Computational Approaches to Single Molecule Force Spectroscopy

项目摘要 可视化蛋白质和RNA分子以及相关复合体的动力学的能力，一 在使用单分子方法的同时，正在戏剧性地改变我们对它们功能的看法，并给我们一个 了解重新设计其功能的可能性，并针对特定的fic区进行药物或 配基结合。要实现单分子牵引实验的全部潜力，必须对它们进行补充 计算不仅产生与测量结果一致的结果，而且还可以使测试 预测。 在这项计算和理论研究提案中，通过协同实验研究合作-- 因此，我们提出了用机械力作为变量的新想法，就像单分子作用力一样 光谱学(SMFS)，研究一组与生物学直接相关的复杂问题。最重要的是 目标是在fic++问题的上下文中使用计算来推动可实现的前沿。 生物物理学，这反过来又将补充实验。fic的三个具体目标是：(1)用于隐藏的SMFS 状态：使用力作为摄动剂，我们提出了表征功能释放的动力学的方法。 蛋白质中大量但稀少布居的激发态。在PDZ域上的应用以及结构上的两个 相似的蛋白质(PrPC和多谱勒)但具有不同的致病机制，旨在说明 在折叠的背景下使用武力和聚集的倾向。(2)张力下的核小体： 染色质的包装单位是核小体核心颗粒(NCP)，它是一种核蛋白，含有大约 147个碱基对的DNA缠绕在高度保守的组蛋白八聚体周围。理解顺序 DNA的依赖动力学对于在分子水平上破译基因表达是至关重要的。新奇的COM- 提出了一种计算方法来理解NCP动力学中令人惊讶的对称性破缺 基于DNA序列的分子术语。(3)用力监测Hsp90的组装：分子 伴侣热休克蛋白90是热休克蛋白家族的一员，在fl中具有不同的(有时)持续的作用。 真核细胞的功能。受最近的激光光钳拉动实验的启发，我们提出了 系统研究包含三个独立折叠结构域的Hsp90组装的方法。 拟议的计算研究与两位领先的实验者密切合作进行 这将极大地促进我们对大型蛋白质复合体的动力学和组装的理解。冰毒- 即将开发的消耗臭氧层物质将标志着fifl在fi领域的应用，并将在加强我们的 了解负责各种不同细胞功能的大型系统。

Project Summary The ability to visualize the dynamics of protein and RNA molecules and the associated complexes, one at a time using single molecule methods, is dramatically altering our view of their functions and giving us a glimpse of what is possible in terms of redesigning their functions and to target specific regions for drug or ligand binding. To realize the full potential of single molecule pulling experiments one has to complement them with computations that not only produce results consistent with measurements but also can make testable predictions. In this computational and theoretical research proposal, with synergistic experimental research collabora- tions, we are advancing new ideas to use mechanical force as a variable, as done in single molecule force spectroscopy (SMFS), to study a set of complex problems of direct relevance to biology. The overarching goal is to push the frontiers of what is achievable using computations in the context of specific problems in biophysics, and which in turn will complement experiments. The three specific aims are: (1) SMFS for hidden states: Using force as a perturbing agent we propose ways to characterize the dynamics of functionally rele- vant but sparsely populated excited states in proteins. Applications to PDZ domain as well as two structurally similar proteins (PrPC and Doppel ) but with different disease causing mechanisms are intended to illustrate the uses of force in the context of folding and the propensity to aggregate. (2) Nucleosome under tension: The packaging unit of Chromatin is the Nucleosome Core Particle (NCP), a nucleoprotein, contains about 147 base pairs of DNA wound around the highly conserved histone octamer. Understanding the sequence dependence dynamics of the DNA is crucial to deciphering gene expression at the molecular level. Novel com- putational methods are proposed to understand the surprising breakage of symmetry in the NCP dynamics in molecular terms based on the DNA sequence. (3) Using force to monitor Hsp90 assembly: The molecular chaperone Hsp90, a member of the heat shock protein family, has diverse (sometimes) conflicting roles in eukaryotic cellular functions. Spurred by the recent Laser Optical Tweezer pulling experiments we propose ways to systematically study the assembly of Hsp90 containing three independent folding domains. The proposed computational studies conducted in close collaboration with two leading experimentalists will greatly advance our understanding of the dynamics and assembly of large protein complexes. The meth- ods to be developed will significantly influence the field, and will be of considerable use in enhancing our understanding of large systems responsible for a variety of diverse cellular functions.