Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator

Calmodulin-dependent kinase II (CaMKII) has long been known to play an important role in learning and memory as well as long term potentiation (LTP). More recently it has been suggested that it might be involved in the time averaging of synaptic signals, which can then lead to the high precision of information stored at a single synapse. However, the role of the scaffolding molecule, neurogranin (Ng), in governing the dynamics of CaMKII is not yet fully understood. In this work, we adopt a rule-based modeling approach through the Monte Carlo method to study the effect of Ca2+ signals on the dynamics of CaMKII phosphorylation in the postsynaptic density (PSD). Calcium surges are observed in synaptic spines during an EPSP and back-propagating action potential due to the opening of NMDA receptors and voltage dependent calcium channels. We study the differences between the dynamics of phosphorylation of CaMKII monomers and dodecameric holoenzymes. The scaffolding molecule Ng, when present in significant concentration, limits the availability of free calmodulin (CaM), the protein which activates CaMKII in the presence of calcium. We show that it plays an important modulatory role in CaMKII phosphorylation following a surge of high calcium concentration. We find a non-intuitive dependence of this effect on CaM concentration that results from the different affinities of CaM for CaMKII depending on the number of calcium ions bound to the former. It has been shown previously that in the absence of phosphatase CaMKII monomers integrate over Ca2+ signals of certain frequencies through autophosphorylation (Pepke et al, Plos Comp. Bio., 2010). We also study the effect of multiple calcium spikes on CaMKII holoenzyme autophosphorylation, and show that in the presence of phosphatase CaMKII behaves as a leaky integrator of calcium signals, a result that has been recently observed in vivo. Our models predict that the parameters of this leaky integrator are finely tuned through the interactions of Ng, CaM, CaMKII, and PP1. This is a possible mechanism to precisely control the sensitivity of synapses to calcium signals.

[1]  D. Storm,et al.  The role of calmodulin as a signal integrator for synaptic plasticity , 2005, Nature Reviews Neuroscience.

[2]  S. Reichow,et al.  The CaMKII holoenzyme structure in activation-competent conformations , 2017, Nature Communications.

[3]  K. Svoboda,et al.  The Life Cycle of Ca2+ Ions in Dendritic Spines , 2002, Neuron.

[4]  Stephen G. Miller,et al.  Sequences of autophosphorylation sites in neuronal type II CaM kinase that control Ca2+-independent activity , 1988, Neuron.

[5]  H. Schulman,et al.  A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme , 2011, Cell.

[6]  Andreas Lüthi,et al.  Modulation of AMPA receptor unitary conductance by synaptic activity , 1998, Nature.

[7]  G. Collingridge,et al.  LTP in hippocampal neurons is associated with a CaMKII‐mediated increase in GluA1 surface expression , 2011, Journal of neurochemistry.

[8]  M. Kennedy,et al.  Activation of type II calcium/calmodulin-dependent protein kinase by Ca2+/calmodulin is inhibited by autophosphorylation of threonine within the calmodulin-binding domain. , 1990, The Journal of biological chemistry.

[9]  J. Lisman A mechanism for memory storage insensitive to molecular turnover: a bistable autophosphorylating kinase. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[10]  H. Cline,et al.  Stabilization of dendritic arbor structure in vivo by CaMKII. , 1998, Science.

[11]  J. Hell,et al.  The CaMKII/GluN2B Protein Interaction Maintains Synaptic Strength* , 2016, The Journal of Biological Chemistry.

[12]  Susan E. Brown,et al.  Kinetic Control of the Dissociation Pathway of Calmodulin-Peptide Complexes* , 1997, The Journal of Biological Chemistry.

[13]  M. Waxham,et al.  RC3/Neurogranin and Ca2+/Calmodulin-dependent Protein Kinase II Produce Opposing Effects on the Affinity of Calmodulin for Calcium* , 2004, Journal of Biological Chemistry.

[14]  Shahid Khan,et al.  Multiple CaMKII Binding Modes to the Actin Cytoskeleton Revealed by Single-Molecule Imaging , 2016, Biophysical journal.

[15]  Dipak Barua,et al.  BioNetGen 2.2: advances in rule-based modeling , 2015, Bioinform..

[16]  A. Zhabotinsky Bistability in the Ca(2+)/calmodulin-dependent protein kinase-phosphatase system. , 2000, Biophysical journal.

