Theoretical and Computational Studies of Pressure Induced Denaturation of Proteins

该项目由生物科学局分子和细胞生物科学部的分子生物物理学和数学和物理科学局物理部的生物物理计划共同支持，其主要目标是利用分子模拟建立压力诱导蛋白质变化的热力学和结构特性之间的关系。压力提供了一种改变蛋白质构型平衡的方法，而不会增加热波动或改变系统组成。静水压力提供了一种探索水合作用在蛋白质稳定性和动力学中的作用的方法。尽管有丰富的实验信息可用，但压力变性的理论和计算研究一直受到系统规模和高压下蛋白质缓慢松弛的限制。随着增强采样技术的发展，大量分布式计算资源的使用，以及蛋白质折叠粗粒度模型的发展，这些限制可以被克服。该项目将研究高压对已知形成α和β发夹结构的多肽稳定性的影响，以确定高压对二级结构稳定性的影响。为了研究三级相互作用对蛋白质稳定性的影响，PI将研究压力对微型蛋白质(Trp-CAGE)和小蛋白质(Protein A)稳定性的影响，这两个系统具有简单的折叠，涉及二级结构元素的堆积。一个主要的挑战将是研究压力对较大蛋白质的影响，如泛素和SNase。对大型蛋白质的研究将涉及粗粒模型，并结合完全溶剂化系统的伞状采样技术。这些模型将通过将它们的结果与在较小系统上无偏见的详细计算中获得的结果进行比较，并通过做出可以进行实验测试的预测来验证。将详细研究展开态和过渡态系综的结构和热力学，以将热力学测量的体积效应与各种系综的水化程度相关联。这项工作将建立一个框架，用于理解水在蛋白质功能和稳定性中的作用，以及解释一些关于压力对生物分子影响的实验研究。这个项目本质上是跨学科的，它将与理论、计算和实验小组合作完成。在这个项目中开发的软件、模型和算法将向科学界提供。所有级别的学生都将接受生物分子系统热力学性质建模方面的培训。PI将培养来自物理系和生物系的研究生和本科生。为了加强代表不足的少数群体对科学的参与，国际和平研究所将接待来自波多黎各大学马亚圭斯大学和胡马考大学的研究人员和学生。

The main objective of this project, jointly supported by Molecular Biophysics in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Biological Physics Program in the Division of Physics in the Mathematical and Physical Sciences Directorate, is to establish relationship between the thermodynamics and the structural properties of pressure induced changes in proteins using molecular simulations. Pressure provides a way of shifting equilibrium of protein configurations without increasing thermal fluctuations or changing the system composition. Hydrostatic pressure provides a way of probing the role of hydration in protein stability and dynamics. In spite of the wealth of experimental information available, theoretical and computational studies of pressure denaturation have been limited by system size and the slow relaxation of proteins at high pressures. With the development of enhanced sampling techniques, the use of large distributed computing resources, and the development of coarse-grained models for protein folding, these limitations can be overcome. This project will study the effect of high pressure on the stability of peptides that are known to form alpha and beta hairpin structures to determine the effect that high pressure has on the secondary structure stability. To study the effect of tertiary interactions in protein stability, the PI will study the effect of pressure on the stability of mini proteins (Trp-cage) and a small protein (protein A), two systems with simple folds that involve the packing of secondary structure elements. A major challenge will be to study the effect of pressure on larger proteins, such as ubiquitin and SNase. The studies on large proteins will involve coarse-grained models, combined with umbrella sampling techniques on fully solvated systems. The models will be validated by comparing their results with those obtained in unbiased detailed calculations on smaller systems, and by making predictions that can be tested experimentally. The structure and thermodynamics of the unfolded and transition state ensembles to correlate volume effects measured thermodynamically to the degree of hydration of the various ensembles will be studied in detail. This work will establish a framework for understanding the role of water in protein function and stability, as well as for the interpretation of a number of experimental studies of pressure effects on biological molecules.This project is inherently interdisciplinary and it will be done in collaboration with theoretical, computational and experimental groups. Software, models, and algorithms developed in this project will be made available to the scientific community. Students at all levels will be trained in the modeling of thermodynamics properties of biomolecular systems. The PI will train graduate and undergraduate students from both Physics and Biology departments. To enhance the participation of under represented minorities in science, the PI will host researchers and students from the University of Puerto Rico Mayaguez and Humacao.