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Ordyan M, Bartol T, Kennedy M, Rangamani P, Sejnowski T. Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. PLoS Comput Biol 2020; 16:e1008015. [PMID: 32678848 PMCID: PMC7390456 DOI: 10.1371/journal.pcbi.1008015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/29/2020] [Accepted: 06/04/2020] [Indexed: 01/10/2023] Open
Abstract
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. Using agent-based models, we computationally investigate 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 Ng 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, providing a mechanism to precisely control the sensitivity of synapses to calcium signals. Author Summary not valid for PLOS ONE submissions.
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Affiliation(s)
- Mariam Ordyan
- Institute for Neural Computation, University of California San Diego, La Jolla, California, United States of America
- Computational Neurobiology Laboratory, Salk Institute for Biological Sciences, La Jolla, California, United States of America
| | - Tom Bartol
- Computational Neurobiology Laboratory, Salk Institute for Biological Sciences, La Jolla, California, United States of America
| | - Mary Kennedy
- The Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (PR), (TS)
| | - Terrence Sejnowski
- Institute for Neural Computation, University of California San Diego, La Jolla, California, United States of America
- Computational Neurobiology Laboratory, Salk Institute for Biological Sciences, La Jolla, California, United States of America
- * E-mail: (PR), (TS)
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Pharris MC, Patel NM, VanDyk TG, Bartol TM, Sejnowski TJ, Kennedy MB, Stefan MI, Kinzer-Ursem TL. A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation. PLoS Comput Biol 2019; 15:e1006941. [PMID: 31869343 PMCID: PMC6957207 DOI: 10.1371/journal.pcbi.1006941] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 01/13/2020] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) accounts for up to 2 percent of all brain protein and is essential to memory function. CaMKII activity is known to regulate dynamic shifts in the size and signaling strength of neuronal connections, a process known as synaptic plasticity. Increasingly, computational models are used to explore synaptic plasticity and the mechanisms regulating CaMKII activity. Conventional modeling approaches may exclude biophysical detail due to the impractical number of state combinations that arise when explicitly monitoring the conformational changes, ligand binding, and phosphorylation events that occur on each of the CaMKII holoenzyme's subunits. To manage the combinatorial explosion without necessitating bias or loss in biological accuracy, we use a specialized syntax in the software MCell to create a rule-based model of a twelve-subunit CaMKII holoenzyme. Here we validate the rule-based model against previous experimental measures of CaMKII activity and investigate molecular mechanisms of CaMKII regulation. Specifically, we explore how Ca2+/CaM-binding may both stabilize CaMKII subunit activation and regulate maintenance of CaMKII autophosphorylation. Noting that Ca2+/CaM and protein phosphatases bind CaMKII at nearby or overlapping sites, we compare model scenarios in which Ca2+/CaM and protein phosphatase do or do not structurally exclude each other's binding to CaMKII. Our results suggest a functional mechanism for the so-called "CaM trapping" phenomenon, wherein Ca2+/CaM may structurally exclude phosphatase binding and thereby prolong CaMKII autophosphorylation. We conclude that structural protection of autophosphorylated CaMKII by Ca2+/CaM may be an important mechanism for regulation of synaptic plasticity.
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Affiliation(s)
- Matthew C. Pharris
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Neal M. Patel
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Tyler G. VanDyk
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Thomas M. Bartol
- Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Terrence J. Sejnowski
- Salk Institute for Biological Studies, La Jolla, California, United States of America
- Institute for Neural Computation, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Mary B. Kennedy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Melanie I. Stefan
- Salk Institute for Biological Studies, La Jolla, California, United States of America
- EMBL-European Bioinformatics Institute, Hinxton, United Kingdom
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- ZJU-UoE Institute, Zhejiang University, Haining, China
- * E-mail: (MIS); (TLKU)
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (MIS); (TLKU)
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Mjolsness E. Prospects for Declarative Mathematical Modeling of Complex Biological Systems. Bull Math Biol 2019; 81:3385-3420. [PMID: 31175549 PMCID: PMC6677696 DOI: 10.1007/s11538-019-00628-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/30/2019] [Indexed: 01/06/2023]
Abstract
Declarative modeling uses symbolic expressions to represent models. With such expressions, one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathematical semantics of a complex biological model. The potential advantages are particularly relevant in the case of developmental modeling, wherein complex spatial structures exhibit dynamics at molecular, cellular, and organogenic levels to relate genotype to multicellular phenotype. Multiscale modeling can benefit from both the expressive power of declarative modeling languages and the application of model reduction methods to link models across scale. Based on previous work, here we define declarative modeling of complex biological systems by defining the operator algebra semantics of an increasingly powerful series of declarative modeling languages including reaction-like dynamics of parameterized and extended objects; we define semantics-preserving implementation and semantics-approximating model reduction transformations; and we outline a “meta-hierarchy” for organizing declarative models and the mathematical methods that can fruitfully manipulate them.