[17]  D. Choquet,et al.  CaMKII Triggers the Diffusional Trapping of Surface AMPARs through Phosphorylation of Stargazin , 2010, Neuron.

[18]  M. Waxham,et al.  Neurogranin controls the spatiotemporal pattern of postsynaptic Ca2+/CaM signaling. , 2007, Biophysical journal.

[19]  A. Chakraborty,et al.  Scaffold proteins confer diverse regulatory properties to protein kinase cascades , 2007, Proceedings of the National Academy of Sciences.

[20]  J. M. Bradshaw,et al.  Thermodynamics of calmodulin trapping by Ca2+/calmodulin-dependent protein kinase II: subpicomolar Kd determined using competition titration calorimetry. , 2007, Biochemistry.

[21]  K. Downing,et al.  Architectural Dynamics of CaMKII-Actin Networks , 2018, Biophysical journal.

[22]  D. Choquet,et al.  A three-step model for the synaptic recruitment of AMPA receptors , 2011, Molecular and Cellular Neuroscience.

[23]  Suzanne Paradis,et al.  The Rac1-GEF Tiam1 Couples the NMDA Receptor to the Activity-Dependent Development of Dendritic Arbors and Spines , 2005, Neuron.

[24]  R. Malinow,et al.  Driving AMPA receptors into synapses by LTP and CaMKII: requirement for GluR1 and PDZ domain interaction. , 2000, Science.

[25]  M. Kennedy,et al.  Structure and regulation of type II calcium/calmodulin-dependent protein kinase in central nervous system neurons. , 1990, Cold Spring Harbor symposia on quantitative biology.

[26]  Thomas Krucker,et al.  Targeted Disruption of RC3 Reveals a Calmodulin-Based Mechanism for Regulating Metaplasticity in the Hippocampus , 2002, The Journal of Neuroscience.

[27]  P. Michalski The delicate bistability of CaMKII. , 2013, Biophysical journal.

[28]  Seok-Jin R. Lee,et al.  CaMKII Autophosphorylation Is Necessary for Optimal Integration of Ca2+ Signals during LTP Induction, but Not Maintenance , 2017, Neuron.

[29]  J. Lisman,et al.  The molecular basis of CaMKII function in synaptic and behavioural memory , 2002, Nature Reviews Neuroscience.

[30]  K. Okamoto,et al.  Regulation of actin dynamics during structural plasticity of dendritic spines: Signaling messengers and actin-binding proteins , 2018, Molecular and Cellular Neuroscience.

[31]  J. Exton,et al.  Phospholipase C‐γ, protein kinase C and Ca2+/calmodulin‐dependent protein kinase II are involved in platelet‐derived growth factor‐induced phosphorylation of Tiam1 , 1998, FEBS letters.

[32]  Stefan Mihalas,et al.  A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II , 2010, PLoS Comput. Biol..

[33]  Michael J Higley,et al.  Calcium Signaling in Dendritic Spines , 2022 .

[34]  R. Zucker,et al.  Selective induction of LTP and LTD by postsynaptic [Ca2+]i elevation. , 1999, Journal of neurophysiology.

[35]  Alcino J. Silva,et al.  Impaired spatial learning in alpha-calcium-calmodulin kinase II mutant mice. , 1992, Science.

[36]  K. Sobue,et al.  Quantitative determinations of calmodulin in the supernatant and particulate fractions of mammalian tissues. , 1982, Journal of biochemistry.

[37]  Eric Mjolsness,et al.  Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics. , 2015, Physical biology.

[38]  J. M. Bradshaw,et al.  Chemical Quenched Flow Kinetic Studies Indicate an Intraholoenzyme Autophosphorylation Mechanism for Ca2+/Calmodulin-dependent Protein Kinase II* , 2002, The Journal of Biological Chemistry.

[39]  James R Faeder,et al.  MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. , 2018, Methods in molecular biology.

[40]  Paul T. Kelly,et al.  Postsynaptic injection of Ca2+/CaM induces synaptic potentiation requiring CaMKII and PKC activity , 1995, Neuron.

[41]  T. Sejnowski,et al.  Computational reconstitution of spine calcium transients from individual proteins , 2015, Front. Synaptic Neurosci..

[42]  F. J. Díez-Guerra,et al.  Neurogranin, a link between calcium/calmodulin and protein kinase C signaling in synaptic plasticity , 2010, IUBMB life.

