酿酒酵母蛋白Prp20p以及人源锌指蛋白DESR1的结构与功能研究
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摘要
在此论文中我们分别用X射线晶体学(X-ray crystallography)和核磁共振波谱学(NMR spectroscopy)的方法解析了酿酒酵母蛋白Prp20p的β-propeller结构域(β-propeller domain)以及人源锌指蛋白DESR1的三维结构。本论文将分三个章节来阐述。
第一章先介绍一下Prp20p所参与的核质输运这一重要的细胞生理过程的背景综述。在真核细胞中,核质的不同物质组成是由具有选择性和方向性的大分子的跨膜运输所维持的。核蛋白经由一类称为输入蛋白(importins)的核转运蛋白(karyopherins)运送至核内,而大半部分的RNA则通过输出蛋白(exportins)转运出核。这种运输的方向性是由RanGTP的梯度(核内是高浓度的RanGTP,而细胞溶质中则是低浓度的RanGTP)决定的。在胞质中缺乏RanGTP的情况下结合货物蛋白,然后在核质中随着RanGTP的结合而将货物蛋白释放。相反在核内,输出蛋白与RanGTP以及货物蛋白形成复合物,运送到胞质中之后随着GTP水解成GDP而解离。GTP的水解需要存在于细胞质中的RanGAP(Ran GTPase-activating protein)。反过来,GTP到GDP的交换是由鸟苷交换因子(GEF,在哺乳动物中是RCC1,在酿酒酵母中是Prp20p)所催化,它存在于核内并与染色质相结合。
第二章则将着重介绍Prp20p这一蛋白质的基本信息,然后是我们所用的实验方法以及随后所得到的实验结果。Prp20p是RCC1(Regulator of Chromosome Condensation 1)在酿酒酵母中的同源蛋白,它是小GTP酶Gsp1p(Ran在酿酒酵母中的同源蛋白)的鸟苷交换因子(guanine nucleotide exchange factor,GEF)。Prp20p主要由类RCC1结构域(RCC1-like domain,RLD)和N端的核定位信号序列(nuclear localization signal)所组成。Prp20p的类RCC1结构域为典型的七叶螺旋桨结构(seven bladesβ-propeller)。在这个结构中,我们发现一个额外的β-wedge,而且随后我们也证明了这个区域参与了Prp20p和Gsp1p的相互作用。然后我们构建了Prp20p-Gsp1p的复合物模型,并用分子动力学模拟(molecular dynamics simulations)进行了优化。此外,我们还研究了Prp20p的组蛋白结合特性,意外地发现其与RCC1的组蛋白结合特性有显著的区别。
第三章则介绍人源锌指蛋白DESR1的溶液结构研究。人源DESR1属于一个高度保守的CSL锌指蛋白家族(Pfam: PF05207)。DESR参与了翻译延伸因子2(translation elongation factor 2,eEF-2)的翻译后修饰的第一步过程,使第715位的组蛋白(H715,在酵母中是H699)生成白喉酰胺(diphthamide),这是ADP核糖基化(ribosylation)的靶位点。另外有实验证实了DESR1在鼠中对于胚胎和胎盘发育的重要性。我们用三维核磁共振波谱的方法解析了这个小蛋白的溶液结构。随后拿它跟其在鼠和酵母中的同源蛋白(mDESR1和KTI11)进行了结构比较,显示出结构的保守性以及些许的微小差异。最后讨论了这一类CSL锌指蛋白的分类问题。
In this thesis, we will present the 1.9 ? crystal structure of Prp20p from Saccharomyces cerevisiae by X-ray crystallography and the solution structure of human DESR1, a CSL zinc-binding protein by multidimensional NMR spectroscopy.
The main part of this thesis will be divided into three chapters.
Chapter 1 is a review of nucleocytoplasmic transport which is an important cellular physiological process that Prp20p participates in and plays key roles in it. In eukaryotic cells, the different composition of the nucleus and cytoplasm is maintained by the transport of macromolecules through the nuclear pore complex (NPC). Nuclear proteins are imported into the nucleus by importins, while most of the RNAs are exported into the cytoplasm by exportins. The directionality of the transport is determined by the RanGTP gradient across the nuclear envelope. Ran in the nucleus is mainly in the GTP-bound form at high concentrations, and mostly in the GDP-bound form in the cytoplasm. Importins bind their cargo in the cytoplasm, with or without the assistance of adaptor proteins, and the cargo will be released by the binding of RanGTP to importins. On the contrary, complexes are formed in the nucleus by exportins and RanGTP and cargo, and then the complexes are dissociated in the cytosol after the hydrolysis of GTP to GDP. GTP hydrolysis requires a RanGAP (Ran GTPase-activating protein) in cytosol, while the exchange of GTP to GDP is catalyzed by a guanine nucleotide exchange factor (GEF, RCC1 in mammals and Prp20p in baker’s yeast) in nuclear.
