Topology, nucleation, and the protein folding barrier

描述(申请人提供)：蛋白质折叠、展开和错误折叠是生物材料的基本物理性质。因此，它们在定义蛋白质稳定性方面发挥着关键作用，是许多疾病状态的根本原因，并成为技术挑战和创新的潜在来源。然而，尽管这些重要问题引发了数十年的仔细研究，但还没有一个定量的、经过实验验证的假说来解释蛋白质折叠是如何发生的，比随机构象搜索快约30个数量级。拟议研究计划的目标是通过一种新颖的、完全原子化的、大规模并行的模拟蛋白质折叠的方法与相关蛋白质在直接可比较的条件下的实验表征的成功结合来加深我们对折叠过程的理解。我们的动机很简单。对简单蛋白质折叠的实验研究充其量只能提供折叠过渡态的有限视角。相比之下，模拟可以提供折叠的任意详细表示(仅受精度和计算复杂性的耦合问题的限制)。然而，它们严重依赖于实验验证，缺乏一种明确的、得到普遍认可的手段来确定过渡国家整体的成员。通过将模拟与实验相结合，我们可以绕过这些困难；这种结合提供了一种“充实”否则对实验隐藏的细节的方法，提供了一种无懈可击的验证模拟的手段，并为识别速率限制转换提供了指导。受这些潜在优势的启发，我们在这里提出了一种新颖的、密切耦合的迭代过程中的模拟和实验，显著提高了两者的实用性。历史上，将模拟和实验联系起来的困难在于，小的、快速折叠的蛋白质很难通过实验检验，而大的和/或缓慢折叠的蛋白质很难通过详细的模拟来检验。然而，正如重要的初步结果所表明的那样，最近在模拟和实验方面的进展现在使我们能够解决这一冲突。我们利用这些进展来达到并测试多用途、完全详细的折叠模拟，提供了一个独特的机会来直接比较详细模拟的结果与实验观察。

DESCRIPTION (provided by applicant): Protein folding, unfolding and misfolding are fundamental physical properties of biomaterials. As such, they play critical roles in defining protein stability, are the underlying cause of many disease states and serve as a potential source of both technological challenges and innovations. Despite the decades of scrutiny motivated by these important issues, however, no quantitative, experimentally verified hypothesis yet explains how protein folding occurs some 30+ orders of magnitude more rapidly than would a random conformational search. The goal of the proposed research program is to further our understanding of the folding process via the successful marriage of a novel, fully atomistic, massively parallel method for simulating protein folding with the experimental characterization of the relevant proteins under directly comparable conditions. Our motivation is straightforward. Experimental studies of the folding of simple proteins provide at best only a limited view of the folding transition-state. Simulations, in contrast, can provide an arbitrarily detailed representation of folding (limited only by the coupled issues of accuracy and computational complexity). They are, however, critically dependent on experimental validation and lack a clear, universally recognized means of identifying members of the transition state ensemble. By coupling simulation with experiment, we can circumvent these difficulties; the combination furnishes a method of "fleshing-out" the details otherwise hidden to experiment, provides an unimpeachable means of validating the simulations and offers guidance in the identification of the rate limiting transition. Inspired by these potential advantages, we propose here a novel, intimate coupling of simulation and experiment in an iterative process that significantly increases the utility of both.The historical difficulty with connecting simulation and experiment has been the conflict that small, rapidly folding proteins are difficult to examine experimentally, whereas large and/or slowly folding proteins are difficult to examine via detailed simulations. As significant preliminary results demonstrate, however, recent advances in both simulation and experiment now allow us to resolve this conflict. We have exploited these advances to reach and test multi-use, fully detailed folding simulations, providing a unique opportunity to directly compare the outcome of detailed simulations with experimental observations.