COMPUTER SIMULATION STUDIES OF PROTEIN AGGREGATION

蛋白质聚集是一个严重的问题。例如，蛋白质聚集可干扰包涵体中重组蛋白质的回收，是阿尔茨海默病或唐氏综合症等疾病的病因或相关症状，并可限制基于蛋白质的药物在包装、运输、储存和给药过程中的稳定性。绕过这个问题的一个有趣的方法是添加具有抑制聚集能力的溶质，例如聚乙二醇(体外)和伴侣(体内)。这项建议描述了一个理论研究计划，旨在了解蛋白质聚集的基本原理，以及溶质防止聚集和促进折叠的机制。我们的目标是开发分子水平的模型，捕捉在没有和存在溶质的情况下管理蛋白质折叠和聚集之间竞争的基本特征。通过在计算机上模拟模型蛋白质和溶质的性质，我们将能够探索蛋白质折叠和动力学如何受到以下因素的影响：蛋白质序列和浓度；变性剂类型和浓度；溶质类型、浓度和大小；以及温度。该建议有两个具体目标：(1)建立基于异核方井链模型的简单、非常通用的非晶格蛋白质模型，然后使用不连续分子动力学(DMD)来模拟在没有或存在模型聚乙二醇分子的情况下蛋白质的折叠和聚集；以及(2)修改更真实的蛋白质模型，如较成功的中等分辨率蛋白质折叠模型之一，用于我们的DMD技术，从而能够模拟特定小蛋白质和多肽的折叠和聚集。预计这些模拟将作为未来对具有重要医学意义的蛋白质聚集建模的基础，例如β淀粉样蛋白，这种蛋白质的聚集与阿尔茨海默病有关。我们的理论工作应该有助于科学家：(1)选择和/或设计溶质来抑制不必要的聚集，(2)通过操纵蛋白质浓度、变性剂浓度等过程变量来优化重组蛋白质的体外复性，以及(3)了解“溶质”是否以及如何促进与医学相关的聚集，例如阿尔茨海默病中的β淀粉样斑块形成。

Protein aggregation is a serious problem. For example, protein aggregation can interfere with the recovery of recombinant proteins from inclusion bodies, is a cause or associated symptom in diseases such as Alzheimer's disease or Downs syndrome, and can limit the stability of protein-based drugs during their packaging, shipping, storage and administration. An intriguing way to circumvent this problem is to add solutes that have the ability to suppress aggregation, e.g. polyethylene glycol (in vitro) and chaperones (in vivo). This proposal describes a program of theoretical research aimed at understanding the basic principles that underlie protein aggregation, and the mechanisms by which solutes prevent aggregation and enhance refolding. The goal is to develop molecular-level models that capture the essential features that govern the competition between protein refolding and aggregation in both the absence and presence of solutes. By simulating the properties of model proteins and solutes on the computer, we will be able to explore how protein folding and kinetics are influenced by: protein sequence and concentration; denaturant type and concentration; solute type, concentration, and size; and temperature. The proposal has two specific aims: (1) to develop simple, very general, off-lattice protein models based an the heteronuclear square-well chain model and then to use discontinuous molecular dynamics (DMD) to simulate protein folding and aggregation in both the absence and presence of model PEG molecules, and (2) to modify a more realistic protein model, such as one of the more successful intermediate resolution protein folding models, for use with our DMD techniques, thereby enabling efforts to simulate the folding and aggregation of specific small proteins and peptides. These simulations are expected to serve as a future basis for modelling the aggregation of medically important proteins such as beta amyloid, the protein whose aggregation is associated with Alzheimer's disease. Our theoretical work should assist scientists in: (1) choosing and/or designing solutes to suppress unwanted aggregation, (2) optimizing the in vitro refolding of recombinant proteins by manipulation of process variables such as protein concentration, denaturant concentration, etc., and (3) understanding if and how "solutes" contribute to medically- relevant aggregation such as beta amyloid plaque formation in Alzheimer's disease.