Computational Approaches to Single Molecule Force Spectroscopy

项目摘要 可视化蛋白质和RNA分子及其相关复合物的动力学的能力， 在使用单分子方法的时候，正在戏剧性地改变我们对它们功能的看法， 在重新设计它们的功能和靶向特定区域进行药物或 配体结合为了实现单分子拉实验的全部潜力，必须对它们进行补充 通过计算，不仅产生与测量一致的结果，而且可以使可测试的 预测。 在这个计算和理论研究的建议，协同实验研究合作， 我们正在提出新的想法，使用机械力作为变量，就像在单分子力中所做的那样。 光谱学（SMFS），研究一系列与生物学直接相关的复杂问题。总体 目标是推动在特定问题的背景下使用计算可以实现的前沿， 生物物理学，这反过来将补充实验。三个具体目标是：（1）SMFS用于隐藏 状态：使用力作为扰动剂，我们提出了表征功能性关系的动态的方法。 在蛋白质中，激发态的数量很少，但数量稀少。应用于PDZ域以及两个结构 类似的蛋白质（PrPC和Doppel）但具有不同的致病机制， 在折叠和聚集的倾向中使用力量。(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），一种核蛋白，含有约 147个碱基对的DNA缠绕在高度保守的组蛋白八聚体周围。了解序列 DNA的依赖动力学对于在分子水平上破译基因表达至关重要。小说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坏， 基于DNA序列的分子术语。(3)使用力监测Hsp90组装：分子 伴侣蛋白Hsp90是热休克蛋白家族的成员，在细胞内具有多种（有时）连接作用。 真核细胞功能。受最近激光光镊牵引实验的激励，我们提出了 系统研究了含有三个独立折叠结构域的Hsp90的组装。 拟议的计算研究与两位领先的实验学家密切合作进行 将极大地推进我们对大型蛋白质复合物的动力学和组装的理解。冰毒- 将开发的ODS将大大提高该领域的效率，并将在提高我们的 理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.