Nuclear export of the HIV genome: A Molecular Dynamics Study of the Interactions

HIV 基因组的核输出：相互作用的分子动力学研究

• 批准号: 8263644
• 负责人: MOHAMMAD RK MOFRAD
• 金额: $ 7.68万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-05-01 至 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8263644
• 关键词: Address; Adverse effects; Antifungal Agents; Antiviral Agents; Atomic Force Microscopy; Binding; Bypass; Cell Nucleus; Characteristics; Complex; Computer Simulation; Computing Methodologies; Databases; Drug Controls; Drug Delivery Systems; Drug resistance; Drug usage; Exportins; Family; Feasibility Studies; Future; Genome; HIV; Hand; Human; Investigation; Leucine; Lytic; Mediating; Messenger RNA; Methods; Modeling; Nuclear Export; Pathway interactions; Pharmaceutical Preparations; Process; Production; Protein Export Pathway; Protein Region; Proteins; RNA; RNA Splicing; RNA Transport; Recruitment Activity; Research; Resistance development; Resolution; Resources; Response Elements; Retroviridae; Ribosomal RNA; Role; Signal Transduction; Source; Staging; Structural Protein; Structure; Subfamily lentivirinae; System; Testing; Time; Transcript; Vaccines; Viral; Viral Genome; Viral Proteins; Virion; Virus; Work; computer studies; exportin 1 protein; falls; field study; genetic regulatory protein; interest; leptomycin B; member; molecular dynamics; monocyte; monomer; nucleocytoplasmic transport; pandemic disease; receptor; research study; spatiotemporal; stem; success

DESCRIPTION (provided by applicant): Nuclear export of the HIV genome: A Molecular Dynamics Study of the Interactions and Structure of HIV Rev and Host CRM1 during Export Summary The HIV virus is a pandemic lentivirus which has no existing cure or vaccine. Current treatments consist of powerful drug cocktails containing multiple drugs targeting multiple aspects of the viral lifecycle. Besides the toxic side effects caused by many of these drugs, in the majority of cases the virus develops resistance to the drugs used, forcing a switch to more toxic and less effective drugs, culminating in the escape of the virus from drug control. Despite the variety of drugs available, no current drugs target a critical part of the viral lifecycle, the Rev and Exportin-1 (Crm1) mediated export of the full viral genome during active viral replication. Here, the viral protein Rev forms a six-part oligomer on the Rev Response Element (RRE) of the viral genome. This oligomer then recruits copies of the host protein crm1 to export the genome out of the cell nucleus, bypassing the standard pathways of mRNA splicing and export. Attempts to target this export pathway are limited by a combination of poor structural and mechanistic understandings of the proteins involved. While experimental methods have been successful in elucidating broad details of the process, the binding regions of the proteins and RNA involved, and even some details of structure and mechanism, the understanding derived so far is incomplete and uncertain, inadequate for use in truly in-depth studies or to support attempts to modify the pathway. Utilizing the fine spatiotemporal resolution of computational and molecular dynamics approaches, these problems can be overcome. In this project, these methods will be used to investigate the entire process of export complex formation, from the attachment of the first Rev monomer to the RRE all the way up the recruitment of multiple crm1 copies, and will use them to address outstanding questions in the field and to open the way for further investigation. Specifically, this study will validate previous proposed mechanisms and structures, deeply investigate the mechanism of Rev oligomer-RRE assembly, including the importance of cooperativity, and provide a complete structure of this assembly. In addition, binding of the assembly with crm1 will be investigated, and the results used to address such topics as the maximal plausible number of bound crm1 proteins and the importance of all six Rev copies in binding. Finally, and most importantly, a structure of the entire export complex will be generated, which can be used in future mechanistic and computational studies, or as a guidepost for future experimental studies. In the long-run it may even be possible to put these results to practical use. PUBLIC HEALTH RELEVANCE: Nuclear export of the HIV genome: A Molecular Dynamics Study of the Interactions and Structure of HIV Rev and Host CRM1 during Export Narrative Despite extensive research, the process by which HIV Rev oligomerizes on the Rev Response Element (RRE) sequence of the viral genome and recruits crm1 to export this genome is not well-characterized. Many of the obstacles to experimental studies that frustrate attempts to fully understand the process fall away when computational methods are considered instead. The greater understanding of the Rev export pathway that will be obtained when such methods are used will prove invaluable to the field of study, and may provide intriguing avenues of exploration into one of the few steps of HIV replication which is not yet the target of therapy.

描述（由申请人提供）：HIV基因组的核出口：对HIV REV和宿主CRM1的相互作用和结构的分子动力学研究，在出口摘要过程中，HIV病毒是一种大流行病病毒，没有现有的治疗或疫苗。当前的处理由强大的药物鸡尾酒组成，其中包含针对病毒生命周期多个方面的多种药物。除了许多这些药物引起的有毒副作用外，在大多数情况下，该病毒会产生对所使用的药物的抗性，迫使转换为更具毒性和效率较低的药物，最终导致病毒从药物控制中逃脱。尽管可用的药物多种多样，但目前没有药物靶向病毒生命周期的关键部分，在主动病毒复制过程中，Rev和Exportin-1（CRM1）介导的全病毒基因组的出口。在这里，病毒蛋白REV在病毒基因组的Rev反应元件（RRE）上形成了六部分的低聚物。然后，这种低聚物募集宿主蛋白CRM1的副本以将基因组从细胞核中输出，绕过mRNA剪接和导出的标准途径。靶向这种出口途径的尝试受到涉及的蛋白质的结构和机械理解的结合而受到限制。尽管实验方法已经成功地阐明了该过程的广泛细节，但涉及蛋白质和RNA的结合区域，甚至是结构和机制的一些细节，到目前为止得出的理解是不完整的，不确定，不足以用于真正的深入研究或支持修改途径的尝试。利用计算和分子动力学方法的精细时空分辨率，可以克服这些问题。在该项目中，这些方法将用于调查出口复杂形成的整个过程，从第一个Rev单体的附着到RRE，一直到招募多个CRM1副本，并将使用它们来解决现场的出色问题，并为进一步的研究打开道路。具体而言，这项研究将验证先前提出的机制和结构，深入研究Rev Poligomer-Rre组装的机制，包括合作的重要性，并提供该组装的完整结构。另外，将研究组件与CRM1的结合，并将结果用于解决诸如最大合理数量的绑定CRM1蛋白以及所有六个REV副本在结合中的重要性。最后，最重要的是，将生成整个出口复合物的结构，该结构可用于未来的机械和计算研究，或作为未来实验研究的指南。从长远来看，甚至有可能将这些结果放在实际使用中。 公共卫生相关性：HIV基因组的核出口：尽管进行了广泛的研究，对HIV REV和宿主CRM1的相互作用和宿主CRM1的相互作用和结构的分子动力学研究，HIV REV对病毒基因组的REV反应元素（RRE）序列（RRE）序列的过程尚未良好地导出。当考虑到计算方法时，实验研究的许多障碍都挫败了试图完全理解该过程的尝试。对使用此类方法时将获得的转速出口途径的更深入的了解对研究领域来说是无价的，并且可能会为尚未成为治疗的艾滋病毒复制步骤提供有趣的探索途径之一。