In chapter 2, we will focus on the introduction of Prp20p and the experimental methods that we used and the subsequent results we obtained. Prp20p, also terms as Srm1, is the functional homolog of mammalian RCC1 (Regulator of Chromosome Condensation 1) in Saccharomyces cerevisiae, and acts as the guanine nucleotide exchange factor (GEF) for Gsp1p (Ran in mammals). Prp20p/RCC1 plays important roles throughout the whole cell cycle, particularly in nucleocytoplasmic transport and mitosis regulation. Prp20p is composed of a NLS (nuclear localization signal)-containing N-terminal tail and a typical RCC1-like domain (RLD) that contains seven RCC1 repeats. Prp20p also functions as a linker between nuclear pore complex (NPC) and chromatin and play important role in the NPC-mediated boundary activity (BA) in the gene regulation. Here we present the 1.9 ? crystal structure of Prp20p, which appears as a classical seven bladesβ-propeller as expected. From this structure, we found an additionalβ-wedge and it was proved to be an important element in the interaction between Prp20p and Gsp1p. We then built the complex model of Prp20p and Gsp1p and optimized it by molecular dynamics (MD) simulations. Besides, we surprisingly discovered that the histone binding properties of Prp20p are different to that of RCC1.
Our work on the solution structure of human DESR1 will present in chapter 3. DESR1, also designated Dph3, is required for the first step in the posttranslational modification of translation elongation factor 2 (eEF-2) at H715 (H699 in yeast) that yields diphthamide, the target site for ADP ribosylation by DT and ETA. Succeeding investigation had attested to the physiological importance of Dph3 in mouse embryonic and placental development. Then we compared the 3D structure of DESR1 with its homologs in mouse (mDESR1) and yeast (KTI11), which showed the conservation and minor difference. Lastly, we discussed the classification of these CSL zinc finger-containing proteins.
第一章先介绍一下Prp20p所参与的核质输运这一重要的细胞生理过程的背景综述。在真核细胞中,核质的不同物质组成是由具有选择性和方向性的大分子的跨膜运输所维持的。核蛋白经由一类称为输入蛋白(importins)的核转运蛋白(karyopherins)运送至核内,而大半部分的RNA则通过输出蛋白(exportins)转运出核。这种运输的方向性是由RanGTP的梯度(核内是高浓度的RanGTP,而细胞溶质中则是低浓度的RanGTP)决定的。在胞质中缺乏RanGTP的情况下结合货物蛋白,然后在核质中随着RanGTP的结合而将货物蛋白释放。相反在核内,输出蛋白与RanGTP以及货物蛋白形成复合物,运送到胞质中之后随着GTP水解成GDP而解离。GTP的水解需要存在于细胞质中的RanGAP(Ran GTPase-activating protein)。反过来,GTP到GDP的交换是由鸟苷交换因子(GEF,在哺乳动物中是RCC1,在酿酒酵母中是Prp20p)所催化,它存在于核内并与染色质相结合。
第二章则将着重介绍Prp20p这一蛋白质的基本信息,然后是我们所用的实验方法以及随后所得到的实验结果。Prp20p是RCC1(Regulator of Chromosome Condensation 1)在酿酒酵母中的同源蛋白,它是小GTP酶Gsp1p(Ran在酿酒酵母中的同源蛋白)的鸟苷交换因子(guanine nucleotide exchange factor,GEF)。Prp20p主要由类RCC1结构域(RCC1-like domain,RLD)和N端的核定位信号序列(nuclear localization signal)所组成。Prp20p的类RCC1结构域为典型的七叶螺旋桨结构(seven bladesβ-propeller)。在这个结构中,我们发现一个额外的β-wedge,而且随后我们也证明了这个区域参与了Prp20p和Gsp1p的相互作用。然后我们构建了Prp20p-Gsp1p的复合物模型,并用分子动力学模拟(molecular dynamics simulations)进行了优化。此外,我们还研究了Prp20p的组蛋白结合特性,意外地发现其与RCC1的组蛋白结合特性有显著的区别。
第三章则介绍人源锌指蛋白DESR1的溶液结构研究。人源DESR1属于一个高度保守的CSL锌指蛋白家族(Pfam: PF05207)。DESR参与了翻译延伸因子2(translation elongation factor 2,eEF-2)的翻译后修饰的第一步过程,使第715位的组蛋白(H715,在酵母中是H699)生成白喉酰胺(diphthamide),这是ADP核糖基化(ribosylation)的靶位点。另外有实验证实了DESR1在鼠中对于胚胎和胎盘发育的重要性。我们用三维核磁共振波谱的方法解析了这个小蛋白的溶液结构。随后拿它跟其在鼠和酵母中的同源蛋白(mDESR1和KTI11)进行了结构比较,显示出结构的保守性以及些许的微小差异。最后讨论了这一类CSL锌指蛋白的分类问题。
In this thesis, we will present the 1.9 ? crystal structure of Prp20p from Saccharomyces cerevisiae by X-ray crystallography and the solution structure of human DESR1, a CSL zinc-binding protein by multidimensional NMR spectroscopy.
