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（由适用提供）：真核细胞取决于肌动蛋白原纤维执行大量潜水功能，包括细胞分裂，粘合剂和运动。它们的形成受细胞的仔细调节，这些细胞以空间和临时特异性来控制各种机制来控制聚合。这样的系统受复杂的蛋白质相互作用网络的控制。该系统在细胞功能中的重要性意味着它在生物故障中具有相应的重要性。任何成分的突变都会导致遗传疾病。病原体还可以滥用这些系统，以帮助通过多种途径感染健康细胞。当细胞自身远离肿瘤体时，就会发生癌细胞转移，这是由于肌动蛋白网络机械的上调而引起的。对肌动蛋白组装和拆卸的充分了解对于治疗人类疾病至关重要。 该系统的中心成分之一是与肌动蛋白相关的蛋白质复合物ARP2/3，该蛋白质由两种蛋白质ARP2和ARP3以及5个辅因子蛋白ARPC1-5组成。 ARP2/3与先前存在的肌动蛋白丝结合，并形成子丝的起点，该丝的角度以70º的角度分支。有证据表明，默认情况下，ARP2/3复合物在不活跃状态下，即不会与其他细胞成分相互作用而启动分支。相反，实验提出了将复合物停用的机制，从而促进了分支。由于该蛋白质组装的大小和复杂性，迄今为止相对较少的计算研究已经研究了ARP2/3系统。我建议使用计算方法研究ARP2/3激活/失活的三个方面，以促进我们对这些蛋白质最近实验结果的理解。 首先，我将研究离子结合在ARP2/3和肌动蛋白之间的接口上的效果。最近的奇迹表明，在界面上可能有特定的位点，其中Arp2/3结合肌动蛋白以开始阳离子可以结合的新细丝。我们将测试以下假设：在这些位点具有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（NPFS）与ARP2/3一起使用的特殊辅助因子通过结合ARP2/3和肌动蛋白和肌动蛋白结合在一起并将其促进ARP2/3中的会议变化来促进分支的方式，从而允许其与新的Actin Monomers形成良好的界面。第三，我将研究对ARP2/3构象的影响，对其将ATP转化为ADP的能力，这是促进分支的控制之一。 这些研究将增强我们在细胞控制肌动蛋白原纤维网络的关键机制原子水平上的理解。我的工作将产生方法论上的改进，而由此产生的数据将有助于解释先前的实验以及新的实验。