BROWNIAN DYNAMICS SIMULATIONS OF ACTINS WITH ALDOLASE

肌动蛋白与醛缩酶的布朗动力学模拟

• 批准号: 6085373
• 负责人: KATHRYN A. THOMASSON
• 金额: $ 14.13万
• 依托单位: UNIVERSITY OF NORTH DAKOTA
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-06-01 至 2003-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6085373
• 关键词: actins; aldehyde lyase; bioenergetics; computer simulation; enzyme complex; glyceraldehyde 3 phosphate dehydrogenase; molecular dynamics; protein isoforms

The proposed study will employ theoretical methods to investigate the interactions between actin and two glycolytic enzymes, aldolase and GAPDH, in order to better understand the nature of their associations. Brownian dynamics (BD) will be employed to study the diffusive dynamics and electrostatic interactions between the glycolytic enzymes and actin, the various kinds of complexes between actin and glycolytic enzymes, and their relative stabilities. This work will initiate adding hydrophobic forces to the existing electrostatic forces during the simulation so that combined free energies can be used to approximate binding constants. The Brownian dynamics (BD) simulation method will be applied to both equilibrium and dynamical aspects of the association of the proteins, with special attention to the electrostatics that affect association. The study will begin with simulations of aldolase interacting with F-actin and F-actin mutants, and subsequently be extended to a large number of BD-docked complexes which provide dynamic snapshots of binding. BD simulations will be used to compute the protein-protein potential of mean force versus the docking coordinate and obtain a free energy curve for the docking between the two proteins. The specific questions to be addressed include a) how do the complexes predicted for aldolase with G- or F-actin compare with the complexes predicted for GAPDH and G- or F-actin? b) Are the predicted energetics for the two glycolytic enzymes comparable? c) Do any of the predicted interactions correspond with experimental observations? d)When F-actin is mutated, how do the energetics and predicted interactions change? e) Is quaternary structure of the glycolytic enzyme important? f) Does a dimer of aldolase bind as effectively to F-actin as the intact tetrameric form of the enzyme? g) Do isolated peptides of pieces of an aldolase or a GAPDH bind in the same fashion as the intact enzyme? Can hydrophobic forces be included so that reasonable predictions of a binding constant can be made? Do the intact enzymes when bound to F-actin exhibit the same affinity for their substrate as they do when they are not bound to F-actin?

本研究将采用理论方法， 肌动蛋白和两种糖酵解酶，醛缩酶和GAPDH之间的相互作用， 以便更好地了解它们之间联系的性质。布朗 动力学（BD）将被用来研究扩散动力学， 糖酵解酶和肌动蛋白之间的静电相互作用， 肌动蛋白和糖酵解酶之间的各种复合物，及其 相对稳定性。这项工作将开始增加疏水力， 现有的静电力在模拟过程中， 能量可用于近似结合常数。布朗动力学 (BD)模拟方法将应用于平衡和动态 蛋白质结合的各个方面，特别注意 影响联想的静电。研究将从模拟开始开始 醛缩酶与F-肌动蛋白和F-肌动蛋白突变体相互作用，随后被 扩展到大量的BD对接复合物，其提供动态的 绑定的快照。BD模拟将用于计算 平均力的蛋白质-蛋白质势能与对接坐标的关系， 获得两种蛋白质之间对接的自由能曲线。的 要解决的具体问题包括：a）如何预测复合物 与GAPDH预测的复合物相比，醛缩酶与G-或F-肌动蛋白的复合物 和G-或F-肌动蛋白B）两种糖酵解的预测能量是 酶的可比性？c）任何预测的相互作用是否符合 实验观察？d）当F-肌动蛋白突变时，能量学和 预测的相互作用会改变吗？e）是糖酵解的四级结构 酵素重要吗？f）醛缩酶的二聚体与F-肌动蛋白的结合是否与 酶的完整四聚体形式？g）将分离的肽片段 醛缩酶或GAPDH以与完整酶相同的方式结合？可以 包括疏水力，使得结合的合理预测 可以使常数？当与F-肌动蛋白结合时，完整的酶是否表现出 它们对底物的亲和力与它们不结合时相同。 肌动蛋白？