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Han Y, Tang Y, Sun S, Kim T, Ju K, Ri S, Du X, Zhou W, Shi W, Li S, Liu G. Modulatory function of calmodulin on phagocytosis and potential regulation mechanisms in the blood clam Tegillarca granosa. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103910. [PMID: 33129883 DOI: 10.1016/j.dci.2020.103910] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 06/11/2023]
Abstract
Unlike vertebrate species, invertebrates lack antigen-antibody mediated immune response and mainly rely on haemocyte phagocytosis to fight against pathogen infection. Recently, studies conducted in model vertebrates demonstrated that the multifunctional protein calmodulin (CaM) plays an important role in regulating immune responses. However, the intrinsic relation between CaM and phagocytosis process remains poorly understood in invertebrate species such as bivalve mollusks. Therefore, in the present study, the immunomodulatory function of CaM on haemocyte phagocytosis was verified in the blood clam, Tegillarca granosa, using the CaM-specific inhibitor N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide hydrochloride (W-7). Results obtained show that CaM inhibition significantly suppressed the phagocytic activity of haemocytes. In addition, CaM inhibition constrained intracellular Ca2+ elevation, hampered actin cytoskeleton assembly, suppressed calcineurin (CaN) activity, and disrupted NF-κB activation in haemocytes upon LPS induction. Furthermore, expression of seven selected genes from the actin cytoskeleton regulation- and immune-related pathways were significantly downregulated whereas those of CaM and CaN from the Ca2+-signaling pathway were significantly upregulated by in vitro incubation of haemocytes with W-7. For the first time, the present study demonstrated that CaM play an important role in phagocytosis modulation in bivalve species. In addition, the intracellular Ca2+ and downstream Ca2+-signaling-, actin cytoskeleton regulation-, and immune-related pathways offer candidate routes through which CaM modulates phagocytosis.
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Affiliation(s)
- Yu Han
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yu Tang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Shuge Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Tongchol Kim
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, Republic of Korea
| | - Kwangjin Ju
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Aquaculture, Wonsan Fisheries University, Wonsan, 999093, Republic of Korea
| | - Sanghyok Ri
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, Republic of Korea
| | - Xueying Du
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Shiguo Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China.
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China.
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2
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Tang S, Deng X, Jiang J, Kirberger M, Yang JJ. Design of Calcium-Binding Proteins to Sense Calcium. Molecules 2020; 25:molecules25092148. [PMID: 32375353 PMCID: PMC7248937 DOI: 10.3390/molecules25092148] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Calcium controls numerous biological processes by interacting with different classes of calcium binding proteins (CaBP’s), with different affinities, metal selectivities, kinetics, and calcium dependent conformational changes. Due to the diverse coordination chemistry of calcium, and complexity associated with protein folding and binding cooperativity, the rational design of CaBP’s was anticipated to present multiple challenges. In this paper we will first discuss applications of statistical analysis of calcium binding sites in proteins and subsequent development of algorithms to predict and identify calcium binding proteins. Next, we report efforts to identify key determinants for calcium binding affinity, cooperativity and calcium dependent conformational changes using grafting and protein design. Finally, we report recent advances in designing protein calcium sensors to capture calcium dynamics in various cellular environments.
