Thermodynamics and structural description of Amyloid-beta 1-42 and pyroglutamate-modified Amyloid-beta 3-42 peptides binding to fibrils.

阿尔茨海默病(AD)是最常见的痴呆类型，其表现为与记忆相关的认知域的恶化。参与AD的蛋白质之一是淀粉样β蛋白(AB)，其聚集行为和小寡聚体与神经元死亡高度相关。最近有证据表明，如果环境中存在纤维，有毒低聚物的产量会大大增加。由纤维表面催化的这种类型的生化反应称为二次成核，导致低聚物的指数生产。然而，关于AB单体与纤维表面之间的基本分子相互作用的细节，包括单体与纤维结合的能量学或这些单体所采用的构象，人们知之甚少。除了AB42外，焦谷氨酸盐AB3-42(pEAB3-42)是淀粉样斑块的主要成分之一，比AB42毒性更大，并被认为与AB42纤维强烈结合。在这个项目中，我们的目标是通过增强的全原子分子动力学模拟和表面等离子体共振实验相结合，从原子细节上阐明AB单体与AB纤维之间的相互作用。我们将集中在AB42和pEAB3-42上，这是淀粉样斑块中发现的毒性最大的AB同种异型。我们的主要目标是通过模拟和实验计算AB42和pEAB3-42单体与AB42纤维的结合亲和力和结合热，并解决结合过程中多肽的结构构象。在计算上，这将通过使用计算平均力势的伞形抽样方法结合哈密顿副本交换模拟来计算单体与纤维的结合亲和力来实现。我们将针对原纤边和原纤侧，并考虑最近派生的包含所有氨基酸的AB42原纤维模型。为了计算结合热，我们将从Arrhenius图和vant Hoff分析研究结合过程的温度依赖性。在实验上，结合亲和力将通过纤维洗涤实验和SPR测量来计算。多肽从纤维表面的分离预计将表现出线性和指数行为的组合，分别是从纤维末端和从纤维表面的分离。对于不同的单体浓度，指数函数的幅值将导致朗缪尔吸附等温线，从而得到与纤维表面结合亲和力相关的临界单体浓度。因此，我们将首次使用计算和实验方法，详细描述AB42和pEAB3-42多肽与纤维结合的能量学和结构。

Alzheimer disease (AD) is the most common type of dementia and it manifests through the deterioration of cognitive domains related to memory. One of the proteins involved in AD is the amyloid beta (AB) protein whose aggregating behaviour and small oligomers are highly associated with neuronal death. The production of toxic oligomers has been recently shown to be greatly enhanced if fibrils are present in the environment. This type of biochemical reaction catalyzed by the fibril surface, known as secondary nucleation, leads to an exponential production of oligomers. However, little information is known about the details of the basic molecular interactions between AB monomers and the fibril surface, including the energetics of monomer binding to the fibril or the conformations adopted by these monomers. Besides AB42, pyroglutamate AB3-42 (pEAB3-42) is one of the main constituents of amyloid plaques, more toxic than AB42, and was hypothesized to strongly attach to AB42 fibrils. In this project we aim at elucidating at atomistic detail the interactions between AB monomers and AB fibrils by combining enhanced all-atom molecular dynamics simulations with surface plasmon resonance experiments. We will focus on AB42 and pEAB3-42, the most toxic alloforms of AB found in amyloid plaques. Our main goal is to calculate the binding affinity and enthalpy of AB42 and pEAB3-42 monomers for AB42 fibrils from simulations and experiments and to resolve the structural conformation of the peptide during binding. Computationally, this will be achieved by calculating the binding affinity of monomers for fibrils using the umbrella sampling method for calculating potentials of mean force in combination with Hamiltonian replica exchange simulations. We will target the fibril edges and the fibril sides and consider a recently derived AB42 fibril model that includes all amino acids. To calculate the binding enthalpy we will study the temperature dependence of the binding process from Arrhenius plots and vant Hoff analysis. Experimentally, the binding affinity will be calculated from fibril washing experiments and SPR measurements. The detachment of peptides from the fibril surface is expected to exhibit a combination of linear and exponential behaviours, specific to detachment from the fibril end and from the fibril surface, respectively. The amplitude of the exponential function for different monomer concentrations will lead to Langmuir adsorption isotherms, and thus the critical monomer concentration associated with the binding affinity for the fibril surface. Thus we will describe thoroughly for the first time, using both computational and experimental methods, the energetics and structure of AB42 and pEAB3-42 peptides binding to the fibrils.