures the molar mass, stoichiometry, and affinity of protein complexes. In 2 mM Ca2+, SKp and CaM bind with three different stoichiometries that depend on the molar ratio of SKp:CaM in solution. These complexes include 28 kD 1SKp/1CaM, 39 kD 2SKp/1CaM, and 44 kD 1SKp/2CaM. A 2SKp/2CaM complex, observed in prior crystallographic studies, is absent. At <5 nM Ca2+, 1SKp/1CaM and 2SKp/1CaM were observed; however, 1SKp/2CaM was absent. Analytical ultracentrifugation was used to characterize the physical properties of the three SKp/CaM stoichiometries. In high Ca2+, the sedimentation coefficient is smaller for a 1SKp:1CaM solution than it is for either 2SKp:1CaM or 1SKp:2CaM. At low Ca2+ and at >100 µM protein concentrations, a molar excess of SKp over CaM causes aggregation. Aggregation is not observed in Ca2+ or with CaM in molar excess. In low Ca2+ both 1SKp:1CaM and 1SKp:2CaM solutions have similar sedimentation coefficients, which is consistent with the absence of a 1SKp/2CaM complex in low Ca2+. These results suggest that complexes with stoichiometries other than 2SKp/2CaM are important in gating.
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Affiliation(s)
- D Brent Halling
- Department of Neuroscience, 2 Center for Learning and Memory, The University of Texas at Austin, Austin, TX 78712
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24
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Russo L, Maestre-Martinez M, Wolff S, Becker S, Griesinger C. Interdomain dynamics explored by paramagnetic NMR. J Am Chem Soc 2013; 135:17111-20. [PMID: 24111622 DOI: 10.1021/ja408143f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An ensemble-based approach is presented to explore the conformational space sampled by a multidomain protein showing moderate interdomain dynamics in terms of translational and rotational motions. The strategy was applied on a complex of calmodulin (CaM) with the IQ-recognition motif from the voltage-gated calcium channel Ca(v)1.2 (IQ), which adopts three different interdomain orientations in the crystal. The N60D mutant of calmodulin was used to collect pseudocontact shifts and paramagnetically induced residual dipolar couplings for six different lanthanide ions. Then, starting from the crystal structure, pools of conformations were generated by free MD. We found the three crystal conformations in solution, but four additional MD-derived conformations had to be included into the ensemble to fulfill all the paramagnetic data and cross-validate optimally against unused paramagnetic data. Alternative approaches led to similar ensembles. Our "ensemble" approach is a simple and efficient tool to probe and describe the interdomain dynamics and represents a general method that can be used to provide a proper ensemble description of multidomain proteins.
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Affiliation(s)
- Luigi Russo
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 37077 Göttingen, Germany
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25
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Prell T, Lautenschläger J, Grosskreutz J. Calcium-dependent protein folding in amyotrophic lateral sclerosis. Cell Calcium 2013; 54:132-43. [DOI: 10.1016/j.ceca.2013.05.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/16/2013] [Accepted: 05/18/2013] [Indexed: 12/25/2022]
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26
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Van Petegem F, Lobo PA, Ahern CA. Seeing the forest through the trees: towards a unified view on physiological calcium regulation of voltage-gated sodium channels. Biophys J 2013; 103:2243-51. [PMID: 23283222 DOI: 10.1016/j.bpj.2012.10.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/26/2012] [Accepted: 10/18/2012] [Indexed: 12/23/2022] Open
Abstract
Voltage-gated sodium channels (Na(V)s) underlie the upstroke of the action potential in the excitable tissues of nerve and muscle. After opening, Na(V)s rapidly undergo inactivation, a crucial process through which sodium conductance is negatively regulated. Disruption of inactivation by inherited mutations is an established cause of lethal cardiac arrhythmia, epilepsy, or painful syndromes. Intracellular calcium ions (Ca(2+)) modulate sodium channel inactivation, and multiple players have been suggested in this process, including the cytoplasmic Na(V) C-terminal region including two EF-hands and an IQ motif, the Na(V) domain III-IV linker, and calmodulin. Calmodulin can bind to the IQ domain in both Ca(2+)-bound and Ca(2+)-free conditions, but only to the DIII-IV linker in a Ca(2+)-loaded state. The mechanism of Ca(2+) regulation, and its composite effect(s) on channel gating, has been shrouded in much controversy owing to numerous apparent experimental inconsistencies. Herein, we attempt to summarize these disparate data and propose a novel, to our knowledge, physiological mechanism whereby calcium ions promote sodium current facilitation due to Ca(2+) memory at high-action-potential frequencies where Ca(2+) levels may accumulate. The available data suggest that this phenomenon may be disrupted in diseases where cytoplasmic calcium ion levels are chronically high and where targeted phosphorylation may decouple the Ca(2+) regulatory machinery. Many Na(V) disease mutations associated with electrical dysfunction are located in the Ca(2+)-sensing machinery and misregulation of Ca(2+)-dependent channel modulation is likely to contribute to disease phenotypes.
