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其功能和设计具有新功能的生物分子的能力的关键。实验取得了惊人的进步， 利用机械力在单分子水平上对生物分子的折叠，提供了前所未有的蛋白质、RNA和配体-蛋白质复合物的折叠图景。需要在与实验中使用的条件相似的条件下进行计算机模拟，以从测量中提取潜在生物物理过程的分子细节。我们描述了新颖的理论和计算工具，这些工具不仅对理解实验不可或缺，而且在预测一系列难以预测的条件下的结果时也很有用。 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粘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，拟议中的研究将提供深入了解绿色荧光蛋白和溶菌酶的弹性的分子基础，以及RNA和蛋白质中的折叠路线对施加力的精确方式的依赖性。应用也是 计划探索在拥挤颗粒存在下泛素的机械稳定性。对细胞粘附分子P选择素和配体之间的复合物的反应的工作旨在提供在低力下复合物的寿命的不寻常增强的分子细节。我们的研究将导致一个全球性的框架来解释广泛的单分子实验，并将证明在设计新的实验，可以探测生物物理过程中至关重要 在细胞条件下。从拟议的研究中预期的一些前沿问题的概念进展和应用将导致我们对生物分子对力的响应的理解的实质性进展-这对一些体外和体内问题至关重要。 公共卫生相关性：了解RNA和蛋白质如何折叠并相互作用是描述其功能的关键。拟议的研究将在单分子水平上给出这些过程的潜在机制的分子观点。这些研究将使我们深入了解与错误折叠有关的疾病以及细胞粘附蛋白对炎症和组织损伤反应的生物物理基础。

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. PUBLIC HEALTH RELEVANCE: Understanding how RNA and proteins fold and interact with each other holds the key to describing their functions. The proposed research will give a molecular view of the underlying mechanisms of these processes at the single molecule level. The studies will give us insights into diseases linked to misfolding and the biophysical basis of response of cell adhesion proteins to inflammation and tissue injury.