1
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Troilo F, Pedretti M, Travaglini-Allocatelli C, Astegno A, Di Matteo A. Rapid kinetics of calcium dissociation from plant calmodulin and calmodulin-like proteins and effect of target peptides. Biochem Biophys Res Commun 2022; 590:103-108. [PMID: 34974297 DOI: 10.1016/j.bbrc.2021.12.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/02/2022]
Abstract
Calcium (Ca2+) signaling represents a universal information code in plants, playing crucial roles spanning developmental processes to stress responses. Ca2+ signals are decoded into defined plant adaptive responses by different Ca2+ sensing proteins, including calmodulin (CaM) and calmodulin-like (CML) proteins. Although major advances have been achieved in describing how these Ca2+ decoding proteins interact and regulate downstream target effectors, the molecular details of these processes remain largely unknown. Herein, the kinetics of Ca2+ dissociation from a conserved CaM and two CML isoforms from A. thaliana has been studied by fluorescence stopped-flow spectroscopy. Kinetic data were obtained for the isolated Ca2+-bound proteins as well as for the proteins complexed with different target peptides. Moreover, the lobe specific interactions between the Ca2+ sensing proteins and their targets were characterized by using a panel of protein mutants deficient in Ca2+ binding at the N-lobe or C-lobe. Results were analyzed and discussed in the context of the Ca2+-decoding and Ca2+-controlled target binding mechanisms in plants.
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Affiliation(s)
- Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy.
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2
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Mahling R, Hovey L, Isbell HM, Marx DC, Miller MS, Kilpatrick AM, Weaver LD, Yoder JB, Kim EH, Andresen CNJ, Li S, Shea MA. Na V1.2 EFL domain allosterically enhances Ca 2+ binding to sites I and II of WT and pathogenic calmodulin mutants bound to the channel CTD. Structure 2021; 29:1339-1356.e7. [PMID: 33770503 PMCID: PMC8458505 DOI: 10.1016/j.str.2021.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 11/23/2022]
Abstract
Neuronal voltage-gated sodium channel NaV1.2 C-terminal domain (CTD) binds calmodulin (CaM) constitutively at its IQ motif. A solution structure (6BUT) and other NMR evidence showed that the CaM N domain (CaMN) is structurally independent of the C-domain (CaMC) whether CaM is bound to the NaV1.2IQp (1,901-1,927) or NaV1.2CTD (1,777-1,937) with or without calcium. However, in the CaM + NaV1.2CTD complex, the Ca2+ affinity of CaMN was more favorable than in free CaM, while Ca2+ affinity for CaMC was weaker than in the CaM + NaV1.2IQp complex. The CTD EF-like (EFL) domain allosterically widened the energetic gap between CaM domains. Cardiomyopathy-associated CaM mutants (N53I(N54I), D95V(D96V), A102V(A103V), E104A(E105A), D129G(D130G), and F141L(F142L)) all bound the NaV1.2 IQ motif favorably under resting (apo) conditions and bound calcium normally at CaMN sites. However, only N53I and A102V bound calcium at CaMC sites at [Ca2+] < 100 μM. Thus, they are expected to respond like wild-type CaM to Ca2+ spikes in excitable cells.
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Affiliation(s)
- Ryan Mahling
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Liam Hovey
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Holly M Isbell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Dagan C Marx
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Mark S Miller
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Adina M Kilpatrick
- Department of Physics and Astronomy, Drake University, Des Moines, IA 50311-4516, USA
| | - Lisa D Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Jesse B Yoder
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Elaine H Kim
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Corinne N J Andresen
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Shuxiang Li
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Madeline A Shea
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
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3
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Sun B, Kekenes-Huskey PM. Assessing the Role of Calmodulin's Linker Flexibility in Target Binding. Int J Mol Sci 2021; 22:ijms22094990. [PMID: 34066691 PMCID: PMC8125811 DOI: 10.3390/ijms22094990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022] Open
Abstract
Calmodulin (CaM) is a highly-expressed Ca2+ binding protein known to bind hundreds of protein targets. Its binding selectivity to many of these targets is partially attributed to the protein’s flexible alpha helical linker that connects its N- and C-domains. It is not well established how its linker mediates CaM’s binding to regulatory targets yet. Insights into this would be invaluable to understanding its regulation of diverse cellular signaling pathways. Therefore, we utilized Martini coarse-grained (CG) molecular dynamics simulations to probe CaM/target assembly for a model system: CaM binding to the calcineurin (CaN) regulatory domain. The simulations were conducted assuming a ‘wild-type’ calmodulin with normal flexibility of its linker, as well as a labile, highly-flexible linker variant to emulate structural changes that could be induced, for instance, by post-translational modifications. For the wild-type model, 98% of the 600 simulations across three ionic strengths adopted a bound complex within 2 μs of simulation time; of these, 1.7% sampled the fully-bound state observed in the experimentally-determined crystallographic structure. By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 × 108 M−1 s−1, which is similar to the diffusion-limited, experimentally-determined rate of 2.2 × 108 M−1 s−1. Furthermore, our simulations recapitulated its well-known inverse relationship between the association rate and the solution ionic strength. In contrast, although over 97% of the labile linker simulations formed tightly-bound complexes, only 0.3% achieved the fully-bound configuration. This effect appears to stem from a difference in the ensembles of extended and collapsed states which are controlled by the linker flexibility. Therefore, our simulations suggest that variations in the CaM linker’s propensity for alpha helical secondary structure can modulate the kinetics of target binding.
