CRCNS: Modeling Activation of CaMKII in Spines

CRCNS：模拟脊柱中 CaMKII 的激活

• 批准号: 8263980
• 负责人: MARY B KENNEDY
• 金额: $ 32.68万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8263980
• 关键词: Actins; Adverse effects; Agreement; Algorithms; Animals; Basic Science; Behavior; Binding; Biological; Biological Assay; Brain; Calcineurin; Calcium/calmodulin-dependent protein kinase; Calmodulin; Calmodulin-Binding Proteins; Catalytic Domain; Cell physiology; Chemical Engineering; Communities; Complex; Computational Technique; Computer Simulation; Cytoskeleton; Cytosol; Dendritic Spines; Development; Disease; Doctor of Philosophy; Drug Addiction; Educational process of instructing; Educational workshop; Egtazic Acid; Employment; Enzymes; Event; Excision; Female; Fire - disasters; Fostering; Foundations; Functional disorder; Glutamate Receptor; Goals; Grant; Hippocampus (Brain); Holoenzymes; Image; In Vitro; Individual; Intervention; Kinetics; Knowledge; Laboratories; Lead; Learning; Location; Long-Term Depression; Long-Term Potentiation; Medical; Membrane; Memory; Memory impairment; Mental disorders; Methods; Minority; Modeling; Molecular; Molecular Models; Multiprotein Complexes; N-Methyl-D-Aspartate Receptors; N-Methylaspartate; Names; Neuraxis; Neurobiology; Neurons; Neurosciences; Output; Pathway interactions; Phosphotransferases; Positioning Attribute; Postdoctoral Fellow; Postsynaptic Membrane; Presynaptic Terminals; Process; Property; Proteins; Publishing; Pump; Reaction; Regulation; Regulatory Pathway; Relative (related person); Research; Research Personnel; Rewards; Role; Schizophrenia; Shapes; Short-Term Memory; Signal Pathway; Signal Transduction; Signaling Protein; Staging; Structure; Students; Surface; Synapses; Synaptic Transmission; Synaptic plasticity; Tail; Techniques; Testing; Time; To specify; Training; Vertebral column; Visual; Work; base; calmodulin-dependent protein kinase II; density; dimer; graduate student; in vivo; knock-down; millisecond; molecular modeling; mutant; neural circuit; photolysis; postsynaptic; programs; protein complex; research study; scaffold; simulation; syntax; undergraduate student