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Affiliation(s)
- Shen Tang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Xiaonan Deng
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Jie Jiang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Michael Kirberger
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA;
| | - Jenny J. Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
- Correspondence: ; Tel.: +1-404-413-5520
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3
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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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4
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Salarian M, Yang H, Turaga RC, Tan S, Qiao J, Xue S, Gui Z, Peng G, Han H, Mittal P, Grossniklaus HE, Yang JJ. Precision detection of liver metastasis by collagen-targeted protein MRI contrast agent. Biomaterials 2019; 224:119478. [DOI: 10.1016/j.biomaterials.2019.119478] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 08/21/2019] [Accepted: 09/05/2019] [Indexed: 12/11/2022]
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5
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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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6
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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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7
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Gorkhali R, Huang K, Kirberger M, Yang JJ. Defining potential roles of Pb(2+) in neurotoxicity from a calciomics approach. Metallomics 2017; 8:563-78. [PMID: 27108875 DOI: 10.1039/c6mt00038j] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions play crucial roles in numerous biological processes, facilitating biochemical reactions by binding to various proteins. An increasing body of evidence suggests that neurotoxicity associated with exposure to nonessential metals (e.g., Pb(2+)) involves disruption of synaptic activity, and these observed effects are associated with the ability of Pb(2+) to interfere with Zn(2+) and Ca(2+)-dependent functions. However, the molecular mechanism behind Pb(2+) toxicity remains a topic of debate. In this review, we first discuss potential neuronal Ca(2+) binding protein (CaBP) targets for Pb(2+) such as calmodulin (CaM), synaptotagmin, neuronal calcium sensor-1 (NCS-1), N-methyl-d-aspartate receptor (NMDAR) and family C of G-protein coupled receptors (cGPCRs), and their involvement in Ca(2+)-signalling pathways. We then compare metal binding properties between Ca(2+) and Pb(2+) to understand the structural implications of Pb(2+) binding to CaBPs. Statistical and biophysical studies (e.g., NMR and fluorescence spectroscopy) of Pb(2+) binding are discussed to investigate the molecular mechanism behind Pb(2+) toxicity. These studies identify an opportunistic, allosteric binding of Pb(2+) to CaM, which is distinct from ionic displacement. Together, these data suggest three potential modes of Pb(2+) activity related to molecular and/or neural toxicity: (i) Pb(2+) can occupy Ca(2+)-binding sites, inhibiting the activity of the protein by structural modulation, (ii) Pb(2+) can mimic Ca(2+) in the binding sites, falsely activating the protein and perturbing downstream activities, or (iii) Pb(2+) can bind outside of the Ca(2+)-binding sites, resulting in the allosteric modulation of the protein activity. Moreover, the data further suggest that even low concentrations of Pb(2+) can interfere at multiple points within the neuronal Ca(2+) signalling pathways to cause neurotoxicity.
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Affiliation(s)
- Rakshya Gorkhali
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Drug Design and Biotechnology, Georgia State University, Atlanta, GA 3030, USA.
| | - Kenneth Huang
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Drug Design and Biotechnology, Georgia State University, Atlanta, GA 3030, USA.
| | - Michael Kirberger
- Department of Chemistry and Physics, Clayton State University, Morrow, GA 30260, USA.
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Drug Design and Biotechnology, Georgia State University, Atlanta, GA 3030, USA.
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8
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Kim TJ, Yoo JY, Shim WS. Substitution with a Single Cysteine in the Green Fluorescent Protein-Based Calcium Indicator GCaMP3 Enhances Calcium Sensitivity. J Fluoresc 2017; 27:2187-2193. [PMID: 28791525 DOI: 10.1007/s10895-017-2159-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/31/2017] [Indexed: 11/25/2022]
Abstract
Genetically encoded calcium indicators (GECI) such as GCaMP3 are attracting significant attention as a good option for measuring intracellular calcium levels. Recently, a modified GCaMP3 called dCys-GCaMP3 was developed by replacing two threonine residues with cysteines. dCys-GCaMP3 proved to be a better calcium indicator, but it was not clear how and why the two cysteine residues were able to enhance the protein's calcium sensitivity. The aim of the present study was to investigate the possible roles of these cysteine residues in dCys-GCaMP3. dCys-GCaMP3 (Thr330Cys;Thr364Cys) exhibited enhanced fluorescence intensity compared to the canonical GCaMP3 in calcium imaging experiments. However, substitution of a single residue at position 330 with cysteine (Thr330Cys) also afforded comparable sensitivity to GCaMP3. In contrast, the other single residue substitution at position 364 with cysteine (Thr364Cys) failed to enhance calcium sensitivity, showing that cysteine at position 330 is essential to improve calcium sensitivity. Thr330Cys substitution in the GCaMP3 or "Cys330-GCaMP3" showed significantly reduced background fluorescence, and the fluorescence intensity was proportional to the amount of DNA used to transfect the cells used in the study. The substitute had to be cysteine, because replacement with other amino acids such as alanine, valine, and aspartate did not improve GCaMP3's calcium sensitivity. Cys330-GCaMP3 outperformed a synthetic calcium-specific indicator, Fluo-3, in various calcium imaging experiments. Thus, the present study asserts that substituting the threonine at position 330 in GCaMP3 with cysteine is essential to enhance calcium sensitivity, and suggests that Cys330-GCaMP3 can be used as a potent fluorescent calcium indicator to measure intracellular calcium levels.
