Brownian Dynamics Simulations of Actins with Aldolase

描述(申请人提供)：细胞骨架结构，F-肌动蛋白，在细胞新陈代谢中起着重要作用，它为各种代谢途径中反应的高度特异性提供了条件。许多糖酵解酶包括果糖-1，6-二磷酸缩醛酶(醛缩酶)、甘油醛-3-磷酸脱氢酶(GAPDH)和乳酸脱氢酶(LDH)可逆地结合肌动蛋白。其他酶，如磷酸三糖异构酶(TIM)，通过与结合酶的相互作用间接结合。这项拟议的研究将使用并加强现有的理论方法，以更好地研究F-肌动蛋白与糖酵解酶的相互作用。布朗动力学(BD)方法预测了F-肌动蛋白和糖酵解酶之间的各种复合体；BD还通过执行自动强制穷举搜索来提供复合体的相对稳定性。BD模拟了受离子效应影响的水中蛋白质-蛋白质的缔合，离子效应介导了生理复合体中的分子相互作用。这些模拟提供了蛋白质-蛋白质缔合的自由能。这项工作将扩展所研究的酶，并继续增强程序包MacroDox中的现有方法。目标是：(1)检测LDH和TIM与F-肌动蛋白的相互作用，并将它们与醛缩酶和GAPDH的预测进行比较；(2)再现实验观察到的结合因素，如离子强度、pH和相对结合亲和力；以及(3)处理酶-酶/F-肌动蛋白复合体的相互作用。提出的这项研究的重要性与F-肌动蛋白在细胞质中创建一种结构的假设有关，糖酵解酶在该结构上动态地关联和解离。这些动态关联对于组织糖酵解途径中的反应和组装广泛的糖酵解酶复合体可能是重要的。这项研究的结果将是更好地理解溶液中蛋白质与肌动蛋白的关联。这将是对F-肌动蛋白形成糖酵解酶在细胞中发挥作用的框架的理论测试。这将加深对细胞质基质中结构组装背后的理论的理解。因此，这项研究的结果应该对细胞质结构和代谢调节具有深远的影响。

DESCRIPTION (provided by applicant): The cytoskeletal structure, F-actin, plays an important role in cellular metabolism by providing conditions for the high specificity of reactions within various metabolic pathways. Many glycolytic enzymes including fructose-1,6-bisphophsate aldolase (aldolase), glycerladehyde-3-phosphate dehydrogenase (GAPDH), and lactate dehydrogenase (LDH) bind actin reversibly. Other enzymes such as triose phosphate isomerase (TIM) bind indirectly through interactions with the enzymes that bind. The proposed study will use and enhance existing theoretical methods to better investigate the interaction of F-actin with glycolytic enzymes. The method of Brownian dynamics (BD) predicts the various kinds of complexes between F-actin and the glycolytic enzymes; BD also provides the relative stability of complexes by performing an automated forceguided exhaustive search. BD simulates the protein-protein associations in water as influenced by the ionic effects that mediate molecular interactions in physiological complexes. The simulations provide free energies of protein-protein associations. This work will expand the enzymes studied and continue to enhance the existing method as found in the program package MacroDox. The goals are: (1) to examine LDH and TIM interactions with F-actin and compare them to predictions for aldolase and GAPDH; (2) to reproduce experimentally observed factors on binding such as ionic strength, pH, and relative binding affinities; and (3) to treat enzyme-enzyme/F-actin complex interactions. The importance of the proposed study relates to the hypothesis that F-actin creates a structure in the cell cytoplasm upon which glycolytic enzymes associate and dissociate dynamically. These dynamic associations may be important to organizing the reactions in the glycolytic pathway and assembling an extensive complex of glycolytic enzymes. The outcome of the research would be an improved understanding of protein association with actin in solution. It will be a theoretical test for F-actin forming a framework for glycolytic enzymes to function in cells. It will further the understanding of the theory behind assembly of structures in the cytoplasmic matrix. Thus, the outcome of this research should have far-reaching implications for cytoplasmic structure and metabolic regulation.