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4
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Mahling R, Rahlf CR, Hansen SC, Hayden MR, Shea MA. Ca 2+-saturated calmodulin binds tightly to the N-terminal domain of A-type fibroblast growth factor homologous factors. J Biol Chem 2021; 296:100458. [PMID: 33639159 PMCID: PMC8059062 DOI: 10.1016/j.jbc.2021.100458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 01/12/2023] Open
Abstract
Voltage-gated sodium channels (Navs) are tightly regulated by multiple conserved auxiliary proteins, including the four fibroblast growth factor homologous factors (FGFs), which bind the Nav EF-hand like domain (EFL), and calmodulin (CaM), a multifunctional messenger protein that binds the NaV IQ motif. The EFL domain and IQ motif are contiguous regions of NaV cytosolic C-terminal domains (CTD), placing CaM and FGF in close proximity. However, whether the FGFs and CaM act independently, directly associate, or operate through allosteric interactions to regulate channel function is unknown. Titrations monitored by steady-state fluorescence spectroscopy, structural studies with solution NMR, and computational modeling demonstrated for the first time that both domains of (Ca2+)4-CaM (but not apo CaM) directly bind two sites in the N-terminal domain (NTD) of A-type FGF splice variants (FGF11A, FGF12A, FGF13A, and FGF14A) with high affinity. The weaker of the (Ca2+)4-CaM-binding sites was known via electrophysiology to have a role in long-term inactivation of the channel but not known to bind CaM. FGF12A binding to a complex of CaM associated with a fragment of the NaV1.2 CTD increased the Ca2+-binding affinity of both CaM domains, consistent with (Ca2+)4-CaM interacting preferentially with its higher-affinity site in the FGF12A NTD. Thus, A-type FGFs can compete with NaV IQ motifs for (Ca2+)4-CaM. During spikes in the cytosolic Ca2+ concentration that accompany an action potential, CaM may translocate from the NaV IQ motif to the FGF NTD, or the A-type FGF NTD may recruit a second molecule of CaM to the channel.
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Affiliation(s)
- Ryan Mahling
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Cade R Rahlf
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Samuel C Hansen
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Matthew R Hayden
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Madeline A Shea
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
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5
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Abstract
The serine/threonine phosphatase calcineurin acts as a crucial connection between calcium signaling the phosphorylation states of numerous important substrates. These substrates include, but are not limited to, transcription factors, receptors and channels, proteins associated with mitochondria, and proteins associated with microtubules. Calcineurin is activated by increases in intracellular calcium concentrations, a process that requires the calcium sensing protein calmodulin binding to an intrinsically disordered regulatory domain in the phosphatase. Despite having been studied for around four decades, the activation of calcineurin is not fully understood. This review largely focuses on what is known about the activation process and highlights aspects that are currently not understood. Video abstract.
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Affiliation(s)
- Trevor P Creamer
- Center for Structural Biology, Department of Molecular & Cellular Biochemistry, 741 S. Limestone Street, Lexington, KY, 40536-0509, USA.
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6
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Cook EC, Creamer TP. Influence of electrostatic forces on the association kinetics and conformational ensemble of an intrinsically disordered protein. Proteins 2020; 88:1607-1619. [PMID: 32654182 DOI: 10.1002/prot.25979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/15/2020] [Accepted: 07/05/2020] [Indexed: 01/26/2023]
Abstract
Recent work has revealed that the association of a disordered region of a protein with a folded binding partner can occur as rapidly as association between two folded proteins. This is the case for the phosphatase calcineurin (CaN) and its association with its activator calmodulin. Calmodulin binds to the intrinsically disordered regulatory domain of CaN. Previous studies have shown that electrostatic steering can accelerate the binding of folded proteins with disordered ligands. Given that electrostatic forces are strong determinants of disordered protein ensembles, the relationship between electrostatics, conformational ensembles, and quaternary interactions is unclear. Here, we employ experimental approaches to explore the impact of electrostatic interactions on the association of calmodulin with the disordered regulatory region of CaN. We find that estimated association rate constants of calmodulin with our chosen calmodulin-substrates are within the diffusion-limited regime. The association rates are dependent on the ionic strength, indicating that favorable electrostatic forces increase the rate of association. Further, we show that charged amino acids outside the calmodulin-binding site modulate the binding rate. Conformational ensembles obtained from computer simulations suggest that electrostatic interactions within the regulatory domain might bias the conformational ensemble such that the calmodulin binding region is readily accessible. Given the prevalence of charged residues in disordered protein chains, our findings are likely relevant to many protein-protein interactions.
