Computational Insights into Assembly, Budding, and Maturation during HIV-1 Replication

HIV-1 复制过程中组装、出芽和成熟的计算见解

• 批准号: 9396905
• 负责人: Alexander Pak
• 金额: $ 5.67万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2020-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9396905
• 关键词: Adverse effects; Anti-Retroviral Agents; Autoantigens; Biochemical; Biophysics; Bundling; C-terminal; Capsid; Capsid Proteins; Cell membrane; Cereals; Cessation of life; Cleaved cell; Collaborations; Computer Simulation; Defect; Development; Dimerization; Dissociation; Drug resistance; Elements; Environment; Foundations; Fullerenes; Future; Goals; Graph; HIV-1; Heterogeneity; Infection; Knowledge; Life; Membrane; Mission; Modeling; Modernization; Modulus; Molecular; Molecular Conformation; Molecular Structure; Morphology; Mutation; Nature; Pathway interactions; Patients; Peptide Hydrolases; Peptides; Phase; Physics; Polyproteins; Process; Protein Analysis; Proteins; Proteolysis; RNA; Replication-Associated Process; Resolution; Risk; Role; Signal Transduction; Site; Sodium Chloride; Stress; Structure; Structure-Activity Relationship; Surface; Testing; Viral; Virion; Virus; Virus Replication; Work; alpha helix; base; combat; cost; design; dimer; drug development; effective therapy; electron tomography; experimental study; gag Gene Products; improved; inhibitor/antagonist; insight; interest; macromolecular assembly; nanometer; novel; novel strategies; novel therapeutics; protein protein interaction; scaffold; self assembly; simulation; treatment strategy; viral RNA; virology

PROJECT SUMMARY Human immunodeficiency virus type 1 (HIV-1) is a virus that has infected and led to the deaths of millions of people since its emergence several decades ago. While modern anti-retroviral treatments (ART) have made the infection manageable for patients, negative side effects, the risk of drug resistance, and the aggregate cost due to life-long usage inspire the need for new, effective treatment strategies. One viable strategy is to disrupt the intrinsically efficient replication cycle of HIV-1. A fundamental understanding of the molecular mechanisms that regulate replication would advance this mission by revealing novel targets and new approaches for ARTs. This proposal focuses on the late stages of HIV-1 replication, which encompasses the assembly of a viral RNA dimer and other constituents, budding of the packaged components (i.e., immature virion), and activation of the virion through maturation. The group specific antigen (Gag) polyprotein is the main structural constituent, which appears to contribute important functionality during this process. For example, Gag self-assemble into an incomplete, asymmetric, and contiguous hexameric lattice; this immature lattice is found along the inner surface of the released immature virion. Proteolytic cleavage of Gag then triggers a morphological change in which the capsid protein and RNA are condensed into a fullerene core (i.e., mature lattice). Most recently, conformational changes throughout Gag have been hypothesized to act as molecular switches that act as regulatory signals. However, specific details have been difficult to experimentally characterize owing to the pleomorphic nature of virions and their associated transition states. I propose to study the molecular structure-function relationships that regulate HIV-1 assembly, budding, and maturation using a systematic, multiscale computer simulation framework. The goals of this project are to (1) predict the structure of native-like immature lattices with molecular resolution, (2) uncover molecular switches throughout Gag that regulate immature lattice assembly, and (3) determine the dynamic morphological changes during viral maturation. I will first develop a coarse-grained model of Gag to study the structure and assembly mechanisms of the immature lattice at the membrane interface in the presence of RNA. Subsequently, these coarse-grained simulations will systematically guide atomistic simulations of key protein interfaces to identify the triggering mechanisms and importance of potential molecular switches, including a noted transition of the spacer peptide 1 (SP1) domain from random coil to alpha helix for Gag oligomerization. Finally, a novel reactive coarse-grained model will be developed to identify disassembly pathways during maturation. During all phases of this project, experimentally tractable predictions will be made and tested through my collaboration with two leading experimentalists, which will enable iterative refinements to the developed models. The insights from this study will have a broad impact on virology, macromolecular assembly, and molecular biophysics.

项目摘要 人类免疫缺陷病毒1型（HIV-1）是一种感染并导致数百万人死亡的病毒， 自几十年前出现以来，虽然现代抗逆转录病毒治疗（ART） 患者可控制的感染、负面副作用、耐药性风险和总成本 由于终身使用激发了对新的、有效的治疗策略的需求。一个可行的策略是 HIV-1固有的高效复制周期。对分子机制的基本理解 通过揭示ART的新靶点和新方法，调控复制将推进这一使命。 这项提案的重点是HIV-1复制的后期阶段，其中包括病毒RNA的组装 二聚体和其它成分，包装组分的出芽（即，未成熟病毒体），以及 病毒体通过成熟。组特异性抗原（Gag）多聚蛋白是主要的结构成分， 在这个过程中发挥了重要作用。例如，Gag自组装成 不完全的、不对称的和连续的六聚体晶格;这种未成熟的晶格被发现沿着内表面沿着 释放的未成熟病毒体的表面。Gag的蛋白水解切割然后触发细胞的形态学变化， 其中衣壳蛋白和RNA凝聚成富勒烯核（即，成熟晶格）。最近， 已经假设整个Gag的构象变化充当分子开关， 监管信号。然而，由于这些因素，难以通过实验表征具体细节。 病毒粒子的多形性及其相关的过渡态。 我建议研究调节HIV-1组装、出芽和表达的分子结构-功能关系。 成熟使用系统的，多尺度的计算机模拟框架。本项目的目标是（1） 用分子分辨方法预测类天然未成熟晶格的结构;（2）揭示分子开关 整个Gag，调节未成熟的晶格组装，和（3）确定动态形态 病毒成熟过程中的变化。我将首先开发一个粗粒度的Gag模型来研究其结构， 组装机制的未成熟的晶格在膜界面在RNA的存在下。 随后，这些粗粒度的模拟将系统地指导关键蛋白质的原子模拟 接口，以确定潜在的分子开关的触发机制和重要性，包括一个 注意到间隔肽1（SP1）结构域从无规卷曲转变为Gag寡聚化的α螺旋。 最后，一个新的反应粗粒度模型将被开发，以确定拆卸过程中的路径 成熟在这个项目的所有阶段，将进行实验性的预测和测试 通过我与两位领先的实验学家的合作，这将使迭代改进 发展模式。这项研究的见解将对病毒学、大分子生物学和生物学产生广泛的影响。 组装和分子生物物理学。