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Affiliation(s)
- Eric Mjolsness
- Department of Computer Science, University of California, Irvine, CA, 92697, USA.
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Ernst OK, Bartol TM, Sejnowski TJ, Mjolsness E. Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions. Phys Rev E 2019; 99:063315. [PMID: 31330605 PMCID: PMC6852890 DOI: 10.1103/physreve.99.063315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/16/2022]
Abstract
Many physical systems are described by probability distributions that evolve in both time and space. Modeling these systems is often challenging due to their large state space and analytically intractable or computationally expensive dynamics. To address these problems, we study a machine-learning approach to model reduction based on the Boltzmann machine. Given the form of the reduced model Boltzmann distribution, we introduce an autonomous differential equation system for the interactions appearing in the energy function. The reduced model can treat systems in continuous space (described by continuous random variables), for which we formulate a variational learning problem using the adjoint method to determine the right-hand sides of the differential equations. This approach can be used to enforce a reduced physical model by a suitable parametrization of the differential equations. The parametrization we employ uses the basis functions from finite-element methods, which can be used to model any physical system. One application domain for such physics-informed learning algorithms is to modeling reaction-diffusion systems. We study a lattice version of the Rössler chaotic oscillator, which illustrates the accuracy of the moment closure approximation made by the method and its dimensionality reduction power.
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Affiliation(s)
- Oliver K Ernst
- Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
| | | | - Terrence J Sejnowski
- Salk Institute for Biological Studies, La Jolla, California 92037, USA and Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093, USA
| | - Eric Mjolsness
- Departments of Computer Science and Mathematics, and Institute for Genomics and Bioinformatics, University of California at Irvine, Irvine, 92697 California, USA
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Henze R, Mu C, Puljiz M, Kamaleson N, Huwald J, Haslegrave J, di Fenizio PS, Parker D, Good C, Rowe JE, Ibrahim B, Dittrich P. Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint. Sci Rep 2019; 9:3902. [PMID: 30846816 PMCID: PMC6405958 DOI: 10.1038/s41598-019-40648-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 02/19/2019] [Indexed: 02/05/2023] Open
Abstract
The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space. A sequence of manual and automatic coarse-grainings finally leads to the coarsest deterministic and stochastic models containing only four molecular species and four states for each kinetochore, respectively. We are able to relate each more coarse-grained level to a finer one, which allows us to relate model parameters between coarse-grainings and which provides a more precise meaning for the elements of the more abstract models. Furthermore, we discuss how organizational coarse-graining can be applied to spatial dynamics by showing spatial organizations during mitotic checkpoint inactivation. We demonstrate how these models lead to insights if the model has different “meaningful” behaviors that differ in the set of (molecular) species. We conclude that understanding, modeling and analyzing complex bio-molecular systems can greatly benefit from a set of coarse-graining methods that, ideally, can be automatically applied and that allow the different levels of abstraction to be related.
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Affiliation(s)
- Richard Henze
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Chunyan Mu
- School of Computing, Teesside University, Teesside, UK
| | - Mate Puljiz
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | | | - Jan Huwald
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | | | | | - David Parker
- School of Computer Science, University of Birmingham, Birmingham, UK
| | | | - Jonathan E Rowe
- School of Computer Science, University of Birmingham, Birmingham, UK
| | - Bashar Ibrahim
- Chair of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University of Jena, Jena, Germany.
| | - Peter Dittrich
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.
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Ernst OK, Bartol T, Sejnowski T, Mjolsness E. Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics. J Chem Phys 2018; 149:034107. [PMID: 30037235 PMCID: PMC6056297 DOI: 10.1063/1.5026403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/01/2018] [Indexed: 11/15/2022] Open
Abstract
Finding reduced models of spatially distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy approximation is constructed that evolves slowly in time. The dynamical model governing the approximation is expressed as a functional, allowing a general treatment of spatial interactions. In contrast to typical machine learning approaches which estimate the interaction parameters of a graphical model, we derive Boltzmann-machine like learning algorithms to estimate directly the functionals dictating the time evolution of these parameters. By incorporating analytic solutions from simple reaction motifs, an efficient simulation method is demonstrated for systems ranging from toy problems to basic biologically relevant networks. The broadly applicable nature of our approach to learning spatial dynamics suggests promising applications to multiscale methods for spatial networks, as well as to further problems in machine learning.
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Affiliation(s)
- Oliver K Ernst
- Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
| | - Thomas Bartol
- Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Eric Mjolsness
- Departments of Computer Science and Mathematics, and Institute for Genomics and Bioinformatics, University of California at Irvine, Irvine, California 92697, USA
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