Computational studies of Arp2/3 activation and deactivation

Arp2/3 激活和失活的计算研究

• 批准号: 8833797
• 负责人: Glen Hocky
• 金额: $ 5.07万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-01 至 2018-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8833797
• 关键词: ATP Hydrolysis; Actins; Adhesions; Affect; Affinity; Binding; Binding Sites; Biochemical; Biological; Biological Factors; Cations; Cell division; Cell physiology; Cells; Cereals; Collaborations; Complex; Computing Methodologies; DNA Sequence Alteration; Data; Daughter; Environment; Eukaryotic Cell; Face; Filament; Fluorescence Resonance Energy Transfer; Goals; Height; Hereditary Disease; Human; Hydrolysis; Infection; Ions; Letters; Measurable; Mechanics; Methodology; Methods; Microfilaments; Modeling; Molecular; Molecular Conformation; Motion; Movement; Mutation; Neoplasm Metastasis; Occupations; Pathway interactions; Physiological; Play; Post-Translational Protein Processing; Process; Proteins; Reaction; Regulation; Role; Series; Site; Specificity; Staging; Structural Models; Structure; System; Testing; Up-Regulation; Work; advanced simulation; base; cancer cell; cofactor; computer studies; computing resources; cost; depolymerization; design; dimer; human disease; improved; molecular assembly/self assembly; monomer; pathogen; polymerization; protein complex; public health relevance; quantum; research study; scaffold; simulation

 DESCRIPTION (provided by applicant): Eukaryotic cells depend on actin fibrils to perform a large number of diverse functions, including cell division, adhesion, and movement. Their formation is carefully regulated by the cells, which employ a variety of mechanisms to control polymerization with spatial and temporal specificity. Such a system is governed by a complex network of protein interactions. The importance of this system in cellular function means it has a commensurately large importance in biological malfunction. Mutations in any component can result in genetic disease. Pathogens can also abuse these systems to aid in infection of healthy cells through several pathways. Cancer cell metastasis occurs when cells move themselves away from a tumorous body, and this results from up-regulation of the actin network machinery. A fuller understanding of actin assembly and disassembly is crucial for the treatment of human disease. One of the central components of this system is the actin-related protein complex Arp2/3, which consists of two proteins, Arp2 and Arp3, as well as 5 cofactor proteins ArpC1-5. Arp2/3 binds to a preexisting actin filament and forms the beginnings of a daughter filament, which branches off at a 70º angle. There is evidence that the Arp2/3 complex is by default in an inactive state, i.e.it does not initiate branching without interaction with other cellular components. Conversely, experiments suggest mechanisms that deactivate the complex, promoting debranching. Due to the size and complexity of this protein assembly, relatively few computational studies to date have investigated the Arp2/3 system. I propose to study three aspects of the activation/deactivation of Arp2/3 using computational methodologies to advance our understanding of recent experimental results on these proteins. First, I will study the effect of ion binding at the interface between Arp2/3 and actin. Recent wor suggests that there may be specific sites at the interface where Arp2/3 binds actin to begin a new filament where cations can bind. We will test the hypothesis that having ions in these sites stabilizes the interface and promotes polymerization. Second, I will study the way in which special cofactors called nucleation promoting factors (NPFs) work with Arp2/3 to promote branching by binding Arp2/3 and actin to bring them together and to cause a conformational change in Arp2/3 that allows it to form a good interface with new actin monomers. Third, I will study the effect on Arp2/3 conformation on its ability to transform ATP to ADP, which is one of the controls that promotes debranching. These studies will enhance our understanding at the atomic level of key mechanisms used by cells to control networks of actin fibrils. My work will produce methodological improvements, and my resulting data will aid in the interpretation of previous experiments as well as the design of new ones.

 描述（由申请人提供）：真核细胞依赖肌动蛋白原纤维来执行大量不同的功能，包括细胞分裂、粘附和运动。它们的形成受到细胞的仔细调节，细胞采用多种机制来控制具有空间和时间特异性的聚合。这样的系统由蛋白质相互作用的复杂网络控制。该系统在细胞功能中的重要性意味着它在生物功能障碍中也具有相当大的重要性。任何成分的突变都可能导致遗传病。病原体还可以滥用这些系统，通过多种途径帮助感染健康细胞。当细胞将自身移离肿瘤体时，就会发生癌细胞转移，这是肌动蛋白网络机制上调的结果。更全面地了解肌动蛋白组装和分解对于人类疾病的治疗至关重要。 该系统的核心组成部分之一是肌动蛋白相关蛋白复合物Arp2/3，它由两种蛋白Arp2和Arp3以及5个辅因子蛋白ArpC1-5组成。 Arp2/3 与预先存在的肌动蛋白丝结合并形成子丝的起点，该子丝以 70° 角分支。有证据表明，Arp2/3 复合体默认处于非活动状态，即，如果不与其他细胞成分相互作用，它不会启动分支。相反，实验表明了使复合物失活、促进脱支的机制。由于这种蛋白质组装体的大小和复杂性，迄今为止研究 Arp2/3 系统的计算研究相对较少。我建议使用计算方法研究 Arp2/3 激活/失活的三个方面，以加深我们对这些蛋白质最新实验结果的理解。 首先，我将研究 Arp2/3 和肌动蛋白界面上离子结合的影响。最近的研究表明，Arp2/3 与肌动蛋白结合的界面上可能存在特定位点，从而开始形成阳离子可以结合的新丝。我们将测试以下假设：这些位点上的离子可以稳定界面并促进聚合。其次，我将研究称为成核促进因子 (NPF) 的特殊辅助因子如何与 Arp2/3 协同作用，通过将 Arp2/3 和肌动蛋白结合在一起来促进分支，并引起 Arp2/3 的构象变化，从而使其与新的肌动蛋白单体形成良好的界面。第三，我将研究 Arp2/3 构象对其将 ATP 转化为 ADP 的能力的影响，ADP 是促进脱支的控制之一。 这些研究将增强我们在原子水平上对细胞控制肌动蛋白原纤维网络的关键机制的理解。我的工作将带来方法上的改进，我得到的数据将有助于解释以前的实验以及新实验的设计。