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Affiliation(s)
- Tae Joon Kim
- College of Pharmacy, Gachon University, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea
| | - Ji Young Yoo
- College of Pharmacy, Gachon University, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea
| | - Won-Sik Shim
- College of Pharmacy, Gachon University, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea. .,Gachon Institute of Pharmaceutical Sciences, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, South Korea.
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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 2016; 292:1385-1395. [PMID: 27927985 PMCID: PMC5270481 DOI: 10.1074/jbc.m116.766253] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [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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Nandigrami P, Portman JJ. Coarse-grained molecular simulations of allosteric cooperativity. J Chem Phys 2016; 144:105101. [DOI: 10.1063/1.4943043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
| | - John J. Portman
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
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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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Lai M, Brun D, Edelstein SJ, Le Novère N. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PLoS Comput Biol 2015; 11:e1004063. [PMID: 25611683 PMCID: PMC4303274 DOI: 10.1371/journal.pcbi.1004063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/26/2014] [Indexed: 01/30/2023] Open
Abstract
Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe) joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines) several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be explained as modulation of a pre-existing dynamic equilibrium between different conformations of calmodulin's lobes, in agreement with linkage theory and MWC-type models.
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Affiliation(s)
- Massimo Lai
- Babraham Institute, Cambridge, United Kingdom
- * E-mail:
| | - Denis Brun
- EMBL-EBI, Hinxton, United Kingdom
- Amadeus IT Group, Sophia Antipolis, France
| | | | - Nicolas Le Novère
- Babraham Institute, Cambridge, United Kingdom
- EMBL-EBI, Hinxton, United Kingdom
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Myoplasmic resting Ca2+ regulation by ryanodine receptors is under the control of a novel Ca2+-binding region of the receptor. Biochem J 2014; 460:261-71. [PMID: 24635445 PMCID: PMC4019983 DOI: 10.1042/bj20131553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Passive SR (sarcoplasmic reticulum) Ca2+ leak through the RyR (ryanodine receptor) plays a critical role in the mechanisms that regulate [Ca2+]rest (intracellular resting myoplasmic free Ca2+ concentration) in muscle. This process appears to be isoform-specific as expression of either RyR1 or RyR3 confers on myotubes different [Ca2+]rest. Using chimaeric RyR3–RyR1 receptors expressed in dyspedic myotubes, we show that isoform-dependent regulation of [Ca2+]rest is primarily defined by a small region of the receptor encompassing amino acids 3770–4007 of RyR1 (amino acids 3620–3859 of RyR3) named as the CLR (Ca2+ leak regulatory) region. [Ca2+]rest regulation by the CLR region was associated with alteration of RyRs’ Ca2+-activation profile and changes in SR Ca2+-leak rates. Biochemical analysis using Tb3+-binding assays and intrinsic tryptophan fluorescence spectroscopy of purified CLR domains revealed that this determinant of RyRs holds a novel Ca2+-binding domain with conformational properties that are distinctive to each isoform. Our data suggest that the CLR region provides channels with unique functional properties that modulate the rate of passive SR Ca2+ leak and confer on RyR1 and RyR3 distinctive [Ca2+]rest regulatory properties. The identification of a new Ca2+-binding domain of RyRs with a key modulatory role in [Ca2+]rest regulation provides new insights into Ca2+-mediated regulation of RyRs. This paper reports the finding of a new class of Ca2+-binding domain of intracellular Ca2+ channels from muscle cells. This domain provides channels with distinctive properties that result in channel-specific modulation of the intracellular resting Ca2+ concentration.