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Affiliation(s)
- Erik C Cook
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Trevor P Creamer
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
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7
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Li L, Lai M, Cole S, Le Novère N, Edelstein SJ. Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies. PLoS Comput Biol 2020; 16:e1006991. [PMID: 32049957 PMCID: PMC7041932 DOI: 10.1371/journal.pcbi.1006991] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 02/25/2020] [Accepted: 11/18/2019] [Indexed: 11/18/2022] Open
Abstract
Calmodulin sits at the center of molecular mechanisms underlying learning and memory. Its complex and sometimes opposite influences, mediated via the binding to various proteins, are yet to be fully understood. Calcium/calmodulin-dependent protein kinase II (CaMKII) and calcineurin (CaN) both bind open calmodulin, favoring Long-Term Potentiation (LTP) or Depression (LTD) respectively. Neurogranin binds to the closed conformation of calmodulin and its impact on synaptic plasticity is less clear. We set up a mechanistic computational model based on allosteric principles to simulate calmodulin state transitions and its interactions with calcium ions and the three binding partners mentioned above. We simulated calcium spikes at various frequencies and show that neurogranin regulates synaptic plasticity along three modalities. At low spike frequencies, neurogranin inhibits the onset of LTD by limiting CaN activation. At intermediate frequencies, neurogranin facilitates LTD, but limits LTP by precluding binding of CaMKII with calmodulin. Finally, at high spike frequencies, neurogranin promotes LTP by enhancing CaMKII autophosphorylation. While neurogranin might act as a calmodulin buffer, it does not significantly preclude the calmodulin opening by calcium. On the contrary, neurogranin synchronizes the opening of calmodulin's two lobes and promotes their activation at specific frequencies. Neurogranin suppresses basal CaN activity, thus increasing the chance of CaMKII trans-autophosphorylation at high-frequency calcium spikes. Taken together, our study reveals dynamic regulatory roles played by neurogranin on synaptic plasticity, which provide mechanistic explanations for opposing experimental findings.
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Affiliation(s)
- Lu Li
- Babraham Institute, Cambridge, United Kingdom
| | - Massimo Lai
- Quantitative Systems Pharmacology, CERTARA, Canterbury, United Kingdom
| | - Stephen Cole
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
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8
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Eriksson O, Jauhiainen A, Maad Sasane S, Kramer A, Nair AG, Sartorius C, Hellgren Kotaleski J. Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models. Bioinformatics 2019; 35:284-292. [PMID: 30010712 PMCID: PMC6330009 DOI: 10.1093/bioinformatics/bty607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 07/10/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours. Results We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building. Availability and implementation Source code is freely available at https://github.com/alexjau/uqsa. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Olivia Eriksson
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.,Swedish e-Science Research Centre (SeRC), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alexandra Jauhiainen
- Biometrics, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | | | - Andrei Kramer
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anu G Nair
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.,Swedish e-Science Research Centre (SeRC), KTH Royal Institute of Technology, Stockholm, Sweden
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9
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Fowler CA, Núñez Hernandez MF, O'Donnell SE, Yu L, Shea MA. Backbone and side-chain resonance assignments of (Ca 2+) 4-calmodulin bound to beta calcineurin A CaMBD peptide. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:275-280. [PMID: 28815458 PMCID: PMC5693717 DOI: 10.1007/s12104-017-9762-7] [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: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Calcineurin (CaN) is a heterodimeric and highly conserved serine/threonine phosphatase (PP2B) that plays a critical role in coupling calcium signals to physiological processes including embryonic cardiac development, NF-AT-regulated gene expression in immune responses, and apoptosis. The catalytic subunit (CaNA) has three isoforms (α, β, and γ,) in humans and seven isoforms in Paramecium. In all eukaryotes, the EF-hand protein calmodulin (CaM) regulates CaN activity in a calcium-dependent manner. The N- and C-domains of CaM (CaMN and CaMC) recognize a CaM-binding domain (CaMBD) within an intrinsically disordered region of CaNA that precedes the auto-inhibitory domain (AID) of CaNA. Here we present nearly complete 1H, 13C, and 15N resonance assignments of (Ca2+)4-CaM bound to a peptide containing the CaMBD sequence in the beta isoform of CaNA (βCaNA-CaMBDp). Its secondary structure elements predicted from the assigned chemical shifts were in good agreement with those observed in the high-resolution structures of (Ca2+)4-CaM bound to CaMBDs of multiple enzymes. Based on the reported literature, the CaMBD of the α isoform of CaNA can bind to CaM in two opposing orientations which may influence the regulatory function of CaM. Because a high resolution structure of (Ca2+)4-CaM bound to βCaNA-CaMBDp has not been reported, our studies serve as a starting point for determining the solution structure of this complex. This will demonstrate the preferred orientation of (Ca2+)4-CaM on the CaMBD as well as the orientations of CaMN and CaMC relative to each other and to the AID of βCaNA.
