Selective Nucleation, Polyproteins, and HIV-1

该奖项支持理论研究和教育，以促进对蛋白质物理学的理解，蛋白质是病毒样颗粒组装的关键。寻找能够有效对抗导致艾滋病的人类免疫缺陷病毒（HIV）的新型抗病毒药物，主要集中在阻断正常细胞中没有对应的病毒蛋白的方法上。这种策略可能会将负面影响降到最低。HIV的关键结构蛋白，被称为“Gag”，是一种在正常细胞中没有对应的HIV蛋白，是这项研究的目标之一。尽管经过多年的深入研究，Gag功能的关键方面仍未被理解。Gag不仅是一种结构蛋白，它还协调HIV病毒的组装过程，首先在被感染的宿主细胞内寻找HIV遗传物质。关于这一主题的大量生命科学文献表明，HIV组装起始的生物物理原理与“标准”病毒的生物物理原理根本不同。实验研究也毫无疑问地表明，Gag蛋白之间的物理相互作用在HIV遗传物质的选择过程中起着关键作用，然而，单个蛋白水平上Gag-Gag相互作用的实验研究受到蛋白-蛋白聚集问题的严重阻碍。Gag本身比许多其他病毒中具有类似功能的蛋白质更复杂，这表明对Gag的研究可能会导致新的物理原理和对病毒组装的见解。该团队将在目前最大的超级计算机上进行Gag蛋白与HIV遗传物质相互作用的计算机模拟。通过建立两个或三个Gag蛋白相互作用以及与HIV遗传物质相互作用的大规模数值模拟模型，可以避免聚集问题。通过数值模拟，对Gag蛋白的动力学和相互作用进行了详细的统计物理分析，为科学探索HIV遗传选择机制提供了直接途径。该研究项目将成为对生物物理学工作感兴趣的年轻物理科学家的培训基地，生物物理学对公共卫生有重要的应用。对物理学对病毒施加的基本限制的全面理解将有助于从事制药行业的年轻科学家。与社区学院和加州州立大学的合作项目将为学生提供获得研究经验的机会，这将进一步促进他们的职业生涯。这两所大学都为洛杉矶地区的少数族裔学生提供服务。技术概述：该奖项支持理论和计算研究及教育，以促进对蛋白质物理学的理解，蛋白质是病毒样颗粒组装的关键。该团队的目标是对HIV-1的主要衣壳蛋白——非常大的多蛋白Gag进行结合分子动力学（MD）和统计力学研究。Gag是病毒形成后包裹RNA基因组分子的衣壳的主要成分。最初，这种多蛋白被认为只起结构作用，Gag的不同部分独立作用。最近的成像实验显示，Gag是一个具有复杂功能能力的综合单元。它从感染细胞内的大量RNA分子中选择少量病毒RNA的能力似乎依赖于Gag结构域组分之间的合作相互作用。尽管有大量关于Gag蛋白的文献，但缺乏一个基于物理的模型来解决围绕Gag的许多难题。例如，Gag可以有效地选择病毒RNA，而不需要在携带病毒RNA的病毒和携带非病毒RNA的病毒之间存在可测量的自由能差。PI旨在解决这一问题和其他挑战，并以选择性成核假说的形式研究统计力学框架。在选择性成核假说中，涉及RNA与Gag结合的远程合作相互作用调节了Gag簇成核和生长的激活自由能垒。该团队计划使用Gag和Gag-Gag相互作用的MD模拟来为成核和生长的统计物理模型提供信息。该团队将根据MD模拟的结果和即将在俄亥俄州立大学进行的实验来测试关于Gag物理的假设。选择性成核假说依赖于一阶跃迁临界核的形成速率对激活自由能势垒的微小变化的敏感性，以便进行选择过程。这个假设的统计物理类似于在蛋白质转录和合成中遇到的动态校对。如果这个假设可以被证实，那么动态校对将是一个统一的原则，将病毒组装与蛋白质转录和合成。第二个假设的确认，即熵变容信号传输可能是Gag子组分之间长距离通信的原理，将导致其扩展到其他多蛋白以及其他小簇弱偶联蛋白的操作，如转录起始复合物。表明大规模MD模拟与统计物理原理的结合可以提供重要的见解，了解像Gag功能这样大的大分子复合物如何有助于刺激生物物理学向结构复杂系统的扩展。该研究项目将成为对生物物理学工作感兴趣的年轻物理科学家的培训基地，生物物理学对公共卫生有重要的应用。对物理学对病毒施加的基本限制的全面理解将有助于从事制药行业的年轻科学家。与社区学院和加州州立大学的合作项目将为学生提供获得研究经验的机会，这将进一步促进他们的职业生涯。这两所大学都为洛杉矶地区的少数族裔学生提供服务。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

NONTECHNICAL SUMMARYThis award supports theoretical research and education to advance understanding of the physics of proteins that are key for the assembly of virus-like particles. The search for new antiviral drugs that are effective against the human immunodeficiency viruses (HIV), which causes AIDS, focuses on ways of obstructing viral proteins that have no counterparts in normal cells. This strategy will likely minimize negative side effects. The key structural protein of HIV, known as "Gag", is an HIV protein with no counterpart in normal cells and is one of the targets for this search. Despite many years of intense research, key aspects of the way Gag functions are not understood. Gag is not only a structural protein, it also coordinates the assembly process of the HIV virus, starting with a search for HIV genetic material inside infected host cells. The large life-science literature on this topic shows that the biophysical principles of HIV assembly initiation are fundamentally different from those of "standard" viruses. Experimental studies also leave no doubt that physical interactions among Gag proteins play a key role during the selection of the HIV genetic material, yet experimental studies of Gag-Gag interactions at the level of individual proteins are very seriously hampered by the problem of protein-protein aggregation. Gag itself is more complex than proteins of analogous function in many other viruses, suggesting that the study of Gag may lead to new physical principles and insights into viral assembly. The team will carry out computer simulations of the interaction of the Gag protein with HIV genetic materials on the largest super-computers currently available. By developing a large-scale numerical simulation model of the interaction of just two or three Gag proteins with each other and with HIV genetic material, the aggregation problem is circumvented. The detailed statistical physics analysis of the dynamics and interactions of the Gag proteins, as obtained from numerical simulations, provides science with a direct route to explore the HIV genetic selection mechanism. The research program will be a training ground for young physical scientists interested in working in biological physics that has important applications for public health. A