COMPUTER SIMULATION STUDIES OF PROTEIN AGGREGATION

蛋白质聚集是一个严重的问题。 例如，蛋白质聚集可干扰重组蛋白质从包涵体中的回收，是诸如阿尔茨海默氏病或唐斯综合征的疾病的原因或相关症状，并且可限制基于蛋白质的药物在其包装、运输、储存和施用期间的稳定性。 一个有趣的方法来规避这个问题是加入溶质，有能力抑制聚集，如聚乙二醇（体外）和伴侣（体内）。该提案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增强重折叠的机制。 我们的目标是开发分子水平的模型，捕捉的基本特征，管理蛋白质的重折叠和聚集在不存在和存在的溶质之间的竞争。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。 该提案有两个具体目标：（1）开发基于异质方阱链模型的简单、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）来模拟在模型PEG分子存在和不存在的情况下的蛋白质折叠和聚集，以及（2）修改更真实的蛋白质模型，例如，最成功的中间分辨率蛋白质折叠模型之一，可与我们的DMD技术一起使用，从而能够模拟特定小蛋白质和肽的折叠和聚集。 这些模拟有望成为未来模拟医学上重要蛋白质聚集的基础，如β淀粉样蛋白，这种蛋白质的聚集与阿尔茨海默病有关。我们的理论工作将有助于科学家：（1）选择和/或设计抑制不需要的聚集的溶质，（2）通过操纵过程变量（如蛋白质浓度，变性剂浓度等）优化重组蛋白的体外重折叠，以及（3）了解“溶质”是否以及如何促成医学相关的聚集，例如阿尔茨海默氏病中β淀粉样蛋白斑块的形成。

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.