Pathways and interactions accounting for the oligomerization of amyloid peptides

淀粉样肽聚集成可溶性低聚物和原纤维是阿尔茨海默氏症的标志 疾病这些聚集体与细胞膜的相互作用是一个重要的原因。 毒性机制，其中低聚物可以在脂膜中形成孔，而淀粉样纤维可以 引起脂质损失。作为单体，即，已经发现单个肽大部分是无毒的， 制定抑制聚集的战略有可能转化为发展 阿尔茨海默病的新的预防性治疗方法。然而，这些努力需要一个深刻的 理解淀粉样蛋白聚集的相互作用。 以前，肽在本体溶液中的聚集，即，初级成核，被认为是 解释低聚物形成的主要机理。最近，这一假设被 通过仔细的动力学实验重新评估，这只能在假设 大多数低聚物在已知为二次成核的过程中形成于现有原纤维的表面上。 目前，对分子相互作用和途径的理解严重缺乏 用于二次成核。这仍然是合理设计药物的一个严重障碍， 抑制原纤维表面的低聚化。这项提议采用了创新的全原子分子动力学 模拟与生物物理和生物化学实验的补充，以填补这一知识空白。它 利用力场发展的改进以及增强的 今天的超级计算机的性能，现在可以跟踪许多原子的位置（~ 250，000 原子）长时间（>10 μs）。此外，该项目为本科生提供了机会， 学生参与本研究的各个方面，包括建立，运行和分析 在不同的超级计算机集群中进行模拟。 全原子模拟将用于本项目的aim 1，以确定肽序列如何影响 途径和相互作用占低聚在本体溶液。目标2和目标3中的模拟 将在含有种子原纤维的大盒子中进行。在目标二中，将对这一问题进行系统的研究 揭示了原纤维表面和肽序列对原纤维伸长的影响。 原纤维表面的低聚途径，即，二次成核，将在目标3中研究。一 将对初级成核和次级成核的低聚途径进行比较研究 以确定使原纤维表面能够催化聚集过程的相互作用。

The aggregation of amyloid peptides into soluble oligomers and fibrils is a hallmark of Alzheimer’s disease. The interaction of these aggregates with the cell membrane accounts for an important mechanism of toxicity wherein oligomers can form pores in lipid membranes and amyloid fibrils can induce lipid loss. As monomers, i.e., individual peptides, have been found to be mostly nontoxic, the development of strategies to inhibit aggregation has the potential to translate into the development of new preventive treatments for Alzheimer’s disease. These efforts require, however, a deep understanding of the interactions accounting for amyloid aggregation. Previously, the aggregation of peptides in bulk solution, i.e., primary nucleation, was assumed to be the main mechanism accounting for the formation of oligomers. More recently, this assumption was reassessed by careful kinetic experiments, which can only be explained quantitatively assuming that most oligomers form on the surface of existing fibrils in a process known as secondary nucleation. Currently, there is a critical lack of understanding of the molecular interactions and pathways accounting for secondary nucleation. This remains a serious impediment for the rational design of drugs that can inhibit oligomerization on the fibril surface. This proposal uses innovative all-atom molecular dynamics simulations complemented with biophysical and biochemical experiments to fill this knowledge gap. It takes advantage of improvements in the development of force fields as well as in the enhanced performance of today’s supercomputers that can now track the position of many atoms (~250,000 atoms) for a long-time (>10 μs). Moreover, this project provides opportunities for undergraduate students to participate in all aspects of this research including setting up, running, and analyzing simulations in different supercomputer clusters. All-atom simulations will be used in aim 1 of this project to determine how the peptide sequence affects pathways and interactions accounting for oligomerization in bulk solution. Simulations in aims 2 and 3 will be performed in large boxes containing a seeded fibril. In aim 2, a systematic study will be carried out to shed light into effects of the fibril surface and the peptide sequence on fibril elongation. Oligomerization pathways at the fibril surface, i.e., secondary nucleation, will be studied in aim 3. A comparative study of oligomerization pathways in primary and secondary nucleation will be performed to determine the interactions enabling the fibril surface to catalyze the aggregation process.