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Affiliation(s)
- Filip Van Petegem
- The Department of Biochemistry and Molecular Biology, Vancouver, British Columbia, Canada.
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27
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Tidow H, Nissen P. Structural diversity of calmodulin binding to its target sites. FEBS J 2013; 280:5551-65. [PMID: 23601118 DOI: 10.1111/febs.12296] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/11/2013] [Accepted: 04/16/2013] [Indexed: 11/28/2022]
Abstract
Calmodulin (CaM) is a ubiquitous, highly conserved, eukaryotic protein that binds to and regulates a number of diverse target proteins involved in different functions such as metabolism, muscle contraction, apoptosis, memory, inflammation and the immune response. In this minireview, we analyze the large number of CaM-complex structures deposited in the Protein Data Bank (i.e. crystal and nuclear magnetic resonance structures) to gain insight into the structural diversity of CaM-binding sites and mechanisms, such as those for CaM-activated protein kinases and phosphatases, voltage-gated Ca(2+)-channels and the plasma membrane Ca(2+)-ATPase.
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Affiliation(s)
- Henning Tidow
- Centre for Membrane Pumps in Cells and Disease - PUMPkin, Aarhus University, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Denmark
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28
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Kovalevskaya NV, van de Waterbeemd M, Bokhovchuk FM, Bate N, Bindels RJM, Hoenderop JGJ, Vuister GW. Structural analysis of calmodulin binding to ion channels demonstrates the role of its plasticity in regulation. Pflugers Arch 2013; 465:1507-19. [PMID: 23609407 DOI: 10.1007/s00424-013-1278-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 04/02/2013] [Indexed: 12/17/2022]
Abstract
The Ca²⁺-binding protein calmodulin (CaM) is a well-known regulator of ion-channel activity. Consequently, the Protein Data Bank contains many structures of CaM in complex with different fragments of ion channels that together display a variety of binding modes. In addition to the canonical interaction, in which CaM engages its target with both its domains, many of the ion-channel-CaM complexes demonstrate alternative non-canonical binding modes that depend on the target and experimental conditions. Based on these findings, several mechanisms of ion-channel regulation by CaM have been proposed, all exploiting its plasticity and flexibility in interacting with its targets. In this review, we focus on complexes of CaM with either the voltage-gated calcium channels; the voltage-gated sodium channels or the small conductance calcium-activated potassium channels, for which both structural and functional data are available. For each channel, the functional relevance of these structural data and possible mechanism of calcium-dependent (in)activation and/or facilitation are discussed in detail.
