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.

项目概要 人类免疫缺陷病毒 1 型 (HIV-1) 是一种已感染并导致数百万人死亡的病毒 人们自几十年前出现以来。虽然现代抗逆转录病毒治疗（ART）已使 患者可控制的感染、副作用、耐药性风险以及总成本 由于终生使用激发了对新的、有效的治疗策略的需求。一种可行的策略是颠覆 HIV-1本质上有效的复制周期。对分子机制的基本了解 调节复制的药物将通过揭示 ART 的新靶标和新方法来推进这一使命。 该提案重点关注 HIV-1 复制的后期阶段，其中包括病毒 RNA 的组装 二聚体和其他成分、包装成分的出芽（即未成熟的病毒颗粒）以及 病毒体通过成熟。群体特异性抗原（Gag）多蛋白是主要结构成分， 在此过程中似乎贡献了重要的功能。例如，Gag 自组装成 不完整、不对称、连续的六聚晶格；这个不成熟的晶格是沿着内部发现的 释放的未成熟病毒粒子的表面。 Gag 的蛋白水解裂解随后引发形态变化 其中衣壳蛋白和RNA浓缩成富勒烯核心（即成熟晶格）。最近， 整个 Gag 的构象变化被假设为充当分子开关， 监管信号。然而，由于 病毒体的多形性及其相关的过渡态。 我建议研究调节 HIV-1 组装、出芽和生长的分子结构-功能关系。 使用系统的、多尺度的计算机模拟框架进行成熟。该项目的目标是 (1) 通过分子分辨率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，以及（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 Gag 的粗粒度模型来研究其结构和 RNA 存在下膜界面上未成熟晶格的组装机制。 随后，这些粗粒度模拟将系统地指导关键蛋白质的原子模拟 接口来识别潜在分子开关的触发机制和重要性，包括 注意到间隔肽 1 (SP1) 结构域从随机卷曲转变为 Gag 寡聚化的 α 螺旋。 最后，将开发一种新颖的反应性粗粒度模型来识别拆卸过程中的拆卸路径 成熟。在该项目的所有阶段，将做出并测试可通过实验处理的预测 通过我与两位领先的实验家的合作，这将使迭代改进成为可能 开发的模型。这项研究的见解将对病毒学、大分子生物学产生广泛影响 组装和分子生物物理学。