Theoretical and computational modeling of amyloid aggregation

描述（由申请人提供）：蛋白质聚集的实验研究利用相对于表征疾病如阿尔茨海默氏病发作的数十年时间尺度加速聚集体形成许多数量级的方案。体内和体外聚集时间尺度之间的差距需要聚集过程的详细理论，以便将实验观察外推到生理条件。目前的理论工具不适合这项任务。分析理论目前缺乏对序列扰动或环境条件进行预测所需的微观基础，并且计算机方法在不牺牲必要分辨率的情况下甚至难以达到体外聚集时间尺度。申请人已经开发了原纤维伸长的微观理论，其与关于以下影响的实验一致： 温度、变性剂和蛋白质浓度。该理论确定的构象搜索H-键合状态的聚集过程中最慢的一步（观察，是在最近的模拟协议），并表明，这种搜索可以有效地建模为一个随机行走在崎岖的一维潜力。这项工作将在两个方面扩展这个模型：1）通过开发新的淀粉样蛋白聚集的微观模型。这些模型将解决聚集途径中的关键步骤，包括成核和新分子结合后原纤维末端的模板效应。他们还将探索不同自缔合模式之间的动力学竞争，包括低聚物和原纤维。2)通过使用的见解，从初步的模型，开发一个多尺度的计算算法来模拟原纤维生长和成核的原子细节。在这 算法，大量的小模拟将被用来计算系统扩散张量在反应坐标空间预测的分析理论。然后，该扩散张量将被用于计算聚集过程的马尔可夫状态轨迹。这项工作的创新之处在于使用分析建模来推导目前无法通过实验或模拟解决的微观动力学中的缓慢步骤，并使用这些见解来开发效率大大提高的模拟方法。结果将是解决小序列扰动的影响的能力，例如区分阿尔茨海默氏症相关肽A的主要形式的两个氨基酸，以及“动力学相图”，这将允许合理操纵聚集途径，并提供一种从体外实验推断生理后果的方法。

DESCRIPTION (provided by applicant): Experimental studies of protein aggregation utilize protocols that accelerate aggregate formation by many orders of magnitude relative to the multi-decade timescales that characterize the onset of dis- eases like Alzheimer's. The gap between in vivo and in vitro aggregation timescales demands detailed theories of the aggregation process in order to extrapolate experimental observations toward physiological conditions. Current theoretical tools are not suitable for this task. Analytic theories presently lack the microscopic basis that is needed to make predictions about sequence perturbations or environmental conditions, and in silico methods struggle to reach even in vitro aggregation timescales without sacrificing necessary resolution. The applicants have developed a microscopic theory of fibril elongation that agrees with experiments with respect to the effects of temperature, denaturants, and protein concentration. This theory identifies the conformational search over H-bonding states as the slowest step in the aggregation process (an observation that is in agreement with recent simulations) and shows that this search can be efficiently modeled as a random walk in a rugged one-dimensional potential. The proposed work will expand on this model in two ways: 1) By developing new microscopic models of amyloid aggregation. These models will resolve key steps in the aggregation pathway including nucleation and the templating effect of the fibril end upon the binding of new molecules. They will also explore the kinetic competition between different modes of self-association, including oligomers and fibrils. 2) By using the insights from the preliminary model to develop a multi-scale computational algorithm to simulate fibril growth and nucleation in atomistic detail. In this algorithm, a large number of small simulations will be used to compute the system diffusion tensor in the reaction coordinate space predicted by the analytic theory. This diffusion tensor wil then be used to compute Markov state trajectories of the aggregation process. The innovation of this work is to use analytic modeling to deduce slow steps in the microscopic kinetics that are not presently resolvable by experiments or simulation, and to use these insights to develop simulation methods with greatly improved efficiency. The outcome will be the ability to resolve the effects of small sequence perturbations, such as the two amino acids differentiating the major forms of the Alzheimer's-related peptide A, as well as a "kinetic phase diagram" that will allow the rational manipulation of aggregation pathways and provide a means to infer physiological consequences from in vitro experiments.