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Affiliation(s)
- C Andrew Fowler
- NMR Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa, IA, 52242-1109, USA
| | - Maria F Núñez Hernandez
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa, IA, 52242-1109, USA
| | - Susan E O'Donnell
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa, IA, 52242-1109, USA
| | - Liping Yu
- NMR Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa, IA, 52242-1109, USA
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa, IA, 52242-1109, USA
| | - Madeline A Shea
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa, IA, 52242-1109, USA.
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10
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Chyan CL, Irene D, Lin SM. The Recognition of Calmodulin to the Target Sequence of Calcineurin-A Novel Binding Mode. Molecules 2017; 22:E1584. [PMID: 28934144 PMCID: PMC6151454 DOI: 10.3390/molecules22101584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/18/2017] [Accepted: 09/18/2017] [Indexed: 11/22/2022] Open
Abstract
Calcineurin (CaN) is a Ca2+/calmodulin-dependent Ser/Thr protein phosphatase, which plays essential roles in many cellular and developmental processes. CaN comprises two subunits, a catalytic subunit (CaN-A, 60 kDa) and a regulatory subunit (CaN-B, 19 kDa). CaN-A tightly binds to CaN-B in the presence of minimal levels of Ca2+, but the enzyme is inactive until activated by CaM. Upon binding to CaM, CaN then undergoes a conformational rearrangement, the auto inhibitory domain is displaced and thus allows for full activity. In order to elucidate the regulatory role of CaM in the activation processes of CaN, we used NMR spectroscopy to determine the structure of the complex of CaM and the target peptide of CaN (CaNp). The CaM/CaNp complex shows a compact ellipsoidal shape with 8 α-helices of CaM wrapping around the CaNp helix. The RMSD of backbone and heavy atoms of twenty lowest energy structures of CaM/CaNp complex are 0.66 and 1.14 Å, respectively. The structure of CaM/CaNp complex can be classified as a novel binding mode family 1-18 with major anchor residues Ile396 and Leu413 to allocate the largest space between two domains of CaM. The relative orientation of CaNp to CaM is similar to the CaMKK peptide in the 1-16 binding mode with N- and C-terminal hydrophobic anchors of target sequence engulfed in the hydrophobic pockets of the N- and C-domain of CaM, respectively. In the light of the structural model of CaM/CaNp complex reported here, we provide new insight in the activation processes of CaN by CaM. We propose that the hydrophobic interactions between the Ca2+-saturated C-domain and C-terminal half of the target sequence provide driving forces for the initial recognition. Subsequent folding in the target sequence and structural readjustments in CaM enhance the formation of the complex and affinity to calcium. The electrostatic repulsion between CaM/CaNp complex and AID may result in the displacement of AID from active site for full activity.
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Affiliation(s)
- Chia-Lin Chyan
- Department of Chemistry, National Dong Hwa University, Hualien 974, Taiwan.
| | - Deli Irene
- Department of Chemistry, National Dong Hwa University, Hualien 974, Taiwan.
| | - Sin-Mao Lin
- Department of Chemistry, National Dong Hwa University, Hualien 974, Taiwan.
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11
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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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12
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Hovey L, Fowler CA, Mahling R, Lin Z, Miller MS, Marx DC, Yoder JB, Kim EH, Tefft KM, Waite BC, Feldkamp MD, Yu L, Shea MA. Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel Na V1.2. Biophys Chem 2017; 224:1-19. [PMID: 28343066 PMCID: PMC5503752 DOI: 10.1016/j.bpc.2017.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 01/26/2023]
Abstract
Several members of the voltage-gated sodium channel family are regulated by calmodulin (CaM) and ionic calcium. The neuronal voltage-gated sodium channel NaV1.2 contains binding sites for both apo (calcium-depleted) and calcium-saturated CaM. We have determined equilibrium dissociation constants for rat NaV1.2 IQ motif [IQRAYRRYLLK] binding to apo CaM (~3nM) and (Ca2+)4-CaM (~85nM), showing that apo CaM binding is favored by 30-fold. For both apo and (Ca2+)4-CaM, NMR demonstrated that NaV1.2 IQ motif peptide (NaV1.2IQp) exclusively made contacts with C-domain residues of CaM (CaMC). To understand how calcium triggers conformational change at the CaM-IQ interface, we determined a solution structure (2M5E.pdb) of (Ca2+)2-CaMC bound to NaV1.2IQp. The polarity of (Ca2+)2-CaMC relative to the IQ motif was opposite to that seen in apo CaMC-Nav1.2IQp (2KXW), revealing that CaMC recognizes nested, anti-parallel sites in Nav1.2IQp. Reversal of CaM may require transient release from the IQ motif during calcium binding, and facilitate a re-orientation of CaMN allowing interactions with non-IQ NaV1.2 residues or auxiliary regulatory proteins interacting in the vicinity of the IQ motif.
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Affiliation(s)
- Liam Hovey
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - C Andrew Fowler
- NMR Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242-1109 Iowa City, United States
| | - Ryan Mahling
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Zesen Lin
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Mark Stephen Miller
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Dagan C Marx
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Jesse B Yoder
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Elaine H Kim
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Kristin M Tefft
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Brett C Waite
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Michael D Feldkamp
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States
| | - Liping Yu
- NMR Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242-1109 Iowa City, United States
| | - Madeline A Shea
- Department of Biochemistry, University of Iowa, 52242-1109 Iowa City, United States.