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Affiliation(s)
- Nadezda V Kovalevskaya
- Department of Physiology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein Zuid 26-28, Nijmegen, 6525, GA, The Netherlands
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29
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Oz S, Benmocha A, Sasson Y, Sachyani D, Almagor L, Lee A, Hirsch JA, Dascal N. Competitive and non-competitive regulation of calcium-dependent inactivation in CaV1.2 L-type Ca2+ channels by calmodulin and Ca2+-binding protein 1. J Biol Chem 2013; 288:12680-91. [PMID: 23530039 DOI: 10.1074/jbc.m113.460949] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CaV1.2 interacts with the Ca(2+) sensor proteins, calmodulin (CaM) and calcium-binding protein 1 (CaBP1), via multiple, partially overlapping sites in the main subunit of CaV1.2, α1C. Ca(2+)/CaM mediates a negative feedback regulation of Cav1.2 by incoming Ca(2+) ions (Ca(2+)-dependent inactivation (CDI)). CaBP1 eliminates this action of CaM through a poorly understood mechanism. We examined the hypothesis that CaBP1 acts by competing with CaM for common interaction sites in the α1C- subunit using Förster resonance energy transfer (FRET) and recording of Cav1.2 currents in Xenopus oocytes. FRET detected interactions between fluorescently labeled CaM or CaBP1 with the membrane-attached proximal C terminus (pCT) and the N terminus (NT) of α1C. However, mutual overexpression of CaM and CaBP1 proved inadequate to quantitatively assess competition between these proteins for α1C. Therefore, we utilized titrated injection of purified CaM and CaBP1 to analyze their mutual effects. CaM reduced FRET between CaBP1 and pCT, but not NT, suggesting competition between CaBP1 and CaM for pCT only. Titrated injection of CaBP1 and CaM altered the kinetics of CDI, allowing analysis of their opposite regulation of CaV1.2. The CaBP1-induced slowing of CDI was largely eliminated by CaM, corroborating a competition mechanism, but 15-20% of the effect of CaBP1 was CaM-resistant. Both components of CaBP1 action were present in a truncated α1C where N-terminal CaM- and CaBP1-binding sites have been deleted, suggesting that the NT is not essential for the functional effects of CaBP1. We propose that CaBP1 acts via interaction(s) with the pCT and possibly additional sites in α1C.
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Affiliation(s)
- Shimrit Oz
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Zhang M, Abrams C, Wang L, Gizzi A, He L, Lin R, Chen Y, Loll PJ, Pascal JM, Zhang JF. Structural basis for calmodulin as a dynamic calcium sensor. Structure 2012; 20:911-23. [PMID: 22579256 DOI: 10.1016/j.str.2012.03.019] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 02/20/2012] [Accepted: 03/08/2012] [Indexed: 12/14/2022]
Abstract
Calmodulin is a prototypical and versatile Ca(2+) sensor with EF hands as its high-affinity Ca(2+) binding domains. Calmodulin is present in all eukaryotic cells, mediating Ca(2+)-dependent signaling. Upon binding Ca(2+), calmodulin changes its conformation to form complexes with a diverse array of target proteins. Despite a wealth of knowledge on calmodulin, little is known on how target proteins regulate calmodulin's ability to bind Ca(2+). Here, we take advantage of two splice variants of SK2 channels, which are activated by Ca(2+)-bound calmodulin but show different sensitivity to Ca(2+) for their activation. Protein crystal structures and other experiments show that, depending on which SK2 splice variant it binds to, calmodulin adopts drastically different conformations with different affinities for Ca(2+) at its C-lobe. Such target protein-induced conformational changes make calmodulin a dynamic Ca(2+) sensor capable of responding to different Ca(2+) concentrations in cellular Ca(2+) signaling.
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Affiliation(s)
- Miao Zhang
- Department of Molecular Physiology and Biophysics, Jefferson Medical College, Philadelphia, PA 19107, USA
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31
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Christel C, Lee A. Ca2+-dependent modulation of voltage-gated Ca2+ channels. Biochim Biophys Acta Gen Subj 2011; 1820:1243-52. [PMID: 22223119 DOI: 10.1016/j.bbagen.2011.12.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 12/15/2011] [Accepted: 12/16/2011] [Indexed: 01/06/2023]
Abstract
BACKGROUND Voltage-gated (Cav) Ca2+ channels are multi-subunit complexes that play diverse roles in a wide variety of tissues. A fundamental mechanism controlling Cav channel function involves the Ca2+ ions that permeate the channel pore. Ca2+ influx through Cav channels mediates feedback regulation to the channel that is both negative (Ca2+-dependent inactivation, CDI) and positive (Ca2+-dependent facilitation, CDF). SCOPE OF REVIEW This review highlights general mechanisms of CDI and CDF with an emphasis on how these processes have been studied electrophysiologically in native and heterologous expression systems. MAJOR CONCLUSIONS Electrophysiological analyses have led to detailed insights into the mechanisms and prevalence of CDI and CDF as Cav channel regulatory mechanisms. All Cav channel family members undergo some form of Ca2+-dependent feedback that relies on CaM or a related Ca2+ binding protein. Tremendous progress has been made in characterizing the role of CaM in CDI and CDF. Yet, what contributes to the heterogeneity of CDI/CDF in various cell-types and how Ca2+-dependent regulation of Cav channels controls Ca2+ signaling remain largely unexplored. GENERAL SIGNIFICANCE Ca2+ influx through Cav channels regulates diverse physiological events including excitation-contraction coupling in muscle, neurotransmitter and hormone release, and Ca2+-dependent gene transcription. Therefore, the mechanisms that regulate channels, such as CDI and CDF, can have a large impact on the signaling potential of excitable cells in various physiological contexts. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signaling.
