Simulations on the early events of TTR amyloidogenesis

我们的长期目标是详细了解各种非同源淀粉样蛋白形成淀粉样蛋白的机制，阐明蛋白质错误折叠与淀粉样蛋白疾病之间的关系，并开发抑制淀粉样蛋白形成的治疗模型。在这个建议中，我们专注于研究早期事件沿着人甲状腺素运载蛋白（TTR）淀粉样蛋白形成的途径，在原子水平上使用计算方法。我们提出了三个具体的目标：目标1：计算研究的能量景观，构象转变途径，和协调运动。单体TTR的稳定性和柔性很可能在淀粉样蛋白形成的早期阶段起着至关重要的作用，因此，表征单体I-FR的初始构象变化是至关重要的。我们开始模拟野生型TTR单体及其突变体，以表征其动力学性质，绘制能量景观，寻找TTR天然状态和中间状态之间可能的构象转换途径。通过比较野生型和淀粉样蛋白突变体，我们将提供差异淀粉样蛋白的见解。目的2：研究pH对结构的影响，pH是影响构象变化的重要因素。溶液pH值对TTR的四元和单体结构有何影响？我们建议在恒定pH值下进行模拟。我们将采用一种新的算法来生成满足玻尔兹曼分布的质子化状态的集合。通过分析人口的每个质子化状态和所产生的轨迹，我们将提供信息的结构变化作为pH值的函数。目的3：为了确定最有利的结合模式的小分子结合TTR和设计Imodifications的配体，优化其最有利的结合模式。我们建议研究蛋白质-小分子相互作用在稳定TTR的四聚体天然状态中的作用，用一种新的自由能计算方法在多种结合模式中确定最有利的配体结合模式，并优化配体以提高结合亲和力。拟议的计算将为干预TTR相关淀粉样蛋白疾病病理的小分子策略提供见解。

Our long-term goal is to understand, in detail, the mechanism of amyloid formation from various non-homologous amyioidogenic proteins, to elucidate the relationship between protein misfolding and amyloid diseases, and to develop therapeutic models for inhibition of amyloid formation. In this proposal, we focus on the study of early events along the pathway of human transthyretin (TTR) amyloid formation using computational approaches at the atomic level. We propose three specific aims: Aim 1: A computational study of the energy landscapes, conformational transition pathways, and concerted motions. It is highly likely that the stability and flexibility of monomedc TTR play crucial roles in the early steps of amyloid formation, thereby, it is essential to characterize the initial conformational changes of monomeric I-FR. We begin with simulations of the wild-type TTR monomer and its mutants to characterize their dynamic properties, map the energy landscapes, and search for likely conformational transition pathways connecting the native state and the intermediate states of TTR. By comparing the wild-type with the amyloidogenic mutants, we will provide insights on the differential amyloidogenesis. Aim 2: To study the pH dependence of structure, pH is a crucial factor of the condition which facilitates conformational changes. How does the solution pH influence the tetramedc and monomeric structure of TTR? We propose to perform simulations at constant pH. We will employ a novel algorithm to generate ensembles of protonation states satisfying Boltzmann distribution. By analyzing the population of each protonation state and the generated trajectories, we will provide information on the structural changes as a function of pH. Aim 3: To identify the most favorable binding mode of small molecules bound to TTR and design Imodifications of the ligand that optimize its most favorable binding mode. We propose to study the role of protein-small molecule interaction in stabilizing the tetrameric native state of TTR, to identify the most favorable ligand binding mode among the multiple binding modes with a novel free energy calculation method, and to optimize the ligands to enhance binding affinity. The proposed calculations will provide insight into the small-molecule strategy for intervening in the pathology of TTR related amyioid diseases.