Theoretical Studies of Protein Folding

蛋白质折叠的理论研究

• 批准号: 8939529
• 负责人: William Eaton
• 金额: $ 22.21万
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8939529
• 关键词: Accounting; Amino Acid Sequence; Annual Reports; Benchmarking; Cereals; Circular Dichroism; Data; Development; Equation; Equilibrium; Fluorescence; Heating; Kinetics; Lasers; Maps; Measurement; Measures; Modeling; Physics; Play; Property; Proteins; Publishing; Role; Science; Set protein; Simulate; Structure; Temperature; Theoretical Studies; Theoretical model; Thermodynamics; Time; Tryptophan; Viscosity; base; millisecond; models and simulation; molecular dynamics; nanosecond; next generation; protein folding; quantum; research study; simulation; single molecule; single-molecule FRET; temperature jump; three dimensional structure; villin

Understanding the mechanism by which proteins fold to their native structure is a central problem in protein science. Clearly, interactions between residues that are in contact in the folded state (native interactions) are likely to be important for folding, but, in principle, nonnative interactions may play a role. We used recently published microsecond to millisecond all-atom molecular dynamics simulations of proteins folding and unfolding to show, remarkably, that nonnative contacts are irrelevant to the mechanism of folding in most cases. This statistical analysis would be very difficult to perform by experiment. Although this is a limited set of proteins, the results nonetheless strongly support coarse-grained theoretical and simulation models of folding in which only native contacts are energetically favorable. A major challenge to advancing our understanding of how proteins fold is the development of an analytical theoretical model capable of calculating the quantities directly measured in both equilibrium and kinetic experiments. That is, we require a partition function to predict thermodynamic properties and a master equation to predict kinetic properties. To this end we have been developing an Ising-like model, with the major input being the contact map of the native structure. This model has been remarkably successful in quantitatively accounting for a wide range of data for the 35-residue subdomain from the villin headpiece, the smallest naturally occurring protein that autonomously folds into a globular structure (see Kubelka et al., PNAS 2008; Cellmer et al., PNAS 2008, Cellmer et al., PNAS 2011). These data include, heat capacity, tryptophan fluorescence quantum yield (QY), and natural circular dichroism spectrum (CD) as a function of temperature in both denaturants and viscogens, while the kinetic data consist of time courses of the QY from nanosecond laser temperature jump experiments as a function of temperature, denaturant concentration, and viscosity. Anticipating the next generation of folding experiments, consisting of measurements of transition paths in single molecule FRET experiments (see annual report on single molecule experiments), we have carried out stochastic kinetic to make closer connections to molecular dynamics simulations. We show that recent simulations by the Shaw group are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter is remarkably similar to the distribution in the molecular-dynamics trajectories.

了解蛋白质折叠到其天然结构的机制是蛋白质科学中的一个核心问题。显然，在折叠状态下接触的残基之间的相互作用（天然相互作用）可能对折叠很重要，但原则上，非本地相互作用可能起作用。我们最近发表的微秒来对蛋白质折叠和展开的毫秒全原子分子动力学模拟，显着地表明，在大多数情况下，非本地接触与折叠机制无关。通过实验执行这种统计分析将非常困难。尽管这是一组有限的蛋白质，但结果仍然强烈支持折叠的粗粒理论和模拟模型，在这种折叠模型中，只有天然接触在能量上有利。 促进我们对蛋白质如何折叠的理解的主要挑战是能够计算直接测量平衡和动力学实验中直接测量数量的分析理论模型的发展。也就是说，我们需要一个分区函数来预测热力学特性和主方程来预测动力学特性。 为此，我们一直在开发一个类似Ising的模型，主要输入是天然结构的触点图。 该模型在定量地考虑了Villin头饰的35个残留子域的广泛数据，这是非常成功的，该数据是自动折叠成球形结构的最小天然蛋白质（参见Kubelka等人，PNAS，PNAS，2008; Cellmer et al。 这些数据包括热容量，色氨酸荧光量子产率（QY）和自然的圆形二角运动光谱（CD）作为变性剂和粘性剂中温度的函数，而动力学数据由Nanosecond Laser温度跳跃实验的QY时间疗程组成。 预期下一代的折叠实验，包括单分子FRET实验中的过渡路径的测量（请参阅单分子实验的年度报告），我们进行了随机动力学，以更紧密地与分子动力学模拟进行了更紧密的联系。我们表明，Shaw组的最新模拟与一个类似ISI​​NG的理论模型的关键假设是一致的，该假设仅在氨基酸序列的几个区域中生长，随着折叠的进展。通过模拟该基准模型的基准模型的主方程为基准villin子域模拟的机制的分布，仅具有两个可调的热力学参数和一个依赖温度的动力学参数，与分子 - 动力学轨迹的分布非常相似。