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Zhou Y, Xue S, Yang JJ. Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems. Metallomics 2013; 5:29-42. [PMID: 23235533 DOI: 10.1039/c2mt20009k] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Calcium ion (Ca(2+)), the fifth most common chemical element in the earth's crust, represents the most abundant mineral in the human body. By binding to a myriad of proteins distributed in different cellular organelles, Ca(2+) impacts nearly every aspect of cellular life. In prokaryotes, Ca(2+) plays an important role in bacterial movement, chemotaxis, survival reactions and sporulation. In eukaryotes, Ca(2+) has been chosen through evolution to function as a universal and versatile intracellular signal. Viruses, as obligate intracellular parasites, also develop smart strategies to manipulate the host Ca(2+) signaling machinery to benefit their own life cycles. This review focuses on recent advances in applying both bioinformatic and experimental approaches to predict and validate Ca(2+)-binding proteins and their interactomes in biological systems on a genome-wide scale (termed "calciomics"). Calmodulin is used as an example of Ca(2+)-binding protein (CaBP) to demonstrate the role of CaBPs on the regulation of biological functions. This review is anticipated to rekindle interest in investigating Ca(2+)-binding proteins and Ca(2+)-modulated functions at the systems level in the post-genomic era.
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Affiliation(s)
- Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, TX 77030, USA
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15
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Kirberger M, Wong HC, Jiang J, Yang JJ. Metal toxicity and opportunistic binding of Pb(2+) in proteins. J Inorg Biochem 2013; 125:40-9. [PMID: 23692958 DOI: 10.1016/j.jinorgbio.2013.04.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
Lead toxicity is associated with various human diseases. While Ca(2+) binding proteins such as calmodulin (CaM) are often reported to be molecular targets for Pb(2+)-binding and lead toxicity, the effect of Pb(2+) on the Ca(2+)/CaM regulated biological activities cannot be described by the primary mechanism of ionic displacement (e.g., ionic mimicry). The focus of this study was to investigate the mechanism of lead toxicity through binding differences between Ca(2+) and Pb(2+) for CaM, an essential intracellular trigger protein with two EF-Hand Ca(2+)-binding sites in each of its two domains that regulates many molecular targets via Ca(2+)-induced conformational change. Fluorescence changes in phenylalanine indicated that Pb(2+) binds with 8-fold higher affinity than Ca(2+) in the N-terminal domain. Additionally, NMR chemical shift changes and an unusual biphasic response observed in tyrosine fluorescence associated with C-terminal domain sites EF-III and EF-IV suggest a single higher affinity Pb(2+)-binding site with a 3-fold higher affinity than Ca(2+), coupled with a second site exhibiting affinity nearly equivalent to that of the N-terminal domain sites. Our results further indicate that Pb(2+) displaces Ca(2+) only in the N-terminal domain, with minimal perturbation of the C-terminal domain, however significant structural/dynamic changes are observed in the trans-domain linker region which appear to be due to Pb(2+)-binding outside of the known calcium-binding sites. These data suggest that opportunistic Pb(2+)-binding in Ca(2+)/CaM has a profound impact on the conformation and dynamics of the essential molecular recognition sites of the central helix, and provides insight into the molecular toxicity of non-essential metal ions.
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Affiliation(s)
- Michael Kirberger
- Department of Chemistry, Center for Diagnostics and Therapeutics and Drug Design and Biotechnology, Georgia State University, Atlanta, GA, 30303, United States
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