A53T突变对α-synuclein错误折叠和聚集影响的分子模拟研究

发布时间：2018-02-13 05:43

本文关键词： 蛋白质构象病 α-突触核蛋白错误折叠聚集突变分子动力学模拟　出处：《兰州大学》2017年硕士论文　论文类型：学位论文

【摘要】：蛋白质聚集是一个高度复杂的过程并伴随出现不同结构和形态的聚合物,其会形成淀粉样沉淀从而引起蛋白质构象病(protein conformational diseases),包括帕金森病、Ⅱ-型糖尿病和亨廷顿氏舞蹈病等。蛋白质发生错误折叠会在很大程度上影响其正常的生物学功能,因而也被认为是神经退行性疾病的主要原因。因此,充分理解这些疾病相关蛋白的错误折叠和聚集机理及由此引发的生理效应是研究聚集过程与细胞毒性之间联系的关键,也是靶向药物设计和开发的重要前提。分子动力学(molecular dynamics,MD)模拟方法作为计算机辅助手段可以和现有实验手段很好的互补,克服了传统实验研究中的局限性,进而从原子水平上认识淀粉样沉淀的形成过程。在对特定蛋白质的错误折叠和聚集的研究过程中,运用计算机模拟的方法可以获取到实验中无法获取的有效信息。在本论文中,我们应用常规分子动力学模拟和副本交换动力学模拟方法对帕金森症特定蛋白质(α-突触核蛋白)的折叠和聚集过程展开了研究,论文内容分为以下四个部分:第一部分主要对神经退行性疾病与蛋白质错误折叠之间的关系进行了阐述,接着说明了神经退行性疾病相关蛋白发生错误折叠与聚集的机制及药物设计的思路,并重点关注α-突触核蛋白的致病机制与帕金森症之间的联系;最后对本论文用到的分子动力学模拟方法的原理与流程步骤进行了详细阐述。第二部分中,我们基于副本交换的分子动力学模拟研究了A53T突变对α-synuclein 47-56序列折叠的影响,对野生型与突变型短肽分别进行了200 ns的REMD模拟。通过对二级结构含量的测定、构象空间特征的比较及溶剂可及化表面积的分布的分析,我们发现A53T突变较野生型有较大的可能来转化成β-sheet结构来增强蛋白质发生聚集的趋势。第三部分主要内容是基于分子动力学模拟方法来研究A53T突变对α-突触核蛋白46-97五聚体折叠和聚集的影响。我们对野生型与突变型-突触核蛋白46-97多肽分别进行了400 ns的分子动力学模拟,结果表明野生型与突变型二级结构均发生了改变,A53T突变的确使得五聚体有向β-sheet结构转变的趋势,使得整体结构更加稳定有利于蛋白质的聚集。这是由于该突变影响到了整个体系的能量发生了变化,有利于五聚体向更稳定的结构转变。A53T突变会影响到自身的折叠,进一步会影响到五聚体的聚集。第四部分研究的是结合分子动力学模拟来观察以α-突触核蛋白46-97五聚体为模板诱导核心肽段低聚化的过程。根据野生型与A53T突变型两组分别诱导其对应的短肽,通过200 ns的模拟过程总结出突变型作为模板诱导的效率较高,并且在五聚体的两侧单体都有明显的β-sheet结构形成,而对应的野生型则只在一侧的临近单体出现了β-sheet结构并且诱导效率较低。研究结果表明A53T突变有助于聚集,使α-突触核蛋白结构发生改变从而引起病症的发生。本论文中,我们对A53T特定突变对α-突触核蛋白错误折叠和聚集的影响进行了系统的分子动力学模拟研究,所得结果可以从原子水平上更好地理解A53T突变型α-突触核蛋白错误折叠和聚集的机理,理解帕金森症的致病机理与靶向药物的设计研究提供理论基础。
[Abstract]:Protein aggregation is a highly complex process with different structure and morphology of the polymer, the formation of amyloid deposition can cause protein conformational disease (protein conformational diseases), including Parkinson's disease, type 2 diabetes and Huntington's disease. Protein misfolding may affect its normal biological function in large degree, which was also thought to be a major cause of neurodegenerative disease. Therefore, to fully understand the physiological effects of these diseases related to protein misfolding and aggregation mechanism and the key link between research aggregation process and cell toxicity, an important prerequisite to drug design and development is also the target of molecular dynamics (molecular dynamics. MD), simulation method as computer aided method and the existing experimental methods can complement each other well, to overcome the traditional experimental study The limitations, and then from the atomic level understanding of amyloid formation process. In the course of the study on the aggregation of misfolded proteins and the specific, effective information using the computer simulation method can get the experiment can not be obtained. In this paper, we apply the conventional molecular dynamics simulation and Parkinson simulation method to copy disease specific protein dynamics exchange (alpha synuclein) folding and aggregation process is studied. The thesis is divided into the following four parts: the first part is mainly about the relationship between neurodegenerative diseases and protein folding errors are discussed, and then explains the neurodegenerative diseases associated with protein misfolding and aggregation the mechanism and drug design ideas, and focus on the pathogenesis of Parkinson's disease and between alpha synuclein links; at the end of this paper to use The molecular dynamics simulation principle and process method are discussed in detail. In the second part, we replica exchange molecular dynamics simulation research based on the effect of A53T mutation on fold alpha -synuclein 47-56 sequence, the wild type and mutant peptides were 200 ns REMD simulation. Through the determination of the content of two level structure the comparison of the characteristics of space and solvent conformation analysis and surface area distribution, we found that A53T mutant compared to the wild type are more likely to convert to the beta -sheet structure to enhance protein aggregation trend. The third part is the molecular dynamics simulation method based on A53T to study the effects of mutations on alpha synuclein 46-97 five mer protein folding and aggregation. The wild type and mutant - synuclein 46-97 polypeptides were 400 ns molecular dynamics simulations. The results show that Wild type and mutant two structures are changed, it makes the A53T mutant dimer has five changes to the beta -sheet structure of the trend, make the whole system more conducive to the stability of protein aggregation. This is due to the mutations affect the energy of the whole system changes, is conducive to the dimer structure to five stable transformation of.A53T mutation affects its own folding, further will affect five dimer accumulation. The fourth part of the study is to observe the alpha synuclein 46-97 five mer peptides as templates to induce the core process of oligomerization. Using the molecular dynamics simulation based on the wild type and A53T mutant groups were two induction of the corresponding peptide, through simulating the process of 200 ns summed up the high efficiency mutant as template to induce the monomer and dimer, both sides in the five have formed beta -sheet structure, and the corresponding wild type Only in the near side of the monomer structure induced by beta -sheet and low efficiency. The results show that A53T mutations contribute to the aggregation of alpha synuclein structural changes caused by the occurrence of the disease. In this paper, we carried out molecular dynamics simulation system of A53T specific mutations affecting misfolding the alpha synuclein aggregation and fault, the results from the atomic level to better understand the mechanism of aggregation of A53T mutant alpha synuclein misfolding and the pathogenesis of Parkinson's disease and target understanding and provide a theoretical basis to the design of drugs.

【学位授予单位】：兰州大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：R742.5

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