DESCRIPTION (provided by applicant): The immediate objective of this proposal is to build an accurate dynamic model of activation and autophosphorylation of the signaling protein Ca2+/calmodulin (CaM)-dependent protein kinase II (CaMKII) during influx of Ca2+ into the postsynaptic spine through NMDA receptors. The work will proceed in three stages. First, investigators will validate a model of activation of individual monomeric catalytic subunits by Ca2+ and CaM and refine its kinetic parameters by comparing the model to experiments. The deterministic model is implemented in Mathematica; the output of the model will be tested against bench assays of the enzymatic activity of monomeric subunits of CaMKII under a wide range of concentrations of the subunits, CaM, and Ca2+. The concentrations will mimic both in vivo and in vitro conditions. In the second stage, investigators will construct a model of activation of the dodecameric holoenzyme of CaMKII, based on the model validated in the first stage. They will model cooperative activation of subunit dimers within the holoenzyme, and three different paths of autophosphorylation of its subunits. The models will be constructed in the program MCell, which supports spatially correct stochastic models of protein interactions and enzymatic activation, within biologically realistic geometries. This model will employ a new rule-based algorithm to specify the locations and behavior of subunits in holoenzymes. It will be constructed in a well-mixed volume to enable testing by comparison to bench experiments with holoenzymes under a wide range of concentrations of subunits, CaM, and Ca2+. The comparisons will be used to optimize four new parameters in the holoenzyme model, and to choose the most accurate model for progression of autophosphorylation within the holoenzyme. In the third stage, investigators will introduce optimized models of the CaMKII holoenzyme into a larger MCell model of Ca2+ influx into spines through NMDA receptors and its removal by pumps and exchangers. Simulations in MCell with this model will be used to test hypotheses about parameters governing activation of CaMKII in spines. The intellectual merit of the proposal lies in its utility in the study of mechanisms of learning in the central nervous system. The regulatory machinery in a spine controls synaptic strength by regulating activity-dependent changes such as LTP and LTD. We know much about the regulatory enzymes in a spine and we have hypotheses about enzymatic networks that regulate the cellular processes controlling synaptic plasticity, including insertion and removal of glutamate receptors and changes in the shape of the spine actin cytoskeleton. However, at the present stage of analysis, qualitative studies with mutant animals, or over-expression and knock-down of particular enzymes are the dominant paradigm in the field and they are not adequate to bring our knowledge to the next level, which is to establish the timing of the action of each of these players, and the precise conditions and position in the regulatory network at which each one becomes important. To reach that level of understanding, we need better quantitative models and methods. CaMKII is one of the the initial enzymes activated by Ca2+ coming through NMDA receptors during induction of LTP. A well-validated quantitative model of its activation in the powerful MCell program will provide a starting point and an example for the construction of dynamic models of successive steps in spine regulatory pathways. The broader impacts include the educational goal of fostering introduction of computational techniques into cellular neurobiological research. A female postdoctoral fellow will be trained in experimental techniques to test computational models, and in the use of MCell. Undergraduate students (including minority students) will be involved in the work through summer research programs at Caltech and Salk. All models will be made available to the community for download. The models of CaMKII holoenzymes will be a first example of simulation in MCell of interactions within a cytosolic multiprotein complex. The syntax for doing this will be published, and taught in the regular workshops on MCell sponsored by NSF. The proposal has medical significance. Deficiencies in spine signaling pathways that use CaMKII are associated with working memory deficits similar to those that underlie schizophrenia and related thought disorders. A quantitative understanding of the factors governing activation of CaMKII during synaptic activity, and its role in controlling synaptic plasticity will facilitate development of clinically useful pharmacological agents that target specific aspects of synaptic dysfunction with fewer undesirable side effects.

描述（由申请人提供）：本提案的直接目标是建立Ca2+/钙调素（CaM）依赖性蛋白激酶II （CaMKII）在Ca2+通过NMDA受体涌入突触后脊柱时激活和自磷酸化的准确动态模型。这项工作将分三个阶段进行。首先，研究人员将验证Ca2+和CaM活化单个单体催化亚基的模型，并通过将模型与实验进行比较来完善其动力学参数。确定性模型在Mathematica中实现；模型的输出将通过CaMKII的单体亚基在广泛的亚基、CaM和Ca2+浓度下的酶活性的台架分析进行测试。浓度将模拟体内和体外条件。在第二阶段，研究人员将基于第一阶段验证的模型构建CaMKII十二聚体全酶的激活模型。他们将模拟全酶内亚基二聚体的协同激活，以及其亚基自磷酸化的三种不同途径。这些模型将在MCell程序中构建，该程序支持蛋白质相互作用和酶激活的空间正确的随机模型，在生物学上是真实的几何形状。该模型将采用一种新的基于规则的算法来指定全酶中亚基的位置和行为。它将在充分混合的体积中构建，以便在广泛的亚基、CaM和Ca2+浓度下与全酶的台架实验进行比较。这些比较将用于优化全酶模型中的四个新参数，并选择最准确的全酶内自磷酸化进程模型。在第三阶段，研究人员将把优化的CaMKII全酶模型引入到一个更大的Ca2+通过NMDA受体流入脊柱并通过泵和交换器去除的mccell模型中。该模型在mccell中的模拟将用于测试关于控制脊髓中CaMKII激活的参数的假设。