A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation
A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation
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DOI：
10.1371/journal.pcbi.1006941
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发表时间：
2019-03
影响因子：
4.3
通讯作者：
Matthew C. Pharris;T. Bartol;T. Sejnowski;M. Kennedy;Melanie I. Stefan;Tamara L. Kinzer-Ursem
中科院分区：
文献类型：
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作者：
Matthew C. Pharris;T. Bartol;T. Sejnowski;M. Kennedy;Melanie I. Stefan;Tamara L. Kinzer-Ursem
钙/钙调蛋白依赖的蛋白激酶II(CaMKII)占所有大脑蛋白质的2%，对记忆功能至关重要。已知CaMKII活性调节神经元连接的大小和信号强度的动态变化，这一过程被称为突触可塑性。越来越多的计算模型被用来探索突触的可塑性和调节CaMKII活性的机制。传统的建模方法可能会排除生物物理细节，因为当显式监测CaMKII全酶12个亚基上发生的构象变化、配体结合和磷酸化事件时，会出现不切实际的状态组合。为了在不造成偏差或生物学准确性损失的情况下管理组合爆炸，我们使用软件MCell中的特殊语法来创建12亚基CaMKII全酶的基于规则的模型。在这里，我们验证了基于规则的模型与以前测量的CaMKII活性，并研究了CaMKII调控的分子机制。具体而言，我们探讨了钙/钙调素结合如何既能稳定CaMKII亚单位的激活，又能调节CaMKII自身磷酸化的维持。注意到Ca~(2+)/CaM和蛋白质磷酸酶在附近或重叠的位点与CaMKII结合，我们比较了Ca~(2+)/CaM和蛋白质磷酸酶在结构上排除或不排除彼此与CaMKII结合的模型场景。我们的结果提示了所谓的“CaM陷阱”现象的作用机制，即钙/CaM在结构上排除了磷酸酶结合，从而延长了CaMKII的自磷酸化。我们认为，钙/钙调素对自磷酸化CaMKII的结构保护可能是调节突触可塑性的重要机制。作者总结在海马体中，神经元连接的大小和强度的动态波动被认为是学习和记忆过程的基础。这些波动被称为突触可塑性，部分由蛋白质钙/钙调蛋白依赖的激酶II(CaMKII)调节。在突触可塑性过程中，CaMKII在钙离子(Ca~(2+))和钙调蛋白(CaM)存在的情况下被激活，使其能够与下游结合伙伴进行酶促相互作用。有趣的是，激活的CaMKII可以自身磷酸化，导致状态变化，使CaMKII功能活跃，而不依赖于钙/钙调素。CaMKII在Thr-286/287处的磷酸化已被证明是学习和记忆的关键组成部分。为了探索调节CaMKII全酶活性的分子机制，我们使用了一种基于规则的方法，该方法降低了计算复杂性，通常与表示CaMKII全酶可以采用的各种功能状态有关。使用这种方法，我们观察到可能被简单化方法所掩盖的调控机制。我们的结果表明，CaMKII在Thr-286/287处的磷酸化是通过CaM结构上排除该位点的磷酸酶结合而稳定的。
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 twelve 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 the twelve-subunit CaMKII holoenzyme. Here we validate the rule-based model against previous 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, such that Ca2+/CaM structurally excludes phosphatase binding and thereby prolongs CaMKII autophosphorylation. We conclude that structural protection of autophosphorylated CaMKII by Ca2+/CaM may be an important mechanism for regulation of synaptic plasticity. Author summary In the hippocampus, the dynamic fluctuation in size and strength of neuronal connections is thought to underlie learning and memory processes. These fluctuations, called synaptic plasticity, are in-part regulated by the protein calcium/calmodulin-dependent kinase II (CaMKII). During synaptic plasticity, CaMKII becomes activated in the presence of calcium ions (Ca2+) and calmodulin (CaM), allowing it to interact enzymatically with downstream binding partners. Interestingly, activated CaMKII can phosphorylate itself, resulting in state changes that allow CaMKII to be functionally active independent of Ca2+/CaM. Phosphorylation of CaMKII at Thr-286/287 has been shown to be a critical component of learning and memory. To explore the molecular mechanisms that regulate the activity of CaMKII holoenzymes, we use a rule-based approach that reduces computational complexity normally associated with representing the wide variety of functional states that a CaMKII holoenzyme can adopt. Using this approach we observe regulatory mechanisms that might be obscured by reductive approaches. Our results newly suggest that CaMKII phosphorylation at Thr-286/287 is stabilized by a mechanism in which CaM structurally excludes phosphatase binding at that site.