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的关系，并开发抑制淀粉样蛋白形成的治疗模型。在这项建议中，我们重点研究人类转甲状腺素(TTR)淀粉样蛋白形成过程中的早期事件，在原子水平上使用计算方法。我们提出了三个具体目标：目标1：对能量景观、构象转变路径和协同运动进行计算研究。单体受体的稳定性和灵活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。我们从模拟野生型TTR单体及其突变体开始，表征它们的动力学性质，绘制能量图，并寻找连接TTR的自然态和中间态的可能的构象转变途径。通过比较野生型和淀粉样变异体，我们将对淀粉样变的差异提供见解。目的：为了研究结构的pH依赖性，pH是促进构象变化的条件的关键因素。溶液pH如何影响TTR四元结构和单体结构？我们建议在恒定pH下进行模拟。我们将使用一种新的算法来产生满足玻尔兹曼分布的质子态系综。通过分析每个质子态的布居和产生的轨迹，我们将提供作为pH函数的结构变化的信息。目的3：确定小分子与TTR结合的最有利结合模式，并设计优化其最有利结合模式的配体的修饰。我们建议研究蛋白质-小分子相互作用在稳定TTR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。拟议的计算将提供对小分子策略的洞察力，以干预TTR型淀粉样变性疾病的病理。

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.