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Affiliation(s)
- Carl Christel
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
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Köster S, Pavkov-Keller T, Kühlbrandt W, Yildiz Ö. Structure of human Na+/H+ exchanger NHE1 regulatory region in complex with calmodulin and Ca2+. J Biol Chem 2011; 286:40954-61. [PMID: 21931166 PMCID: PMC3220496 DOI: 10.1074/jbc.m111.286906] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/06/2011] [Indexed: 11/06/2022] Open
Abstract
The ubiquitous mammalian Na(+)/H(+) exchanger NHE1 has critical functions in regulating intracellular pH, salt concentration, and cellular volume. The regulatory C-terminal domain of NHE1 is linked to the ion-translocating N-terminal membrane domain and acts as a scaffold for signaling complexes. A major interaction partner is calmodulin (CaM), which binds to two neighboring regions of NHE1 in a strongly Ca(2+)-dependent manner. Upon CaM binding, NHE1 is activated by a shift in sensitivity toward alkaline intracellular pH. Here we report the 2.23 Å crystal structure of the NHE1 CaM binding region (NHE1(CaMBR)) in complex with CaM and Ca(2+). The C- and N-lobes of CaM bind the first and second helix of NHE1(CaMBR), respectively. Both the NHE1 helices and the Ca(2+)-bound CaM are elongated, as confirmed by small angle x-ray scattering analysis. Our x-ray structure sheds new light on the molecular mechanisms of the phosphorylation-dependent regulation of NHE1 and enables us to propose a model of how Ca(2+) regulates NHE1 activity.
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Affiliation(s)
- Stefan Köster
- From the Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany and
| | - Tea Pavkov-Keller
- From the Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany and
- the Department of Structural Biology, Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010 Graz, Austria
| | - Werner Kühlbrandt
- From the Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany and
| | - Özkan Yildiz
- From the Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany and
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Evans TIA, Hell JW, Shea MA. Thermodynamic linkage between calmodulin domains binding calcium and contiguous sites in the C-terminal tail of Ca(V)1.2. Biophys Chem 2011; 159:172-87. [PMID: 21757287 DOI: 10.1016/j.bpc.2011.06.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 06/15/2011] [Accepted: 06/15/2011] [Indexed: 11/30/2022]
Abstract
Calmodulin (CaM) binding to the intracellular C-terminal tail (CTT) of the cardiac L-type Ca(2+) channel (Ca(V)1.2) regulates Ca(2+) entry by recognizing sites that contribute to negative feedback mechanisms for channel closing. CaM associates with Ca(V)1.2 under low resting [Ca(2+)], but is poised to change conformation and position when intracellular [Ca(2+)] rises. CaM binding Ca(2+), and the domains of CaM binding the CTT are linked thermodynamic functions. To better understand regulation, we determined the energetics of CaM domains binding to peptides representing pre-IQ sites A(1588), and C(1614) and the IQ motif studied as overlapping peptides IQ(1644) and IQ'(1650) as well as their effect on calcium binding. (Ca(2+))(4)-CaM bound to all four peptides very favorably (K(d)≤2 nM). Linkage analysis showed that IQ(1644-1670) bound with a K(d)~1 pM. In the pre-IQ region, (Ca(2+))(2)-N-domain bound preferentially to A(1588), while (Ca(2+))(2)-C-domain preferred C(1614). When bound to C(1614), calcium binding in the N-domain affected the tertiary conformation of the C-domain. Based on the thermodynamics, we propose a structural mechanism for calcium-dependent conformational change in which the linker between CTT sites A and C buckles to form an A-C hairpin that is bridged by calcium-saturated CaM.
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Affiliation(s)
- T Idil Apak Evans
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, United States.