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13
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Li S, Fell SM, Surova O, Smedler E, Wallis K, Chen ZX, Hellman U, Johnsen JI, Martinsson T, Kenchappa RS, Uhlén P, Kogner P, Schlisio S. The 1p36 Tumor Suppressor KIF 1Bβ Is Required for Calcineurin Activation, Controlling Mitochondrial Fission and Apoptosis. Dev Cell 2016; 36:164-78. [PMID: 26812016 DOI: 10.1016/j.devcel.2015.12.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 11/23/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
KIF1Bβ is a candidate 1p36 tumor suppressor that regulates apoptosis in the developing sympathetic nervous system. We found that KIF1Bβ activates the Ca(2+)-dependent phosphatase calcineurin (CN) by stabilizing the CN-calmodulin complex, relieving enzymatic autoinhibition and enabling CN substrate recognition. CN is the key mediator of cellular responses to Ca(2+) signals and its deregulation is implicated in cancer, cardiac, neurodegenerative, and immune disease. We show that KIF1Bβ affects mitochondrial dynamics through CN-dependent dephosphorylation of Dynamin-related protein 1 (DRP1), causing mitochondrial fission and apoptosis. Furthermore, KIF1Bβ actuates recognition of all known CN substrates, implying a general mechanism for KIF1Bβ in Ca(2+) signaling and how Ca(2+)-dependent signaling is executed by CN. Pathogenic KIF1Bβ mutations previously identified in neuroblastomas and pheochromocytomas all fail to activate CN or stimulate DRP1 dephosphorylation. Importantly, KIF1Bβ and DRP1 are silenced in 1p36 hemizygous-deleted neuroblastomas, indicating that deregulation of calcineurin and mitochondrial dynamics contributes to high-risk and poor-prognosis neuroblastoma.
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Affiliation(s)
- Shuijie Li
- Ludwig Institute for Cancer Research Ltd., 17177 Stockholm, Sweden; Department of Microbiology and Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Stuart M Fell
- Ludwig Institute for Cancer Research Ltd., 17177 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Olga Surova
- Ludwig Institute for Cancer Research Ltd., 17177 Stockholm, Sweden
| | - Erik Smedler
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Karin Wallis
- Ludwig Institute for Cancer Research Ltd., 17177 Stockholm, Sweden
| | - Zhi Xiong Chen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Ulf Hellman
- Ludwig Institute for Cancer Research Ltd., Biomedical Center, 75124 Uppsala, Sweden
| | - John Inge Johnsen
- Department of Women's and Children's Health, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Tommy Martinsson
- Department of Clinical Genetics, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, 41345 Göteborg, Sweden
| | - Rajappa S Kenchappa
- Neuro-Oncology Program, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Per Uhlén
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Susanne Schlisio
- Ludwig Institute for Cancer Research Ltd., 17177 Stockholm, Sweden; Department of Microbiology and Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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14
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Abstract
![]()
Calcineurin
is a Ser/Thr phosphatase that is important for key
biological processes, including immune system activation. We previously
identified a region in the intrinsically disordered regulatory domain
of calcineurin that forms a critical amphipathic α-helix (the
“distal helix”) that is required for complete activation
of calcineurin. This distal helix was shown to have a Tm close to that of human body temperature. Because the Tm was determined in dilute buffer, we hypothesized
that other factors inherent to a cellular environment might modulate
the stability of the distal helix. One such factor that contributes
to stability in other proteins is macromolecular crowding. The cell
cytoplasm is comprised of up to 400 g/L protein, lipids, nucleic acids,
and other compounds. We hypothesize that the presence of such crowders
could increase the thermal stability of the distal helix and thus
lead to a more robust activation of calcineurin in vivo. Using biophysical and biochemical approaches, we show that the
distal helix of calcineurin is indeed stabilized when crowded by the
synthetic polymers dextran 70 and ficoll 70, and that this stabilization
of the distal helix increases the activity of calcineurin.
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Affiliation(s)
- Erik C Cook
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Trevor P Creamer
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
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15
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Modelling intracellular competition for calcium: kinetic and thermodynamic control of different molecular modes of signal decoding. Sci Rep 2016; 6:23730. [PMID: 27033299 PMCID: PMC4817061 DOI: 10.1038/srep23730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/14/2016] [Indexed: 02/06/2023] Open
Abstract
Frequently, a common chemical entity triggers opposite cellular processes, which implies that the components of signalling networks must detect signals not only through their chemical natures, but also through their dynamic properties. To gain insights on the mechanisms of discrimination of the dynamic properties of cellular signals, we developed a computational stochastic model and investigated how three calcium ion (Ca2+)-dependent enzymes (adenylyl cyclase (AC), phosphodiesterase 1 (PDE1), and calcineurin (CaN)) differentially detect Ca2+ transients in a hippocampal dendritic spine. The balance among AC, PDE1 and CaN might determine the occurrence of opposite Ca2+-induced forms of synaptic plasticity, long-term potentiation (LTP) and long-term depression (LTD). CaN is essential for LTD. AC and PDE1 regulate, indirectly, protein kinase A, which counteracts CaN during LTP. Stimulations of AC, PDE1 and CaN with artificial and physiological Ca2+ signals demonstrated that AC and CaN have Ca2+ requirements modulated dynamically by different properties of the signals used to stimulate them, because their interactions with Ca2+ often occur under kinetic control. Contrarily, PDE1 responds to the immediate amplitude of different Ca2+ transients and usually with the same Ca2+ requirements observed under steady state. Therefore, AC, PDE1 and CaN decode different dynamic properties of Ca2+ signals.