sound understanding of the fundamental limitations imposed by physics on viruses in general will help young scientists with careers in the pharmaceutical industry. A collaborative program with a community college and Cal State University, both of which serve under-represented minority students in the LA area, will provide students with the opportunity to obtain research experience that would further their career. TECHNICAL SUMMARYThis award supports theoretical and computational research and education to advance understanding of the physics of proteins that are key to the assembly of virus like particles. The team aims to carry out combined molecular dynamics (MD) and statistical mechanics studies of the very large poly-protein Gag, the main capsid protein of HIV-1. Gag is the main component of the capsid that surrounds the RNA genome molecule after formation of the virus. Originally the poly-protein was thought to play only a structural role with the different parts of Gag acting independently. More recent imaging experiments have revealed that Gag functions as an integrated unit with complex functional abilities. Its ability to select a small number of viral RNA from a large number of RNA molecules inside an infected cell, appears to rely on cooperative interactions between the domain components of Gag. Despite the large literature on the Gag protein, a physics-based model that can address the many puzzles surrounding Gag is lacking. For example, Gag can select viral RNA efficiently without a measurable free energy difference between a virus that packs viral RNA versus a virus that packs non-viral RNA. The PI aims to address this and other challenges, and investigate a statistical mechanical framework in the form of the selective nucleation hypothesis. In the selective nucleation hypothesis, long-range cooperative interactions that involve binding of RNA to Gag modulates the activation free energy barrier for the nucleation and growth of Gag clusters. The team plans to use MD simulations of Gag and Gag-Gag interactions to inform statistical physics models of nucleation and growth. The team will test hypotheses about the physics of Gag against the outcomes of MD simulations and against experiments to be carried out at The Ohio State University.The selective nucleation hypothesis depends on the sensitivity of the formation rate of the critical nucleus of a first-order transition to small changes in the activation free energy barrier in order to carry out a selection process. The statistical physics of this hypothesis is akin to that of kinetic proofreading as encountered in protein transcription and synthesis. If this hypothesis can be confirmed, then kinetic proofreading would be a unifying principle relating viral assembly to protein transcription and synthesis. Confirmation of a second hypothesis, namely that entropic allosteric signal transmission could be the principle that allows long-distance communication between the sub-components of Gag, would lead to its extension to other poly-proteins as well as to the operation of other small clusters of weakly coupled proteins, such as transcription initiation complexes. Showing that the combination of large-scale MD simulations with the principles of statistical physics can provide important insights into how a macromolecular complex as large as Gag functions could help stimulate the extension of biological physics to structurally complex systems.The research program will be a training ground for young physical scientists interested in working in biological physics that has important applications for public health. A sound understanding of the fundamental limitations imposed by physics on viruses in general will help young scientists with careers in the pharmaceutical industry. A collaborative program with a community college and Cal State University, both of which serve under-represented minority students in the LA area, will provide students with the opportunity to obtain research experience that would further their career.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.