Computational approaches to single molecule force spectroscopy

描述(由申请人提供)：对蛋白质和RNA折叠方式以及它们如何相互响应的分子理解是描述它们的功能和设计具有新功能的生物分子的能力的关键。在实验中的惊人进步，操纵 生物分子在单分子水平上使用机械力，提供了一幅前所未有的蛋白质、RNA和配体-蛋白质复合体的折叠图景。为了从测量中提取潜在生物物理过程的分子细节，需要在与实验中使用的条件类似的条件下进行计算机模拟。我们描述了新的理论和计算工具，这些工具不仅对于理解实验是不可或缺的，而且在预测一系列难以预测的条件下的结果也是有用的 在实验室里探索。利用计算方法，我们准备在定量描述蛋白质和RNA的折叠机制以及细胞黏附分子与其同源配体之间的相互作用方面取得实质性进展。特别是，拟议的研究将提供对绿色荧光蛋白和溶菌酶弹性的分子基础，以及RNA和蛋白质中折叠路径对精确作用力方式的依赖。应用程序也是 计划探索泛素在拥挤颗粒存在下的机械稳定性。关于细胞黏附分子PSelectin和配体之间的复合体的响应的工作旨在提供在低作用力下复合体寿命异常延长的分子细节。我们的研究将导致一个解释广泛的单分子实验的全球框架，并将被证明是设计能够探索生物物理过程的新实验的关键 在细胞条件下。拟议的研究有望在概念上取得进展，并应用于一些前沿问题，这将使我们对生物分子对力的反应的理解有实质性的进步-这是许多体外和体内问题的关键。

DESCRIPTION (provided by applicant): A molecular understanding of the way proteins and RNA fold and how they respond to each other holds the key to describing their functions and the ability to design biological molecules with novel functions. Spectacular advances in experiments, that manipulate biomolecules at the single molecule level using mechanical force, are providing an unprecedented picture of the folding landscapes of proteins, RNA, and ligand-protein complexes. Computer simulations that can be done under conditions that are similar to those used in experiments are required to extract molecular details of the underlying biophysical processes from measurements. We describe novel theoretical and computational tools that are not only integral to the understanding of the experiments but are also useful in predicting their outcomes over a range of conditions that are difficult to explore in the laboratory. Using computational methods, we are poised to make substantial progress in quantitatively describing the folding mechanisms of proteins and RNA and the interactions between cell adhesion molecules and their cognate ligands. In particular, the proposed research will offer insights into the molecular basis of elasticity of Green Fluorescent Protein and Lysozyme and the dependence of folding routes in RNA and proteins on the precise way force is applied. Applications are also planned to explore mechanical stability of Ubiquitin in the presence of crowding particles. The work on the response of the complex between the cell adhesion molecule PSelectin and the ligand is intended to provide molecular details of the unusual enhancement of the lifetime of the complex at low forces. Our studies will lead to a global framework for interpreting a wide range of single molecule experiments and will prove essential in the design of new experiments that can probe biophysical processes under cellular conditions. The conceptual progress and applications to a number of cutting edge problems that is expected from the proposed researches will lead to a substantial advance in our understanding of the response of biological molecules to force - which is pivotal to a number of in vitro and in vivo problems.