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16
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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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17
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Dunlap TB, Guo HF, Cook EC, Holbrook E, Rumi-Masante J, Lester TE, Colbert CL, Vander Kooi CW, Creamer TP. Stoichiometry of the calcineurin regulatory domain-calmodulin complex. Biochemistry 2014; 53:5779-90. [PMID: 25144868 DOI: 10.1021/bi5004734] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Calcineurin is an essential serine/threonine phosphatase that plays vital roles in neuronal development and function, heart growth, and immune system activation. Calcineurin is unique in that it is the only phosphatase known to be activated by calmodulin in response to increasing intracellular calcium concentrations. Calcium-loaded calmodulin binds to the regulatory domain of calcineurin, resulting in a conformational change that removes an autoinhibitory domain from the active site of the phosphatase. We have determined a 1.95 Å crystal structure of calmodulin bound to a peptide corresponding to its binding region from calcineurin. In contrast to previous structures of this complex, our structure has a stoichiometry of 1:1 and has the canonical collapsed, wraparound conformation observed for many calmodulin-substrate complexes. In addition, we have used size-exclusion chromatography and time-resolved fluorescence to probe the stoichiometry of binding of calmodulin to a construct corresponding to almost the entire regulatory domain from calcineurin, again finding a 1:1 complex. Taken in sum, our data strongly suggest that a single calmodulin protein is necessary and sufficient to bind to and activate each calcineurin enzyme.
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Affiliation(s)
- Tori B Dunlap
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
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18
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Antunes G, Sebastião AM, Simoes de Souza FM. Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. PLoS One 2014; 9:e105531. [PMID: 25144232 PMCID: PMC4140790 DOI: 10.1371/journal.pone.0105531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/23/2014] [Indexed: 12/11/2022] Open
Abstract
Olfactory adaptation is a fundamental process for the functioning of the olfactory system, but the underlying mechanisms regulating its occurrence in intact olfactory sensory neurons (OSNs) are not fully understood. In this work, we have combined stochastic computational modeling and a systematic pharmacological study of different signaling pathways to investigate their impact during short-term adaptation (STA). We used odorant stimulation and electroolfactogram (EOG) recordings of the olfactory epithelium treated with pharmacological blockers to study the molecular mechanisms regulating the occurrence of adaptation in OSNs. EOG responses to paired-pulses of odorants showed that inhibition of phosphodiesterases (PDEs) and phosphatases enhanced the levels of STA in the olfactory epithelium, and this effect was mimicked by blocking vesicle exocytosis and reduced by blocking cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) and vesicle endocytosis. These results suggest that G-coupled receptors (GPCRs) cycling is involved with the occurrence of STA. To gain insights on the dynamical aspects of this process, we developed a stochastic computational model. The model consists of the olfactory transduction currents mediated by the cyclic nucleotide gated (CNG) channels and calcium ion (Ca2+)-activated chloride (CAC) channels, and the dynamics of their respective ligands, cAMP and Ca2+, and it simulates the EOG results obtained under different experimental conditions through changes in the amplitude and duration of cAMP and Ca2+ response, two second messengers implicated with STA occurrence. The model reproduced the experimental data for each pharmacological treatment and provided a mechanistic explanation for the action of GPCR cycling in the levels of second messengers modulating the levels of STA. All together, these experimental and theoretical results indicate the existence of a mechanism of regulation of STA by signaling pathways that control GPCR cycling and tune the levels of second messengers in OSNs, and not only by CNG channel desensitization as previously thought.
