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300种蛋白质的2300多个模拟。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约占所有已知蛋白质结构的80%。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，正在对多个高密度折叠的代表进行研究，以确定序列特异性的影响。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路径，并且一旦模拟了大量的蛋白质折叠，就可以确定蛋白质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调查三个具有不同结构的常见折叠家族的多个成员来确定。此外，关于分离的蛋白质在水中的热展开通常适用于蛋白质可能发现自己的许多条件的假设正在通过“试管”模拟进行测试，在该模拟中，在一大盒水中一起模拟蛋白质的多个副本，以确定分子间相互作用如何扰乱折叠和展开的过程。最后，研究了有机溶剂对该过程的影响。这一提议本质上是假说驱动的发现科学。与公共卫生相关的蛋白质折叠仍然是分子生物学中最重要的悬而未决的问题之一，它是充分利用基因组序列图谱中可用信息所必需的重要缺失环节。无论是从充分理解基本的生化现象的角度，还是从揭示折叠过程的角度来看，对展开过程的表征都同样重要。对蛋白质折叠/展开的了解对所有生物过程也具有重要意义，包括蛋白质降解、蛋白质移位、衰老和许多人类疾病，包括淀粉样蛋白疾病。

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 over 2300 simulations of more than 300 proteins. 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 approximately 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. 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 three common fold families with different architectures. In addition, the assumption that the thermal unfolding of an isolated protein in water is generally valid for the many conditions in which a protein may find itself is being tested through `test tube' simulations in which multiple copies of a protein are simulated together in a large box of water to determine how intermolecular interactions perturb the processes of folding and unfolding. Finally, the effect of aqueous organic solvents on the process is being investigated. This proposal is essentially hypothesis-driven discovery science. PUBLIC HEALTH RELEVANCE Protein folding remains one of the most important unsolved problems in molecular biology, and it represents an important missing link necessary for full utilization of the information becoming available from the mapping of genomic sequences. Characterization of the unfolding process is equally important, both from the perspective of fully understanding a fundamental biochemical phenomenon and for the light shed on the folding process. An understanding of protein folding/unfolding also has important implications for all biological processes, including protein degradation, protein translocation, aging, and many human diseases, including amyloid diseases.