CAREER: Computational studies of the structure and biological activity of amyloid forming peptides

淀粉样肽具有很强的膜相关能力，可通过改变膜的完整性和通透性诱导神经元细胞毒性。越来越多的证据表明：(1)可溶性低分子量淀粉样蛋白低聚物是主要的毒性物质；(2)导致细胞死亡的细胞毒性可能是由淀粉样蛋白低聚物与细胞膜之间的直接相互作用介导的。然而，肽介导裂解的分子机制，即这些肽是否形成孔或诱导膜缺陷，在原子水平上仍不清楚。缺乏详细的低聚物结构和复杂的天然细胞膜的参与，阻碍了建立低聚物结构从水环境到膜环境的转变与其在细胞膜中的生物活性之间的直接关系的努力。智力优势：本项目最重要的目标是建立淀粉样肽引起毒性机制的一般性，特别关注两种类型的淀粉样肽（来自阿尔茨海默病的淀粉样肽与来自血液透析的k2 -微球蛋白）和两种膜相互作用模型（位于膜上与嵌入膜上），使用四步计算策略与不同的计算方法相结合。本提案的具体目标是：(i)使用内部肽包装程序预测淀粉样低聚物，（ii）识别溶液中稳定的淀粉样低聚物，（iii）确定有毒的膜结合低聚物及其相关的膜破坏机制，以及（iv）设计突变体和配体来破坏稳定的有毒低聚物的形成。提出的协同四步计算策略也可以应用于其他蛋白质错误折叠疾病的研究，如帕金森病和朊病毒疾病。这项提案的资金将允许PI的小组扩展目前的模拟工作，使用控制良好的自组装单层来捕获淀粉样蛋白低聚物，并开发基于聚合物的抑制剂来防止实验中低聚物的形成。在更广泛的背景下，了解淀粉样蛋白低聚物的详细结构并了解它们与脂质的分子行为将(i)促进我们对淀粉样蛋白毒性机制的基本理解，（ii）合理设计抑制淀粉样蛋白形成的药物。广泛影响：PI正在与学术界和国家实验室的各种实验和理论小组合作进行这个抗淀粉样蛋白项目。通过这项研究，可以从分子水平上了解错误折叠蛋白聚集体与细胞膜之间的结构、稳定性和生物活性之间的关系，这对于开发针对神经退行性疾病（如阿尔茨海默病、帕金森病和II型糖尿病）的治疗策略至关重要，有利于科学界和整个社会。该项目还将教育研究生、本科生和大学预科学生，特别是那些来自代表性不足群体的学生，了解研究蛋白质聚集体的概念和模拟工具。本提案的发现和方法将被纳入生物分子系统的分子建模和模拟的新课程和现有的本科热力学课程中。从提案中获得的知识将通过出版物、演讲、讲习班、课程、实习和其他外联活动传播。

0952624ZhengAmyloid peptides have a strong membrane associated ability that can induce cytotoxicity to neurons by altering membrane integrity and permeability. Accumulating evidences suggest that (i) soluble, low molecular weight amyloid oligomers are major toxic species and (ii) the cytotoxicity leading to the cell death could be mediated by direct interactions between amyloid oligomers and cell membrane. However, the molecular mechanism underlying peptide-mediated lysis, i.e. whether these peptides form pores or induce membrane defects, remains unclear at the atomic level. The lack of detailed oligomer structures and the involvement of complex natural cell membrane have hampered efforts to establish a direct correlation between oligomer structural transition from the aqueous to the membrane environment and their biological activity in cell membranes. Intellectual Merit: The most important goal of this project is to establish the generality of the mechanism of toxicity caused by amyloid peptides, with particular attention to two types of amyloid peptides (Aâ from Alzheimer disease vs. K3 of â2-microglobulin from hemodialysis) and two membrane interaction models (reside on the membrane vs. embed in the membrane), using a four step computational strategy coupled with different computational approaches. The specific aims of this proposal are: (i) to predict amyloid oligomers using an in house peptide packing program, (ii) to identify stable amyloid oligomers in solution, (iii) to determine toxic membrane bound oligomers and their related mechanism of membrane disruption, and (iv) to design mutants and ligands to disrupt the formation of stable toxic oligomers. The proposed synergistic four step computational strategy can be also applied to study other protein misfolding diseases such as Parkinson's and Prion diseases. Funding of this proposal will allow PI's group to extend current simulation works to capture amyloid oligomers using well controlled self-assembled monolayers and to develop polymer based inhibitors to prevent oligomer formation in experiments. In a broader context, knowing the detailed structures of amyloid oligomers and understanding their molecular behavior with lipids will (i) advance our fundamental understanding of amyloid toxicity mechanism and (ii) rationally design drugs for inhibiting amyloid formation. Broad Impact: The PI is collaborating with various experimental and theoretical groups in academia and national laboratories on this anti amyloid project. Through this research, a molecular level understanding of the relationship between structure, stability, and biological activity of misfolded protein aggregates and cell membranes can be obtained, which is vital in the development of therapeutic strategies against neurodegenerative diseases such as Alzheimer's, Parkinson's, and diabetes II, benefiting both scientific community and entire society. The project will also educate graduate, undergraduate, and precollege students, particularly those from underrepresented groups, to the concepts and simulation tools for studying protein aggregates. The discoveries and methods from this proposal will be incorporated into a new course of Molecular Modeling and Simulation of Biomolecular Systems and an existing undergraduate thermodynamics course. The knowledge derived from the proposal will be disseminated through publications, presentations, workshops, courses, internships, and other outreach activities.