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Affiliation(s)
- Gabriela Antunes
- Neurosciences Unit, Institute of Molecular Medicine, University of Lisbon, Lisbon, Portugal; Laboratory of Neural Systems, Psychobiology Sector, Department of Psychology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Maria Sebastião
- Institute of Pharmacology and Neurosciences, Faculty of Medicine, University of Lisbon, Lisbon, Portugal; Neurosciences Unit, Institute of Molecular Medicine, University of Lisbon, Lisbon, Portugal
| | - Fabio Marques Simoes de Souza
- Neurosciences Unit, Institute of Molecular Medicine, University of Lisbon, Lisbon, Portugal; Center for Mathematics, Computation and Cognition, Federal University of ABC, São Bernardo do Campo, Brazil
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19
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Calcium-dependent energetics of calmodulin domain interactions with regulatory regions of the Ryanodine Receptor Type 1 (RyR1). Biophys Chem 2014; 193-194:35-49. [PMID: 25145833 DOI: 10.1016/j.bpc.2014.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
Abstract
Calmodulin (CaM) allosterically regulates the homo-tetrameric human Ryanodine Receptor Type 1 (hRyR1): apo CaM activates the channel, while (Ca(2+))4-CaM inhibits it. CaM-binding RyR1 residues 1975-1999 and 3614-3643 were proposed to allow CaM to bridge adjacent RyR1 subunits. Fluorescence anisotropy titrations monitored the binding of CaM and its domains to peptides encompassing hRyR(11975-1999) or hRyR1(3614-3643). Both CaM and its C-domain associated in a calcium-independent manner with hRyR1(3614-3643) while N-domain required calcium and bound ~250-fold more weakly. Association with hRyR1(11975-1999) was weak. Both hRyR1 peptides increased the calcium-binding affinity of both CaM domains, while maintaining differences between them. These energetics support the CaM C-domain association with hRyR1(3614-3643) at low calcium, positioning CaM to respond to calcium efflux. However, the CaM N-domain affinity for hRyR(11975-1999) alone was insufficient to support CaM bridging adjacent RyR1 subunits. Other proteins or elements of the hRyR1 structure must contribute to the energetics of CaM-mediated regulation.
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20
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Nair AG, Gutierrez-Arenas O, Eriksson O, Jauhiainen A, Blackwell KT, Kotaleski JH. Modeling intracellular signaling underlying striatal function in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 123:277-304. [PMID: 24560149 DOI: 10.1016/b978-0-12-397897-4.00013-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Striatum, which is the input nucleus of the basal ganglia, integrates cortical and thalamic glutamatergic inputs with dopaminergic afferents from the substantia nigra pars compacta. The combination of dopamine and glutamate strongly modulates molecular and cellular properties of striatal neurons and the strength of corticostriatal synapses. These actions are performed via intracellular signaling networks, containing several intertwined feedback loops. Understanding the role of dopamine and other neuromodulators requires the development of quantitative dynamical models for describing the intracellular signaling, in order to provide precise unambiguous descriptions and quantitative predictions. Building such models requires integration of data from multiple data sources containing information regarding the molecular interactions, the strength of these interactions, and the subcellular localization of the molecules. Due to the uncertainty, variability, and sparseness of these data, parameter estimation techniques are critical for inferring or constraining the unknown parameters, and sensitivity analysis evaluates which parameters are most critical for a given observed macroscopic behavior. Here, we briefly review the modeling approaches and tools that have been used to investigate biochemical signaling in the striatum, along with some of the models built around striatum. We also suggest a future direction for the development of such models from the, now becoming abundant, high-throughput data.
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Affiliation(s)
- Anu G Nair
- School of Computer Science and Communication, Royal Institute of Technology, Stockholm, Sweden
| | - Omar Gutierrez-Arenas
- School of Computer Science and Communication, Royal Institute of Technology, Stockholm, Sweden
| | - Olivia Eriksson
- Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
| | - Alexandra Jauhiainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kim T Blackwell
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Jeanette H Kotaleski
- School of Computer Science and Communication, Royal Institute of Technology, Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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21
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Dunlap TB, Cook EC, Rumi-Masante J, Arvin HG, Lester TE, Creamer TP. The Distal Helix in the Regulatory Domain of Calcineurin Is Important for Domain Stability and Enzyme Function. Biochemistry 2013; 52:8643-51. [DOI: 10.1021/bi400483a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tori B. Dunlap
- Center for Structural Biology,
Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Erik C. Cook
- Center for Structural Biology,
Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Julie Rumi-Masante
- Center for Structural Biology,
Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Hannah G. Arvin
- Center for Structural Biology,
Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Terrence E. Lester
- Center for Structural Biology,
Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Trevor P. Creamer
- Center for Structural Biology,
Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
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22
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Creamer TP. Transient disorder: Calcineurin as an example. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26412. [PMID: 28516023 PMCID: PMC5424781 DOI: 10.4161/idp.26412] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 01/11/2023]
Abstract
How intrinsically disordered proteins and regions evade degradation by cellular machinery evolved to recognize unfolded and misfolded chains remains a vexing question. One potential means by which this can occur is the disorder is transient in nature. That is, the disorder exists just long enough for it to be bound by a partner biomolecule and fold. A review of 30 y of studies of calmodulin’s activation of calcineurin suggests that the regulatory domain of this vital phosphatase is a transiently disordered region. During activation, the regulatory domain progresses from a folded state, to disordered, followed by folding upon being bound by calmodulin. The transient disordered state of this domain is part of a critical intermediate state that facilitates the rapid binding of calmodulin. Building upon “fly-casting” as a means of facilitating partner binding, the mechanism by which calcineurin undergoes activation and subsequent deactivation could be considered “catch and release.”