The main part of this thesis will be divided into three chapters.
Chapter 1 is a review of nucleocytoplasmic transport which is an important cellular physiological process that Prp20p participates in and plays key roles in it. In eukaryotic cells, the different composition of the nucleus and cytoplasm is maintained by the transport of macromolecules through the nuclear pore complex (NPC). Nuclear proteins are imported into the nucleus by importins, while most of the RNAs are exported into the cytoplasm by exportins. The directionality of the transport is determined by the RanGTP gradient across the nuclear envelope. Ran in the nucleus is mainly in the GTP-bound form at high concentrations, and mostly in the GDP-bound form in the cytoplasm. Importins bind their cargo in the cytoplasm, with or without the assistance of adaptor proteins, and the cargo will be released by the binding of RanGTP to importins. On the contrary, complexes are formed in the nucleus by exportins and RanGTP and cargo, and then the complexes are dissociated in the cytosol after the hydrolysis of GTP to GDP. GTP hydrolysis requires a RanGAP (Ran GTPase-activating protein) in cytosol, while the exchange of GTP to GDP is catalyzed by a guanine nucleotide exchange factor (GEF, RCC1 in mammals and Prp20p in baker’s yeast) in nuclear.
In chapter 2, we will focus on the introduction of Prp20p and the experimental methods that we used and the subsequent results we obtained. Prp20p, also terms as Srm1, is the functional homolog of mammalian RCC1 (Regulator of Chromosome Condensation 1) in Saccharomyces cerevisiae, and acts as the guanine nucleotide exchange factor (GEF) for Gsp1p (Ran in mammals). Prp20p/RCC1 plays important roles throughout the whole cell cycle, particularly in nucleocytoplasmic transport and mitosis regulation. Prp20p is composed of a NLS (nuclear localization signal)-containing N-terminal tail and a typical RCC1-like domain (RLD) that contains seven RCC1 repeats. Prp20p also functions as a linker between nuclear pore complex (NPC) and chromatin and play important role in the NPC-mediated boundary activity (BA) in the gene regulation. Here we present the 1.9 ? crystal structure of Prp20p, which appears as a classical seven bladesβ-propeller as expected. From this structure, we found an additionalβ-wedge and it was proved to be an important element in the interaction between Prp20p and Gsp1p. We then built the complex model of Prp20p and Gsp1p and optimized it by molecular dynamics (MD) simulations. Besides, we surprisingly discovered that the histone binding properties of Prp20p are different to that of RCC1.
Our work on the solution structure of human DESR1 will present in chapter 3. DESR1, also designated Dph3, is required for the first step in the posttranslational modification of translation elongation factor 2 (eEF-2) at H715 (H699 in yeast) that yields diphthamide, the target site for ADP ribosylation by DT and ETA. Succeeding investigation had attested to the physiological importance of Dph3 in mouse embryonic and placental development. Then we compared the 3D structure of DESR1 with its homologs in mouse (mDESR1) and yeast (KTI11), which showed the conservation and minor difference. Lastly, we discussed the classification of these CSL zinc finger-containing proteins.
引文
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