CAREER: CDS&E: Developing Reaction-Diffusion Models of Non-Equilibrium Virion Assembly and Budding

约翰霍普金斯大学的Margaret E. Johnson教授获得了生命过程化学和化学系化学理论、模型和计算方法项目的奖励，以开发和应用新的理论和计算机模拟方法来研究病毒粒子的形成、出芽和导致病毒粒子在细胞膜上释放的膜重塑。病毒粒子是具有传染性的病毒颗粒，由蛋白质外壳包裹的病毒DNA或RNA组成。约翰逊博士正在研究逆转录病毒Gag（群特异性抗原）蛋白如何通过在感染细胞的膜上组装新的病毒粒子来使病毒感染永久化。对感染性病毒粒子生命周期中这一关键步骤的分子理解可以帮助确定针对病毒感染的治疗干预目标。Johnson博士为这个项目开发的新的反应-扩散建模软件提供了连接短分子长度尺度（化学）与细胞自组装和膜出芽（膜力学）的慢时间尺度的缺失环节。这些模型正在进行测试，并根据活细胞实验不断改进。建模软件、图形用户界面和基于规则的模型定义框架正在作为开源软件传播，并与其他广泛使用的生物物理建模工具兼容，为理解和控制基本细胞过程提供了一种变革性的新方法，包括那些涉及细胞分裂或病毒感染的过程。该研究与一项教育推广计划紧密结合，该计划旨在通过向巴尔的摩市小学的学生教授计算机编程来提高STEM领域的多样性，从而提高成果。课后模块向学生介绍计算机在解决生物和化学方面的突出问题方面的力量，目的是促进和鼓励未来在STEM领域的职业发展。该项目的目标是建立一个基于速率的病毒粒子在细胞内形成的计算模型，以确定膜上中心逆转录病毒Gag蛋白的募集和组装机制。虽然最终病毒粒子的组成成分是已知的，但由于动力学对蛋白质生产、动力学、膜组成和细胞辅助因子敏感，因此对组装途径知之甚少。在本项目中，将病毒粒子组件的计算机模拟与活细胞实验直接进行比较，以确定和描述Gag晶格在体内组装的时空和结构依赖机制，并为迭代模型改进提供机制。计算方法是通过实现新的非平衡组装和膜重塑的反应扩散方法。对病毒粒子形成和机制途径的深入了解，可以应用于病毒成功退出感染细胞的预测控制，并为治疗干预策略提供信息。这项研究有助于更广泛的科学界以前所未有的分辨率研究细胞非平衡动力学机制，通过公众访问为该项目开发的强大的新方法和软件。该研究与一项教育外展计划相结合，通过教授计算机编程及其在化学和生物学中的应用，积极促进和鼓励巴尔的摩市来自不同背景的学生考虑STEM的未来。通过关注小学生，这个研究项目将有助于培养他们对STEM领域的兴趣，使用约翰逊教授的计算研究项目作为动力和应用。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。

Professor Margaret E. Johnson of Johns Hopkins University is supported by an award from the Chemistry of Life Processes and Chemical Theory, Models, and Computational Methods programs in the Division of Chemistry to develop and apply novel theoretical and computer simulation methods for studying virion formation, budding, and membrane remodeling leading to virion release at the cell membrane. Virions are the infective virus particles, and consist of viral DNA or RNA enclosed by a protein shell. Dr. Johnson is investigating how retroviral Gag (Group-specific Antigen) proteins perpetuate viral infection by assembling new virions on the membranes of infected cells. A molecular understanding of this critical step in the lifecycle of infectious virions can help identify targets for therapeutic intervention against viral infection. The new reaction-diffusion modeling software being developed by Dr. Johnson for this project provides the missing link coupling short molecular length-scales (chemistry) with the slow time-scales of cellular self-assembly and membrane budding (membrane mechanics). The models are being tested and iteratively refined against live cell experiments. The modeling software, graphical user interface, and rule-based model definition framework are being disseminated as open-source software and made compatible with other widely-used biophysical modeling tools, providing a transformative new approach for understanding and controlling essential cellular processes, including those involved in cell division or in viral infections. The research is closely integrated with an educational outreach program designed to improve diversity and therefore outcomes in STEM fields by teaching computer programming to Baltimore City Elementary School students. The after-school module introduces students to the power of computers in solving outstanding problems in biology and chemistry, with the goal of promoting and encouraging future careers in STEM.The goal of this project is to develop a rate-based computational model of virion formation in the cell, to determine the mechanisms of recruitment and assembly of the central retroviral Gag protein on the membrane. While the components of the final virion are known, pathways of assembly are poorly understood because the dynamics is sensitive to protein production, kinetics, membrane composition, and cellular co-factors. In this project, computer simulations of the virion components are directly compared with live-cell experiments to determine and describe the time- and space- and structure-dependent mechanisms of Gag lattice assembly in vivo, and provide a mechanism for iterative model refinement. The computational approach is made possible by the implementation of new reaction-diffusion methods for non-equilibrium assembly and membrane remodeling. The deepened understanding of virion formation and mechanistic pathways has application to predictive control over successful viral exit from infected cells, and informing strategies for therapeutic intervention. This research is contributing to the ability of the broader scientific community to study mechanisms of non-equilibrium dynamics of the cell at unprecedented resolution through public access to the powerful new methods and software being developed for the project. The research is integrated with an educational outreach program to actively promote and encourage students from diverse backgrounds in Baltimore city to consider futures in STEM by teaching them computer programming and its applications in chemistry and biology. By focusing on elementary school students, this research program will help to foster, early on, interest in STEM fields, using Professor Johnson's computational research program as a motivation and application.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.