Combining Molecular Simulations and Biophysical Methods to Characterize Conformational Dynamics of the HIV-1 Envelope Glycoprotein

结合分子模拟和生物物理方法来表征 HIV-1 包膜糖蛋白的构象动力学

• 批准号: 10749273
• 负责人: CAMERON F ABRAMS
• 金额: $ 82.51万
• 依托单位: DREXEL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-10 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10749273
• 关键词: 3-Dimensional; Acceleration; Antigens; Antiviral Therapy; Binding; Biophysics; Cells; Characteristics; Complex; Crosslinker; Data; Development; Equilibrium; Fluorescence Resonance Energy Transfer; Future; Generations; Glycoproteins; HIV-1; Immune; Immune Evasion; Immune system; Length; Lysine; Mass Spectrum Analysis; Mediating; Membrane; Methods; Modeling; Molecular; Molecular Conformation; Molecular Machines; Molecular Target; Monitor; Outcome; Positioning Attribute; Predisposition; Resolution; Role; Sampling; Schedule; Specific qualifier value; Spectrum Analysis; Structure; Surface; Techniques; Temperature; Testing; Time; Vaccines; Viral; Viral Proteins; Virion; Virus; Work; biophysical techniques; biophysical tools; crosslink; design; experimental study; flexibility; fluorophore; immunogenicity; improved; inhibitor; molecular dynamics; simulation; single molecule; single-molecule FRET; small molecule; small molecule inhibitor; vaccine development; viral entry inhibitor

PROJECT SUMMARY The HIV-1 envelope glycoprotein spike (Env) mediates viral entry into target cells. Because Env is the only viral protein on the virion surface, it is central to the development of potential vaccines and small-molecule entry inhibitors. Env is a uniquely flexible molecular machine, and deep understanding of its immunogenicity and susceptibility to inhibition requires an appreciation of its atomically resolved conformational dynamics. Structural studies using truncated, solubilized, and stabilized Env constructs have yielded detailed atomic models of its main open and closed conformational states. Emerging structural studies of full-length Env support identification of asymmetric closed conformations as the “default intermediate state” (DIS), revealing details of a potentially pivotal role of quaternary asymmetry in Env conformational dynamics. At the same time, both single-molecule FRET (smFRET) and crosslinking mass spectrometry (XL-MS) of Env suggest the existence of at least one, sometimes dominant conformational state that has not been structurally characterized. This “State-1” conformation nonetheless seems relevant for both immune recognition and susceptibility to small-molecule inhibitors. We will leverage advanced Molecular Dynamics (MD) methods including targeted MD, temperature-accelerated MD, and string method to provide atomic level models for the opening of HIV-1 Env from closed (State 2) to open (State 3) conformational states and to identify critical structural changes separating State-2 from the poorly understood State-1 Env. The MD simulation methods we use will incorporate biases from multi-perspective smFRET and XL-MS, and they will in turn provide direction for expanding the set of Env constructs used in those experiments, establishing an iterative approach that progressively better defines transition mechanisms and State 1. An atomic-level understanding of HIV-1 Env conformational dynamics, identification of a yet to be structurally characterized pre-triggered conformational states, as well as the mechanism of Env activation for fusion will inform immunogen design and antiviral therapies.

项目摘要 HIV-1包膜糖蛋白尖峰（ENV）介导病毒进入靶细胞。因为env是唯一的 病毒蛋白在病毒体表面上，这对于潜在疫苗的发展和小分子的发展至关重要 env是一种独特的柔性分子机，对其免疫原性有深刻的了解 并且对抑制作用的敏感性需要欣赏其原子解决的构象动力学。 使用截短，可溶性和稳定的ENV结构的结构研究产生了详细的原子 其主要开放和封闭构象状态的模型。全长ENV的新兴结构研究 支持识别不对称闭合构象为“默认中间状态”（DIS），揭示 第四纪不对称性在ENV构象动力学中的潜在关键作用的细节。同时， ENV的单分子fret（SMFRET）和交联的质谱（XL-MS）表明 至少存在一个尚未在结构上的构象状态的存在 特征。但是，这种“状态1”构象似乎与免疫认知和 对小分子抑制剂的敏感性。我们将利用高级分子动力学（MD）方法 包括针对目标的MD，温度加速的MD和String方法，以提供原子水平模型 从封闭（状态2）开放HIV-1 Env以打开（状态3）构象状态并确定关键 结构性变化将状态-2与知名度不佳的状态1所区分开。 MD仿真方法我们 使用将融合来自多角度SMFRET和XL-MS的偏见，它们又将提供方向 用于扩大这些实验中使用的ENV结构集，建立一种迭代方法 逐渐更好地定义了过渡机制和状态1。 构象动力学，鉴定尚未结构表征的预触发构象 状态以及融合活化的机制将为免疫原和抗病毒提供信息 疗法。