[43]  H. Cline,et al.  Postsynaptic Calcium/Calmodulin-Dependent Protein Kinase II Is Required to Limit Elaboration of Presynaptic and Postsynaptic Neuronal Arbors , 1999, The Journal of Neuroscience.

[44]  Alcino J. Silva,et al.  Autophosphorylation at Thr286 of the alpha calcium-calmodulin kinase II in LTP and learning. , 1998, Science.

[45]  M Neal Waxham,et al.  βCaMKII Regulates Actin Assembly and Structure* , 2009, Journal of Biological Chemistry.

[46]  H. Schulman,et al.  Calmodulin Trapping by Calcium-Calmodulin-Dependent Protein Kinase , 1992, Science.

[47]  M. Zaccolo,et al.  The Role of Type 4 Phosphodiesterases in Generating Microdomains of cAMP: Large Scale Stochastic Simulations , 2010, PloS one.

[48]  Rafael Yuste,et al.  Imaging calcium dynamics in dendritic spines , 1996, Current Opinion in Neurobiology.

[49]  Terrence J Sejnowski,et al.  Complexity of calcium signaling in synaptic spines. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[50]  R. Malinow,et al.  Ras and Rap Control AMPA Receptor Trafficking during Synaptic Plasticity , 2002, Cell.

[51]  T. Schikorski,et al.  Inactivity Produces Increases in Neurotransmitter Release and Synapse Size , 2001, Neuron.

[52]  K. Svoboda,et al.  The Number of Glutamate Receptors Opened by Synaptic Stimulation in Single Hippocampal Spines , 2004, The Journal of Neuroscience.

[53]  Tobias Meyer,et al.  CaMKIIβ Functions As an F-Actin Targeting Module that Localizes CaMKIIα/β Heterooligomers to Dendritic Spines , 1998, Neuron.

[54]  S. Linse,et al.  Calcium binding to calmodulin and its globular domains. , 1991, The Journal of biological chemistry.

[55]  Yasunori Hayashi,et al.  The role of CaMKII as an F-actin-bundling protein crucial for maintenance of dendritic spine structure , 2007, Proceedings of the National Academy of Sciences.

[56]  S. Halpain,et al.  Computational Modeling Reveals Frequency Modulation of Calcium-cAMP/PKA Pathway in Dendritic Spines , 2019, bioRxiv.

[57]  Stefan Mihalas,et al.  Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums , 2006, Proceedings of the National Academy of Sciences.

[58]  J. Connor,et al.  Micromolar Ca2+ transients in dendritic spines of hippocampal pyramidal neurons in brain slice , 1995, Neuron.

[59]  T. Sejnowski,et al.  Nanoconnectomic upper bound on the variability of synaptic plasticity , 2015, eLife.

[60]  Seok-Jin R. Lee,et al.  Activation of CaMKII in single dendritic spines during long-term potentiation , 2009, Nature.

[61]  A. Persechini,et al.  Different Mechanisms for Ca Dissociation from Complexes of Calmodulin with Nitric Oxide Synthase or Myosin Light Chain Kinase (*) , 1996, The Journal of Biological Chemistry.

[62]  Nicolas Brunel,et al.  STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways , 2007, PLoS Comput. Biol..

[63]  Robert A. Copeland,et al.  Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis , 1996 .

[64]  Andy Hudmon,et al.  Neuronal CA2+/calmodulin-dependent protein kinase II: the role of structure and autoregulation in cellular function. , 2002, Annual review of biochemistry.

[65]  Michael G. Rosenfeld,et al.  Expression of a multifunctional Ca2+/calmodulin-dependent protein kinase and mutational analysis of its autoregulation , 1989, Neuron.

[66]  M. Waxham,et al.  Calcium-calmodulin-dependent protein kinase II isoforms differentially impact the dynamics and structure of the actin cytoskeleton. , 2013, Biochemistry.

[67]  T. Bliss,et al.  Autonomous activity of CaMKII is only transiently increased following the induction of long‐term potentiation in the rat hippocampus , 2004, The European journal of neuroscience.

[68]  James R Faeder,et al.  Efficient modeling, simulation and coarse-graining of biological complexity with NFsim , 2011, Nature Methods.

[69]  K. Roche,et al.  Autonomous CaMKII mediates both LTP and LTD using a mechanism for differential substrate site selection. , 2014, Cell reports.

