FORCE-MODULATED BINDING AFFINITY: COMPUTATIONAL STUDY OF FAT-PAXILLIN INTERACTI

力调节结合亲和力：脂肪-桩蛋白相互作用的计算研究

• 批准号: 7956235
• 负责人: BRUCE TIDOR
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956235
• 关键词: Affinity; Apoptosis; Behavior; Binding; Biochemical; Biological; Biomedical Research; Cells; Chemicals; Computer Retrieval of Information on Scientific Projects Database; Cues; Devices; Environment; Focal Adhesion Kinase 1; Focal Adhesions; Free Energy; Funding; Gene Expression; Grant; High Performance Computing; Institution; Lead; Mechanics; Methods; Molecular; Peptides; Physiological; Play; Process; Property; Protein Analysis; Proteins; Protocols documentation; Research; Research Personnel; Resources; Role; Sampling; Signal Transduction; Site; Source; Speed; Therapeutic; Tissue Engineering; United States National Institutes of Health; Weight; Work; cell growth; cell motility; computer studies; design; driving force; extracellular; insight; paxillin; protein complex; response; simulation

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Mechanical signals have been shown to regulate various physiological behaviors, including cell growth, differentiation, apoptosis, motility and gene expression. The details of the processes by which mechanical cues result in biochemical and cellular change, or mechanotransduction, are largely unknown. One proposed mechanism is that a force-driven conformational change results in altered binding affinity, essentially converting a mechanical signal into a concentration change. We will characterize properties of force-induced binding changes, through detailed structural and energetic analysis of protein pulling simulations. Methodologically the work uses a multi-dimensional replica exchange protocol, which speeds up convergence through better sampling, and the Weighted Histogram Analysis Method (WHAM) to compute free energy changes induced by mechanical perturbation. We are focusing our efforts on the focal adhesion targeting (FAT) domain of focal adhesion kinase binding to a paxillin peptide. Focal adhesions, the cell anchor points to the extracellular environment, are dynamical protein complexes known to act as mechanosensory devices, where mechanical forces can regulate the assembly of the site and trigger signaling. While the precise identity of proteins responsive to force is not elucidated, interactions between FAT and paxillin play an important role in focal adhesion formation and are thought to be part of the mechanosensing machinery. Preliminary simulations have shown that force can induce strengthening of FAT-paxillin binding interactions through activation of new contacts. We plan to investigate variable effects along different pulling directions to gain insight into the robustness of this response in a biological context, as well as to carry out mutational studies of force-bearing residues. Detailed understanding of the molecular mechanisms of mechanotransduction could lead to advances in therapeutics and tissue engineering, with design of culture conditions mimicking the cells natural chemical and mechanical environment.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 机械信号已被证明可以调节各种生理行为，包括细胞生长，分化，凋亡，运动性和基因表达。机械提示导致生化和细胞变化或机械转传的过程的细节在很大程度上尚不清楚。提出的一种机制是，力驱动的构象变化会导致结合亲和力改变，从而将机械信号转化为浓度变化。我们将通过蛋白质拉动模拟的详细结构和能量分析来表征力诱导的结合变化的性质。从方法上讲，工作使用多维复制交换协议，该协议通过更好的采样来加快收敛性，加权直方图分析方法（WHAM）来计算机械扰动引起的自由能变化。我们将精力集中在局灶性靶标（脂肪）结构域的局灶性粘附激酶与帕西林肽的结合。局灶性粘连（细胞锚指向细胞外环境）是动态蛋白质复合物，被称为机械感觉装置，机械力可以调节位点的组装并触发信号传导。尽管未阐明对力的蛋白质的精确认同，但脂肪和帕西林之间的相互作用在局灶性粘附形成中起着重要作用，被认为是机械传感器机械的一部分。初步模拟表明，力可以通过激活新接触来诱导脂肪 - 同蛋白结合相互作用的增强。我们计划研究沿着不同的拉动方向的可变效应，以深入了解在生物学环境中这种反应的鲁棒性，并对含力残基进行突变研究。详细了解机械转导的分子机制可能会导致治疗和组织工程的进步，并设计模仿细胞天然化学和机械环境的培养条件的设计。