Structural Analysis of TF and Interacting Molecules

TF 和相互作用分子的结构分析

• 批准号: 7237998
• 负责人: ARTHUR J. OLSON
• 金额: $ 10.61万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-06-01 至 2009-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7237998
• 关键词: binding sites; biological signal transduction; blood coagulation; calorimetry; chemical models; chemical synthesis; circular dichroism; clotting factor; coagulation factor IX; coagulation factor VII; coagulation factor X; computational biology; computer simulation; fluorescence spectrometry; high performance liquid chromatography; mathematical model; model design /development; molecular dynamics; nuclear magnetic resonance spectroscopy; phosphorylation; protein binding; protein protein interaction; protein purification; protein structure function; thromboplastin; thrombosis

The ability to precisely identify and characterize the molecular sites of interaction, both for the coagulation protease pathway and for the signaling pathways related to thrombogenesis, will open the door for computational and experimental screening of chemical agents that may beneficially modulate these processes. The identification of such agents may generate new classes of interventional molecules to study these mechanisms in greater detail and may lead to new diagnostic and therapeutic approaches to the detection and treatment of the thrombotic and related diseases. The goal of this project is to produce a physical picture of the interactions of Tissue Factor (TF) with its functionally relevant partners, and to utilize this information to help select targets and design chemical agents that can modulate TF function in vitro and in vivo. To accomplish this we will determine and analyze the structural aspects of the intracellular and extracellular molecular interactions of Tissue Factor by utilizing and combining computational modeling, NMR and other biophysical methods. We will use these structures to define binding sites and interaction "hot spots", computationally screen small molecule libraries, and design specific ligands to modulate particular interactions. Specifically we will utilize computational docking, and molecular mechanics to develop improved models of the temary complexes of tissue factor/factor Vlla with factors IXa and Xa; model interactions of peptide inhibitors with the ternary complex containing Xa; develop models for the extracellular interactions of the initiation complex with the protease activated receptors PAR-1 and PAR-2; and develop models of the interaction of TF with relevant integrin structures. Utilizing NMR, and other biophysical techniques in conjunction with computational modeling, we will characterize the intracellular interactions of the cytoplasmic TF C-terminal domain (TFCD) in both its phosphorylated and unphosphorylated states with signaling partners. From these structural analyses we will define interaction targets and screen small molecule databases for ligands that can modulate these interactions. To enable these studies we will extend and enhance our computational docking codes to deal with the complexity of these multi-component, flexible molecular systems.

精确识别和表征相互作用的分子位点的能力，既适用于 凝血蛋白酶途径和与血栓形成相关的信号途径，将为计算和实验筛选可能有益地调节这些过程的化学制剂打开大门。此类药物的鉴定可能会产生新类别的介入分子，以更详细地研究这些机制，并可能导致检测和治疗血栓及相关疾病的新诊断和治疗方法。该项目的目标是生成组织因子 (TF) 与其功能相关伙伴相互作用的物理图像，并利用该信息帮助选择靶标并设计可在体外和体内调节 TF 功能的化学制剂。为了实现这一目标，我们将利用并结合计算模型、核磁共振和其他生物物理方法来确定和分析组织因子的细胞内和细胞外分子相互作用的结构方面。我们将使用这些结构来定义结合位点和相互作用“热点”，通过计算筛选小分子库，并设计特定配体来调节特定相互作用。具体来说，我们将利用计算对接和分子力学来开发组织因子/因子VIIa与因子IXa和Xa的三元复合物的改进模型；肽抑制剂与含有 Xa 的三元复合物的相互作用模型；开发起始复合物与蛋白酶激活受体 PAR-1 和 PAR-2 的细胞外相互作用模型；并开发 TF 与相关整合素结构相互作用的模型。利用 NMR 和其他生物物理技术与计算模型相结合，我们将表征磷酸化和非磷酸化状态下的细胞质 TF C 末端结构域 (TFCD) 与信号传导伴侣的细胞内相互作用。根据这些结构分析，我们将定义相互作用目标并筛选小分子数据库以寻找可以调节这些相互作用的配体。为了实现这些研究，我们将扩展和增强我们的计算对接代码，以处理这些多组分、灵活的分子系统的复杂性。