Molecular Dynamics Simulations of Protein Unfolding

描述（由申请人提供）：本提案的目标是蛋白质展开的分子水平描述，并通过扩展折叠，使用现实分子动力学（MD）模拟溶液。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来研究。此外，还将添加新的轨迹。到目前为止，这个数据库包含了300多种蛋白质的2300多个模拟。这个仓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，从最多到最少的折叠。目前的蛋白质结构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。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展开的一般规则。此外，正在研究多个密集折叠的代表，以确定序列特异性影响。我们的假设是，溶液中分离蛋白质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，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，一个折叠家庭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，序列特异性效应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。此外，一个分离的蛋白质在水中的热展开的假设通常适用于蛋白质可能发现自己的许多条件，通过“试管”模拟进行测试，其中一个蛋白质的多个拷贝在一个大的水盒子中一起模拟，以确定分子间相互作用如何干扰折叠和展开的过程。最后，研究了有机溶剂对反应的影响。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问题之一，它代表了充分利用基因组序列图谱所提供的信息所必需的重要缺失环节。从充分理解基本生化现象的角度和从折叠过程的角度来看，对展开过程的表征同样重要。对蛋白质折叠/展开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.