Molecular Dynamics Simulations of Protein Unfolding

描述(由申请人提供)：本提案的目标是使用真实的分子动力学(MD)模拟在溶液中描述蛋白质展开以及延伸折叠的分子水平。既要遵循一般的展开规则，也要遵循特定的程序规则。一般规律将通过利用实验室中已有的蛋白质展开轨迹的大型数据库进行研究。此外，还将添加新的轨迹。到目前为止，这个数据库包含了超过2200个蛋白质和多肽系统的近11,000个模拟。这个资料库代表了世界上最大的蛋白质模拟和蛋白质结构集合。这些模拟的设计是为了最终研究所有蛋白质折叠的代表，从最多的折叠到最少的折叠。目前的SET代表了所有已知蛋白质结构的80%以上。我们已经开发了一个新的关系/多维数据库来存储这些数据。这项提案的具体目标1试图通过挖掘这个数据库来确定蛋白质展开的一般规则。此外，人们正在研究多个高密度折叠的代表，以确定特定目的2的序列特异性效应。我们的假设是，对分离蛋白质在溶液中的全原子分子动力学模拟可以提供连续和真实的蛋白质展开途径，并且一旦模拟了大量蛋白质折叠，就可以确定展开和折叠的一般规则。虽然根据实验研究，一个折叠家族中的大多数亲属都使用相同的折叠机制，但也有一些例外。因此，序列特异性效应将通过研究具有不同结构的四个常见折叠家族的多个成员来确定。具体目标3侧重于在孤立的和不同的结构背景下，即在不同的结构内展开结构主题。最后，特定目标4重点描述了一对设计的蛋白质的展开行为和展开的序列决定因素，这些蛋白质具有高度的序列同源性，但它们采用不同的折叠，具有不同的功能。

DESCRIPTION (provided by applicant): The goal of this proposal is a molecular level description of protein unfolding, and by extension folding, using realistic molecular dynamics (MD) simulations in solution. Both the general and sequence-specific rules of unfolding will be pursued. The general rules will be investigated by making use of a large database of protein unfolding trajectories that already exist in the lab. In addition, new trajectories will be added. So far, this database contains nearly 11,000 simulations of more than 2200 protein and peptide systems. This repository represents the largest collection of protein simulations and protein structures in the world. The simulations were designed so that representatives of all proteins folds will eventually be investigated, working from the most to least populated folds. The current set represents over 80% of all known protein structures. We have already developed a novel relational/multidimensional database to house these data. Specific Aim 1 of this proposal seeks to determine the general rules of protein unfolding by mining this database. In addition, multiple representatives of highly populated folds are being investigated to determine sequence-specific effects in Specific Aim 2. Our hypothesis is that all-atom molecular dynamics simulations of isolated proteins in solution can provide continuous and realistic protein unfolding pathways and that the general rules for unfolding and folding can be determined once a large number of protein folds have been simulated. While most relatives within a fold family fold by the same mechanism based on experimental studies, there are some exceptions. Consequently, sequence-specific effects will be determined by investigating multiple members of four common fold families with different architectures. Specific Aim 3 focuses on the unfolding of structural motifs in isolation and in different structural contexts, i.e., within different structures. Finally, Specific Aim 4 focuses on characterizing the unfolding behavior and sequence determinants of unfolding for a pair of designed proteins with high sequence identity but they adopt different folds with different functions.