AF9 YEATS识别乙酰化组蛋白H3K9ac机制的分子动力学模拟研究

发布时间：2018-12-23 20:49

【摘要】：在真核细胞中,核小体是构成染色质的基本结构单位。核小体由组蛋白H2A、H2B、H3、H4各两个分子形成一个扁平圆柱状八聚体,约每146bp的染色质DNA以左手螺旋的方式围绕八聚体组蛋白形成一个核小体,无数个核小体又构成了染色质。DNA与组蛋白借助组蛋白分子中碱性氨基酸的正电荷和DNA双螺旋中磷酸基负电荷以静电引力维持结构稳定。一般来说,组蛋白是非常稳定的,但是组蛋白暴露在外部的N端尾部经常会发生大量的翻译后修饰(包括赖氨酸和精氨酸的乙酰化和甲基化,丝氨酸和苏氨酸的磷酸化,赖氨酸的泛素化和类泛素化等)。这些翻译后修饰在真核细胞调节染色体动力学和DNA的可接近性中发挥着重要的作用。组蛋白乙酰化是最常见也最具有代表性的组蛋白修饰方式,组蛋白赖氨酸乙酰化更是被当作活化转录的标志。目前,一共有三个蛋白结构域被发现可以特异性识别并结合乙酰化组蛋白:布罗莫结构域(Bromodomain BRD),串联植物同源结构域(tandem plant homeodomain PHD)以及最新发现的AF9 YEATS蛋白结构域。AF9蛋白是一类非常重要的转录调控因子,它可以招募组蛋白H3K79甲基化转移酶和超级延伸复合物(Super Elongation Complex)在转录开始和延伸期间发挥着重要的作用。YEATS结构域可以特异性识别并结合赖氨酸乙酰化的组蛋白(H3K9ac),并发挥相应的下游功能。与布罗莫结构域(BRD)和串联植物同源结构域(PHD)不同,YEATS结构采取了一种类似免疫球蛋白的折叠,并且利用了芳香族环来形成一种类似“三明治”的结合口袋来识别和容纳乙酰化赖氨酸。但是关于YEATS蛋白域特异性识别并结合乙酰化赖氨酸的具体细节尚不清楚。本论文中,我们使用分子动力学模拟(molecular dynamics simulations,MD)方法并结合MM-PBSA(molecular mechanics/Poisson-Boltzmann surface area)方法来探究AF9 YEATS与乙酰化组蛋白H3K9ac之间的相互作用。在本论文中,我们主要关注在以下几个方面:(1)探索AF9 YEATS蛋白是如何特异性结合乙酰化组蛋白H3K9ac的;(2)通过计算结合自由能来评估突变对AF9 YEATS与H3K9ac结合能力的影响;(3)筛选在结合中发挥重要作用的氨基酸残基;(4)通过比较野生型和突变型体系来确定重要残基的功能;(5)通过研究AF9同家族蛋白Taf14来帮助我们了解YEATS蛋白家族与乙酰化组蛋白H3K9ac之间的结合细节;(6)疏水相互作用在YEATS蛋白家族与乙酰化组蛋白H3K9ac的结合中发挥着决定性的作用。
[Abstract]:In eukaryotes, nucleosomes are the basic structural units that form chromatin. The nucleosome consists of two molecules of histone H _ 2A, H _ 2B, H _ 3H _ 3 and H _ 3H _ 4, each of which forms a flat cylindrical octamer. The chromatin DNA of about every 146bp forms a nucleosome around the histone in a left-handed manner. Numerous nucleosomes make up chromatin. DNA and histone keep their structure stable by electrostatic force with positive charge of basic amino acid in histone molecule and negative charge of phosphate group in DNA double helix. Generally speaking, histone is very stable, but histone exposure to external N-terminal tail often occurs a large number of post-translational modifications (including acetylation and methylation of lysine and arginine, phosphorylation of serine and threonine, and phosphorylation of serine and threonine). Ubiquidization and ubiquitization of lysine. These posttranslational modifications play an important role in eukaryotic regulation of chromosome dynamics and accessibility of DNA. Histone acetylation is the most common and representative histone modification, and histone lysine acetylation is used as a marker for activation of transcription. At present, three protein domains have been found to specifically recognize and bind to acetylated histones: the Bromo domain (Bromodomain BRD), Tandem plant homologous domain (tandem plant homeodomain PHD) and newly discovered AF9 YEATS protein domain. AF9 protein is a very important transcriptional regulator. It can recruit histone H3K79 methyltransferase and superextension complex (Super Elongation Complex) to play an important role in the beginning and extension of transcription. YEATS domain can specifically recognize and bind to lysine acetylated histone (H3K9ac). And give play to the corresponding downstream function. Different from the Bromo domain (BRD) and the tandem plant homologous domain (PHD), the YEATS structure adopts a kind of immunoglobulin-like folding. Aromatic rings are used to form a sandwich-like binding pocket to recognize and accommodate acetyllysine. However, the specific details of YEATS domain specific recognition and binding to acetyllysine are unclear. In this paper, we used the molecular dynamics simulation of (molecular dynamics simulations,MD method and MM-PBSA (molecular mechanics/Poisson-Boltzmann surface area) method) to explore the interaction between AF9 YEATS and acetylated histone H3K9ac. In this thesis, we mainly focus on the following aspects: (1) to explore how AF9 YEATS protein specifically binds to acetylated histone H3K9ac, (2) to evaluate the effect of mutation on the binding ability of AF9 YEATS to H3K9ac by calculating binding free energy; (3) screening amino acid residues which play an important role in binding, (4) determining the function of important residues by comparing wild type and mutant system; (5) to help us understand the binding details between YEATS protein family and acetylated histone H3K9ac by studying AF9 and family protein Taf14; (6) hydrophobic interaction plays a decisive role in the binding of YEATS protein family to acetylated histone H3K9ac.
【学位授予单位】：吉林大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q51

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