Dynamics and Energetics of Viral DNA Packaging and Ejection

病毒 DNA 包装和喷射的动力学和能量学

• 批准号: 0848905
• 负责人: Douglas Smith
• 金额: $ 90万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0848905&HistoricalAwards=false
• 关键词: Dynamics; Energetics; Viral; DNA; Packaging

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).In this project the PI will study the physical principles of viral genome packaging using phi29 as a model system. The study will use previously developed technique based on optical tweezers for real time visualization of viral packaging processes. The project will examine the following effects on viral DNA packaging and ejection: (1) Screening of DNA by polyamine ions: Host cell polyamines including putrescine2+, spermidine3+, and spermine4+ are expected to substantially influence DNA packaging dynamics by affecting DNA mechanics and electrostatics, packing forces, and motor function. (2) Non-equilibrium dynamics: DNA packing forces will be investigated by studying the time-dependence of the internal forces resulting from changes in motor velocity induced by varying ATP concentration, and pauses in packaging induced with non-hydrolyzable ATP analogs at various capsid filling levels. Potential heterogeneity in packaging dynamics and force, as predicted in recent theoretical simulations, will also be investigated with ensembles of single molecule measurements. (3) Capsid shape: Different viruses have different capsid shapes that may affect DNA packaging dynamics. (4) DNA binding proteins: The PI will study the effect of protein "roadblocks" that interact with the DNA and create an additional load on the packaging motor. Topics of broad interest in physics and biology will be addressed, including polymer (DNA) conformation and dynamics, molecular motor function, ionic screening, protein-DNA interactions, and principles of viral assembly. Graduate and undergraduate students will be supervised by PIs with varying backgrounds and the students will perform research involving concepts and methods from the physical and biological sciences. Undergraduates will participate in this research and new undergraduate physics and biology course materials will be developed. Materials for K-12 science education will also be developed in collaboration with the R. H. Fleet Science Museum in San Diego.

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。在该项目中，PI将使用phi 29作为模型系统研究病毒基因组包装的物理原理。这项研究将使用以前开发的技术的基础上，光学镊子的真实的时间可视化的病毒包装过程。（1）多胺离子对DNA的筛选：宿主细胞中的多胺，包括腐胺2+、亚精胺3+和精胺4+，通过影响DNA的力学和静电、包装力和运动功能，对DNA包装动力学产生实质性影响。(2)非平衡动力学：将通过研究由不同ATP浓度诱导的电机速度变化引起的内力的时间依赖性，以及在各种衣壳填充水平下用不可水解的ATP类似物诱导的包装暂停来研究DNA包装力。包装动力学和力的潜在异质性，在最近的理论模拟预测，也将与单分子测量的合奏进行研究。(3)衣壳形状：不同的病毒有不同的衣壳形状，可能会影响DNA包装动力学。(4)DNA结合蛋白：PI将研究与DNA相互作用的蛋白质“路障”的影响，并在包装电机上产生额外的负载。在物理学和生物学的广泛兴趣的主题将得到解决，包括聚合物（DNA）的构象和动力学，分子马达功能，离子筛选，蛋白质-DNA相互作用，和病毒组装的原则。研究生和本科生将由具有不同背景的PI监督，学生将进行涉及物理和生物科学概念和方法的研究。本科生将参与这项研究，并将开发新的本科物理和生物课程材料。K-12科学教育材料也将与R。H.位于圣地亚哥的舰队科学博物馆。