A Lumry-Eyring nucleated polymerization model of protein aggregation kinetics: 1. Aggregation with pre-equilibrated unfolding
A Lumry-Eyring nucleated polymerization model of protein aggregation kinetics: 1. Aggregation with pre-equilibrated unfolding
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DOI：
10.1021/jp070212j
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发表时间：
2007-07-12
影响因子：
3.3
通讯作者：
Roberts, Christopher J.
中科院分区：
文献类型：
--
作者：
Andrews, Jennifer M.;Roberts, Christopher J.
提出了一个结合 Lumry-Eyring 和有核聚合 (LENP) 描述的非天然蛋白质聚集动力学数学模型。 LENP 模型针对与折叠-展开平衡相比聚集速率较慢的情况进行了求解，并且被证明是许多先前提出的非天然和天然蛋白质聚集的成核和生长模型的概括。模型解表现出许多定性动力学机制。每个状态都有一组特征性的实验特征，这些特征与生长和成核的相对速率以及聚集体凝结形成高阶结构或其他相的阈值尺寸相关。近似模型解提供了实用的速率方程，可以根据典型的实验动力学数据进行回归，以获得表征聚集途径的机械参数。在所有动力学机制中，我们发现从反应程度测量中获得的观察到的速率系数 (k(obs)) 或半衰期 (t(50)) 是路径中多个阶段的卷积，除非发生纯粹的种子生长。尽管存在这种卷积，表观反应顺序（时域）以及 k(obs) 或 t(50) 与初始蛋白质浓度的缩放的组合提供了一种确定每种情况下主导核大小值的方法。需要额外的信息，例如平衡展开热力学和限制聚集体尺寸分布，以进一步将 k(obs) 解卷积为成核、生长和构象变化的内在贡献。该模型和分析预计普遍适用于形成非天然聚集体的各种蛋白质和多肽。
A mathematical model is presented of the kinetics of non-native protein aggregation that combines Lumry-Eyring and nucleated polymerization (LENP) descriptions. The LENP model is solved for cases in which aggregation rates are slow compared to folding-unfolding equilibration and is shown to be a generalization of a number of previously proposed nucleation-and-growth models for non-native and native protein aggregation. The model solutions exhibit a number of qualitative kinetic regimes. Each regime has a characteristic set of experimental signatures that are related to the relative rates of growth and nucleation as well as to the threshold size at which aggregates condense to form higher-order structures or other phases. Approximate model solutions provide practical rate equations that can be regressed against typical experimental kinetic data to obtain mechanistic parameters characterizing the aggregation pathway. In all kinetic regimes, it is found that observed rate coefficients (k(obs)) or half-lives (t(50)) obtained from extent-of-reaction measurements are convolutions of more than one stage in the pathway unless purely seeded growth occurs. Despite this convolution, the combination of apparent reaction order (time domain) and the scaling of k(obs) or t(50) with initial protein concentration provides a means to determine a value for the dominant nucleus size in each case. Additional information, such as equilibrium unfolding thermodynamics and the limiting aggregate size distribution, are required to further deconvolute k(obs) into intrinsic contributions from nucleation, growth, and conformational changes. The model and analysis are expected to be generally applicable to a wide range of proteins and polypeptides that form non-native aggregates.