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Minor DL, Findeisen F. Progress in the structural understanding of voltage-gated calcium channel (CaV) function and modulation. Channels (Austin) 2011; 4:459-74. [PMID: 21139419 DOI: 10.4161/chan.4.6.12867] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Voltage-gated calcium channels (CaVs) are large, transmembrane multiprotein complexes that couple membrane depolarization to cellular calcium entry. These channels are central to cardiac action potential propagation, neurotransmitter and hormone release, muscle contraction, and calcium-dependent gene transcription. Over the past six years, the advent of high-resolution structural studies of CaV components from different isoforms and CaV modulators has begun to reveal the architecture that underlies the exceptionally rich feedback modulation that controls CaV action. These descriptions of CaV molecular anatomy have provided new, structure-based insights into the mechanisms by which particular channel elements affect voltage-dependent inactivation (VDI), calcium‑dependent inactivation (CDI), and calcium‑dependent facilitation (CDF). The initial successes have been achieved through structural studies of soluble channel domains and modulator proteins and have proven most powerful when paired with biochemical and functional studies that validate ideas inspired by the structures. Here, we review the progress in this growing area and highlight some key open challenges for future efforts.
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Affiliation(s)
- Daniel L Minor
- Cardiovascular Research Institute, University of California-San Francisco, CA, USA.
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Chagot B, Chazin WJ. Solution NMR structure of Apo-calmodulin in complex with the IQ motif of human cardiac sodium channel NaV1.5. J Mol Biol 2010; 406:106-19. [PMID: 21167176 DOI: 10.1016/j.jmb.2010.11.046] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 12/19/2022]
Abstract
The function of the human voltage-gated sodium channel Na(V)1.5 is regulated in part by intracellular calcium signals. The ubiquitous calcium sensor protein calmodulin (CaM) is an important part of the complex calcium-sensing apparatus in Na(V)1.5. CaM interacts with an IQ (isoleucine-glutamine) motif in the large intracellular C-terminal domain of the channel. Using co-expression and co-purification, we have been able to isolate a CaM-IQ motif complex and to determine its high-resolution structure in absence of calcium using multi-dimensional solution NMR. Under these conditions, the Na(V)1.5 IQ motif interacts with the C-terminal domain (C-lobe) of CaM, with the N-terminal domain remaining free in solution. The structure reveals that the C-lobe adopts a semi-open conformation with the IQ motif bound in a narrow hydrophobic groove. Sequence similarities between voltage-gated sodium channels and voltage-gated calcium channels suggest that the structure of the CaM-Na(V)1.5 IQ motif complex can serve as a general model for the interaction between CaM and ion channel IQ motifs under low-calcium conditions. The structure also provides insight into the biochemical basis for disease-associated mutations that map to the IQ motif in Na(V)1.5.
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Affiliation(s)
- Benjamin Chagot
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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Lanner JT, Georgiou DK, Joshi AD, Hamilton SL. Ryanodine receptors: structure, expression, molecular details, and function in calcium release. Cold Spring Harb Perspect Biol 2010; 2:a003996. [PMID: 20961976 DOI: 10.1101/cshperspect.a003996] [Citation(s) in RCA: 537] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ryanodine receptors (RyRs) are located in the sarcoplasmic/endoplasmic reticulum membrane and are responsible for the release of Ca(2+) from intracellular stores during excitation-contraction coupling in both cardiac and skeletal muscle. RyRs are the largest known ion channels (> 2MDa) and exist as three mammalian isoforms (RyR 1-3), all of which are homotetrameric proteins that interact with and are regulated by phosphorylation, redox modifications, and a variety of small proteins and ions. Most RyR channel modulators interact with the large cytoplasmic domain whereas the carboxy-terminal portion of the protein forms the ion-conducting pore. Mutations in RyR2 are associated with human disorders such as catecholaminergic polymorphic ventricular tachycardia whereas mutations in RyR1 underlie diseases such as central core disease and malignant hyperthermia. This chapter examines the current concepts of the structure, function and regulation of RyRs and assesses the current state of understanding of their roles in associated disorders.
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Affiliation(s)
- Johanna T Lanner
- Baylor College of Medicine, Department of Molecular Physiology and Biophysics, Houston, Texas 77030,USA
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