[70]  Alcino J. Silva,et al.  Deficient hippocampal long-term potentiation in alpha-calcium-calmodulin kinase II mutant mice. , 1992, Science.

[71]  G. Oster,et al.  Paradoxical signaling regulates structural plasticity in dendritic spines , 2016, Proceedings of the National Academy of Sciences.

[72]  First demonstration of bistability in CaMKII, a memory-related kinase. , 2014, Biophysical journal.

[73]  Padmini Rangamani,et al.  Geometric control of frequency modulation of cAMP oscillations due to Ca2+-bursts in dendritic spines , 2019, bioRxiv.

[74]  James R Faeder,et al.  Rule-based modeling of biochemical systems with BioNetGen. , 2009, Methods in molecular biology.

[75]  H. Schulman,et al.  Substrate-directed Function of Calmodulin in Autophosphorylation of Ca2+/Calmodulin-dependent Protein Kinase II* , 1998, The Journal of Biological Chemistry.

[76]  R. Yasuda,et al.  Mechanisms of Ca2+/calmodulin-dependent kinase II activation in single dendritic spines , 2019, Nature Communications.

[77]  Lubert Stryer,et al.  Dual role of calmodulin in autophosphorylation of multifunctional cam kinase may underlie decoding of calcium signals , 1994, Neuron.

[78]  Hiroshi Okamoto,et al.  Switching characteristics of a model for biochemical-reaction networks describing autophosphorylation versus dephosphorylation of Ca2+/calmodulin-dependent protein kinase II , 2000, Biological Cybernetics.

[79]  M. Bear,et al.  Regulation of distinct AMPA receptor phosphorylation sites during bidirectional synaptic plasticity , 2000, Nature.

[80]  M K Bennett,et al.  Purification and characterization of a calmodulin-dependent protein kinase that is highly concentrated in brain. , 1983, The Journal of biological chemistry.

[81]  Tobias Meyer,et al.  An ultrasensitive Ca2+/calmodulin-dependent protein kinase II-protein phosphatase 1 switch facilitates specificity in postsynaptic calcium signaling , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[82]  William S. Hlavacek,et al.  BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains , 2004, Bioinform..

[83]  K. Reymann,et al.  Involvement of neurogranin in the modulation of calcium/calmodulin-dependent protein kinase II, synaptic plasticity, and spatial learning: a study with knockout mice. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Xiao-Jing Wang,et al.  The Stability of a Stochastic CaMKII Switch: Dependence on the Number of Enzyme Molecules and Protein Turnover , 2005, PLoS biology.

[85]  J. Falke,et al.  Intermolecular tuning of calmodulin by target peptides and proteins: Differential effects on Ca2+ binding and implications for kinase activation , 1997, Protein science : a publication of the Protein Society.

[86]  Jay T. Groves,et al.  A Mechanism for Tunable Autoinhibition in the Structure of a Human Ca2+/Calmodulin- Dependent Kinase II Holoenzyme , 2011, Cell.

[87]  A. Miyawaki,et al.  Visualization of Synaptic Ca2+ /Calmodulin-Dependent Protein Kinase II Activity in Living Neurons , 2005, The Journal of Neuroscience.

[88]  John Lisman,et al.  Synaptic Strength of Individual Spines Correlates with Bound Ca2+–Calmodulin-Dependent Kinase II , 2007, The Journal of Neuroscience.

[89]  J. Lisman,et al.  A Model of Synaptic Memory A CaMKII/PP1 Switch that Potentiates Transmission by Organizing an AMPA Receptor Anchoring Assembly , 2001, Neuron.

[90]  E. Neher,et al.  Calcium gradients and buffers in bovine chromaffin cells. , 1992, The Journal of physiology.

[91]  T. Sejnowski,et al.  Addendum: Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium , 2019, The Journal of general physiology.

[92]  B. Finn,et al.  The evolving model of calmodulin structure, function and activation. , 1995, Structure.

[93]  T. Soderling,et al.  Regulatory phosphorylation of AMPA-type glutamate receptors by CaM-KII during long-term potentiation. , 1997, Science.

[94]  H. Schulman,et al.  Inhibitory autophosphorylation of multifunctional Ca2+/calmodulin-dependent protein kinase analyzed by site-directed mutagenesis. , 1992, The Journal of biological chemistry.

[95]  R. Yasuda,et al.  PKCα integrates spatiotemporally distinct Ca2+ and autocrine BDNF signaling to facilitate synaptic plasticity , 2018, Nature Neuroscience.

