Molecular Dynamics Simulations of Protein Unfolding

描述（由申请人提供）：本提案的目标是在溶液中使用现实分子动力学（MD）模拟对蛋白质展开和延伸折叠进行分子水平描述。展开的一般规则和序列特定规则都将被追求。一般规则将通过利用实验室中已经存在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，该数据库包含300多种蛋白质的2300多个模拟。这个知识库代表了世界上最大的蛋白质模拟和蛋白质结构的集合。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。目前的集合代表了所有已知蛋白质结构的大约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。本提案的具体目标1旨在通过挖掘该数据库来确定蛋白质解折叠的一般规则。此外，正在研究高度聚集的折叠的多个代表，以确定序列特异性效应。我们的假设是，全原子分子动力学模拟分离的蛋白质在溶液中可以提供连续的和现实的蛋白质展开途径和展开和折叠的一般规则，可以确定一旦大量的蛋白质折叠已经模拟。虽然根据实验研究，一个褶皱家族中的大多数亲属都是通过相同的机制折叠的，但也有一些例外。因此，将通过研究具有不同结构的三个常见折叠家族的多个成员来确定序列特异性效应。此外，一种假设是，一种分离的蛋白质在水中的热解折叠对于蛋白质可能发现自身的许多条件通常是有效的，这一假设正在通过“试管”模拟进行检验，在这种模拟中，在一个大盒子的水中一起模拟一种蛋白质的多个拷贝，以确定分子间相互作用如何干扰折叠和解折叠的过程。最后，研究了含水有机溶剂对该过程的影响。这个提议本质上是假设驱动的发现科学。蛋白质折叠仍然是分子生物学中最重要的未解决的问题之一，它代表了充分利用从基因组序列图谱中获得的信息所必需的重要缺失环节。展开过程的表征同样重要，无论是从充分理解一个基本的生物化学现象的角度来看，还是为了阐明折叠过程。对蛋白质折叠/解折叠的理解也对所有生物过程具有重要意义，包括蛋白质降解、蛋白质易位、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.