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Affiliation(s)
- Trevor P Creamer
- Center for Structural Biology; Department of Molecular and Cellular Biochemistry; University of Kentucky; Lexington, KY USA
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23
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Slupe AM, Merrill RA, Flippo KH, Lobas MA, Houtman JCD, Strack S. A calcineurin docking motif (LXVP) in dynamin-related protein 1 contributes to mitochondrial fragmentation and ischemic neuronal injury. J Biol Chem 2013; 288:12353-65. [PMID: 23486469 PMCID: PMC3636919 DOI: 10.1074/jbc.m113.459677] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fission and fusion events dynamically control the shape and function of mitochondria. The activity of the mitochondrial fission enzyme dynamin-related protein 1 (Drp1) is finely tuned by several post-translational modifications. Phosphorylation of Ser-656 by cAMP-dependent protein kinase (PKA) inhibits Drp1, whereas dephosphorylation by a mitochondrial protein phosphatase 2A isoform and the calcium-calmodulin-dependent phosphatase calcineurin (CaN) activates Drp1. Here, we identify a conserved CaN docking site on Drp1, an LXVP motif, which mediates the interaction between the phosphatase and mechanoenzyme. We mutated the LXVP motif in Drp1 to either increase or decrease similarity to the prototypical LXVP motif in the transcription factor NFAT, and assessed stability of the mutant Drp1-CaN complexes by affinity precipitation and isothermal titration calorimetry. Furthermore, we quantified effects of LXVP mutations on Drp1 dephosphorylation kinetics in vitro and in intact cells. With tools for bidirectional control of the CaN-Drp1 signaling axis in hand, we demonstrate that the Drp1 LXVP motif shapes mitochondria in neuronal and non-neuronal cells, and that CaN-mediated Drp1 dephosphorylation promotes neuronal death following oxygen-glucose deprivation. These results point to the CaN-Drp1 complex as a potential target for neuroprotective therapy of ischemic stroke.
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Affiliation(s)
- Andrew M Slupe
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242, USA
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24
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Reyes-Bermudez A, Miller DJ, Sprungala S. The Neuronal Calcium Sensor protein Acrocalcin: a potential target of calmodulin regulation during development in the coral Acropora millepora. PLoS One 2012; 7:e51689. [PMID: 23284743 PMCID: PMC3524228 DOI: 10.1371/journal.pone.0051689] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 11/05/2012] [Indexed: 12/28/2022] Open
Abstract
To understand the calcium-mediated signalling pathways underlying settlement and metamorphosis in the Scleractinian coral Acropora millepora, a predicted protein set derived from larval cDNAs was scanned for the presence of EF-hand domains (Pfam Id: PF00036). This approach led to the identification of a canonical calmodulin (AmCaM) protein and an uncharacterised member of the Neuronal Calcium Sensor (NCS) family of proteins known here as Acrocalcin (AmAC). While AmCaM transcripts were present throughout development, AmAC transcripts were not detected prior to gastrulation, after which relatively constant mRNA levels were detected until metamorphosis and settlement. The AmAC protein contains an internal CaM-binding site and was shown to interact in vitro with AmCaM. These results are consistent with the idea that AmAC is a target of AmCaM in vivo, suggesting that this interaction may regulate calcium-dependent processes during the development of Acropora millepora.
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Affiliation(s)
- Alejandro Reyes-Bermudez
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - David J. Miller
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
| | - Susanne Sprungala
- ARC Centre of Excellence for Coral Reef Studies and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- * E-mail:
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25
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Ogura K, Kumeta H, Takahasi K, Kobashigawa Y, Yoshida R, Itoh H, Yazawa M, Inagaki F. Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin. Genes Cells 2012; 17:159-72. [DOI: 10.1111/j.1365-2443.2012.01580.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Rumi-Masante J, Rusinga FI, Lester TE, Dunlap TB, Williams TD, Dunker AK, Weis DD, Creamer TP. Structural basis for activation of calcineurin by calmodulin. J Mol Biol 2011; 415:307-17. [PMID: 22100452 DOI: 10.1016/j.jmb.2011.11.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/02/2011] [Accepted: 11/04/2011] [Indexed: 11/29/2022]
Abstract
The highly conserved phosphatase calcineurin (CaN) plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin (CaM). CaM binds to a regulatory domain (RD) within CaN, causing a conformational change that displaces an autoinhibitory domain (AID) from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which CaM activates CaM-dependent protein kinases. Previously published data have hinted that the RD of CaN is intrinsically disordered. In this work, we demonstrate that the RD is unstructured and that it folds upon binding CaM, ousting the AID from the catalytic site. The RD is 95 residues long, with the AID attached to its C-terminal end and the 24-residue CaM binding region toward the N-terminal end. This is unlike the CaM-dependent protein kinases that have CaM binding sites and AIDs immediately adjacent in sequence. Our data demonstrate that not only does the CaM binding region folds but also an ∼25- to 30-residue region between it and the AID folds, resulting in over half of the RD adopting α-helical structure. This appears to be the first observation of CaM inducing folding of this scale outside of its binding site on a target protein.
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Affiliation(s)
- Julie Rumi-Masante
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA
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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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