Creating a Unified RAS Structural Nomenclature to Compare the Impact of Oncogenic Mutations on KRAS, NRAS, and HRAS

创建统一的 RAS 结构命名法以比较致癌突变对 KRAS、NRAS 和 HRAS 的影响

• 批准号: 10734916
• 负责人: Mitchell Isaac Parker
• 金额: $ 0.25万
• 依托单位: DREXEL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-07 至 2025-11-06
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10734916
• 关键词: 3-Dimensional; Agreement; Alanine; Antibodies; Behavior; Binding; Biochemical; Biological; Canada; Classification; Complex; Computer software; Databases; Europe; Event; Future; GTP Binding; Genes; Guanosine Triphosphate; Homodimerization; Human; KRAS2 gene; Ligand Binding; Ligands; Malignant Neoplasms; Missense Mutation; Molecular Conformation; Mutate; Mutation; Mutation Analysis; Nomenclature; Oncogenes; Oncogenic; Output; Patients; Pattern; Pharmaceutical Preparations; Phosphotransferases; Proteins; RAS genes; Resources; Roentgen Rays; SWI1; Scanning; Signal Pathway; Site; Statistical Data Interpretation; Structure; Testing; United States; Update; Visualization; Work; cancer therapy; cohort; computational suite; computerized tools; conformer; design; electron density; experimental group; experimental study; improved; inhibitor; insight; molecular dynamics; mutational status; novel; preference; protein data bank; protein protein interaction; protein structure; ras Proteins; tumor; web server

Abstract: RAS proteins (KRAS, NRAS, and HRAS) are the most extensively studied set of mutationally activated oncogenes. Yet we do not completely understand the structural impact of RAS mutations in cancer. As of August 2020, there are 333 experimentally solved wild-type (WT) and mutated RAS structures in the Protein Data Bank (PDB), comprising 175 HRAS, 155 KRAS, and 3 NRAS structures. This growing structural ensemble provides a valuable resource to discover novel insights into RAS activity through statistical analyses that enable quantitative determination of biological correlates. In recent years, NMR studies and molecular dynamic (MD) simulations (using experimental structures as templates) have shown that the conserved RAS switch 1 (SW1) and 2 (SW2) regions display dynamic conformational behaviors that modify RAS activity. Conformational changes in SW1/SW2 facilitate the concerted binding of regulator and effector proteins at these regional interfaces, in turn promoting proper switching of RAS proteins from an active GTP-conformer to an inactive GDP-conformer. In addition, biochemical studies have provided evidence for the existence of a GTP-bound RAS homodimer required for activation of certain signaling pathways. While we know that RAS homodimerization occurs in a GTP-bound state, we do not know if a specific RAS conformational arrangement is required for RAS homodimer formation and associated protein-protein interaction (PPI) events. Further complicating this issue, there is no consolidated understanding of how mutations on RAS proteins may shift SW1/SW2 conformation in ways favoring or disfavoring RAS PPIs, including RAS homodimerization. The objective of this proposal is to create a unified RAS structural classification to assess the impact of oncogenic mutations on KRAS, HRAS, and NRAS, ligands (GTP, GDP, inhibitors, or none), and PPIs/homodimerization. In preliminary work, I created a unified RAS structural nomenclature based on clustering SW1/SW2 conformations across experimental structures of KRAS, HRAS, and NRAS. I have also performed a pan-cancer analysis of 18,841 RAS missense mutations from a cohort of 100,707 patients, providing the most comprehensive existing resource for KRAS, NRAS, and HRAS mutational patterns in human tumors. In Aim 1, I will compare the conformational and PPI preferences of RAS mutated and WT forms with experimentally solved structures. Following this, in Aim 2, I will predict the conformational and PPI preferences of RAS mutated and WT forms by examining energy distributions of generated structural ensembles. If we can reproduce the effects of some known mutations, then we can confidently predict the consequence for novel mutations that have not been experimentally studied. In completing this proposal, I will present the unified RAS structural nomenclature, including the determined impact of RAS mutations, in a database that will be continually updated upon solving of new experimental structures. This work will serve as a biological resource, informing future studies stratifying RAS WT and mutated structures and efforts to create drugs directly targeting RAS proteins for cancer treatment.

翻译后摘要：RAS蛋白（KRAS，NRAS和HRAS）是最广泛研究的突变激活的一组 致癌基因然而，我们并不完全了解RAS突变在癌症中的结构影响。截至八 到2020年，蛋白质数据库中有333个实验解决的野生型（WT）和突变的RAS结构 (PDB)包括175个HRAS、155个KRAS和3个NRAS结构。这种不断增长的结构合奏提供了一个 有价值的资源，通过统计分析发现RAS活动的新见解， 确定生物学相关因素。近年来，核磁共振研究和分子动力学（MD）模拟 （使用实验结构作为模板）已经表明，保守的RAS开关1（SW 1）和2（SW 2） 区域显示改变RAS活性的动态构象行为。的构象变化 SW 1/SW 2依次促进调节蛋白和效应蛋白在这些区域界面的协同结合 促进RAS蛋白从活性GTP-构象异构体到非活性GDP-构象异构体的适当转换。在 此外，生物化学研究提供了存在GTP结合RAS同源二聚体的证据 激活某些信号通路所必需的。虽然我们知道RAS同源二聚化发生在 GTP结合状态，我们不知道RAS同源二聚体是否需要特定的RAS构象排列 形成和相关的蛋白质-蛋白质相互作用（PPI）事件。使这个问题更加复杂的是， 巩固了对RAS蛋白突变如何改变SW 1/SW 2构象的理解， 有利于或不利于RAS PPI，包括RAS同源二聚化。这项建议的目的是建立一个 统一RAS结构分类，以评估致癌突变对KRAS、HRAS和NRAS的影响， 配体（GTP、GDP、抑制剂或无）和PPI/同源二聚化。在初步工作中，我创建了一个统一的 RAS结构命名法基于跨实验结构的SW 1/SW 2构象聚类， KRAS、HRAS和NRAS。我还对18,841例RAS错义突变进行了泛癌症分析， 100，707例患者的队列，为KRAS、NRAS和HRAS提供最全面的现有资源 人类肿瘤的突变模式。在目标1中，我将比较RAS的构象和PPI偏好 突变和WT形式与实验解决的结构。在目标2中，我将预测 通过检查RAS突变和WT形式的能量分布， 生成的结构集合。如果我们能重现一些已知突变的影响， 有信心地预测尚未实验研究的新突变的后果。在完成 在这个建议中，我将提出统一的RAS结构命名法，包括RAS的确定影响 突变，在一个数据库中，将不断更新后，解决新的实验结构。这项工作 将作为一个生物资源，告知未来的研究分层RAS WT和突变的结构和努力 来创造直接靶向RAS蛋白的癌症治疗药物。