[96]  W. Kolch Coordinating ERK/MAPK signalling through scaffolds and inhibitors , 2005, Nature Reviews Molecular Cell Biology.

[97]  Angus C. Nairn,et al.  Structure of the Autoinhibited Kinase Domain of CaMKII and SAXS Analysis of the Holoenzyme , 2005, Cell.

[98]  M. Waxham,et al.  Neurogranin Alters the Structure and Calcium Binding Properties of Calmodulin* , 2014, The Journal of Biological Chemistry.

[99]  S. Martin,et al.  Stopped-flow studies of calcium dissociation from calcium-binding-site mutants of Drosophila melanogaster calmodulin. , 1992, European journal of biochemistry.

[100]  K. Hempel,et al.  Calmodulin content in specific brain areas , 2004, Experimental Brain Research.

[101]  S. Raghavachari,et al.  Mechanisms of CaMKII action in long-term potentiation , 2012, Nature Reviews Neuroscience.

[102]  D. Surmeier,et al.  Kalirin-7 Controls Activity-Dependent Structural and Functional Plasticity of Dendritic Spines , 2007, Neuron.

[103]  Paul De Koninck,et al.  CaMKII control of spine size and synaptic strength: Role of phosphorylation states and nonenzymatic action , 2010, Proceedings of the National Academy of Sciences.

[104]  Jeanette Kotaleski,et al.  Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration , 2016, PLoS Comput. Biol..

[105]  R. Colbran,et al.  Protein Phosphatases and Calcium/Calmodulin-Dependent Protein Kinase II-Dependent Synaptic Plasticity , 2004, The Journal of Neuroscience.

[106]  Shin Ishii,et al.  In vitro reconstitution of a CaMKII memory switch by an NMDA receptor-derived peptide. , 2014, Biophysical journal.

[107]  T. Vanaman,et al.  Structural similarities between the Ca2+-dependent regulatory proteins of 3':5'-cyclic nucleotide phosphodiesterase and actomyosin ATPase. , 1976, The Journal of biological chemistry.

[108]  S. Coultrap,et al.  CaMKII regulation in information processing and storage , 2012, Trends in Neurosciences.

[109]  M. Kennedy,et al.  Regulation of brain Type II Ca 2+ calmodulin -dependent protein kinase by autophosphorylation: A Ca2+-triggered molecular switch , 1986, Cell.

[110]  Irving R Epstein,et al.  Role of the Neurogranin Concentrated in Spines in the Induction of Long-Term Potentiation , 2006, The Journal of Neuroscience.

[111]  G. Bi,et al.  Synaptic Modifications in Cultured Hippocampal Neurons: Dependence on Spike Timing, Synaptic Strength, and Postsynaptic Cell Type , 1998, The Journal of Neuroscience.

[112]  Ling Zhong,et al.  Neurogranin enhances synaptic strength through its interaction with calmodulin , 2009, The EMBO journal.

[113]  M. Kennedy,et al.  SynGAP Regulates Steady-State and Activity-Dependent Phosphorylation of Cofilin , 2008, The Journal of Neuroscience.

[114]  Terrence J. Sejnowski,et al.  A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation , 2019, bioRxiv.

[115]  D. Clapham,et al.  SynGAP-MUPP1-CaMKII Synaptic Complexes Regulate p38 MAP Kinase Activity and NMDA Receptor- Dependent Synaptic AMPA Receptor Potentiation , 2004, Neuron.

[116]  Masanobu Kano,et al.  Nonlinear decoding and asymmetric representation of neuronal input information by CaMKIIα and calcineurin. , 2013, Cell reports.

[117]  B. Sakmann,et al.  Spine Ca2+ Signaling in Spike-Timing-Dependent Plasticity , 2006, The Journal of Neuroscience.

[118]  D. Lovinger,et al.  Translocation of Autophosphorylated Calcium/Calmodulin-dependent Protein Kinase II to the Postsynaptic Density* , 1997, The Journal of Biological Chemistry.

[119]  U. Bhalla,et al.  Subunit exchange enhances information retention by CaMKII in dendritic spines , 2018, bioRxiv.

[120]  Caleb J Bashor,et al.  The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway , 2006, Science.

[121]  P. Greengard,et al.  A Network of Control Mediated by Regulator of Calcium/Calmodulin-Dependent Signaling , 2004, Science.