Computational studies of Arp2/3 activation and deactivation

Arp2/3 激活和失活的计算研究

• 批准号: 9093581
• 负责人: Glen Hocky
• 金额: $ 5.43万
• 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/9093581
• 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（通过应用程序证明）：肌动蛋白原纤维上的真核细胞执行大量不同的功能，adhe sion和运动。 。机械。 与肌动蛋白相关的蛋白质复合物ARP2/3 TOR蛋白ARPC1-5的中心成分之一结合了预先存在的肌动蛋白丝，并以ATA70º的角度形成女儿的开始。相反，实验表明，E ARP2/3系统提出了使用计算方法来研究ARP2/3的三分之一的机制。 首先，在此处，ARP2/3之间的离子结合在ARP2/3之间结合了阳离子，我们将结合阳离子促进因子（NPF）与ARP2/3一起使用，通过结合ARP2/3和肌动蛋白将其促进分支，以使它们聚集在一起并引起ARP2/3，从而使其与新的Actin单体形成良好的界面。能够将ATP转换为ADP的能力，ADP是促进分裂桥梁的控制之一。 这些研究将磨损磨损，而我所产生的数据将有助于对先前的实验进行解释。