臺灣博碩士論文加值系統

人類在日常生活中常常因曝露在化學物質或紫外光下造成體內的氧化壓力(Reactive oxygen species)增加，而其中一種的氧化壓力來源是7,8-dihydro-8-oxodeoxyguanine (8-oxodG)，它可以欺騙A base跟它配對而造成突變。在人體內，專門移除這8-oxodG的酵素是一種糖苷酶：hOGG1，這酵素是base excision repair中的參與酵素之一，它可以移除8-oxodG，使受損的DNA恢復正常。

在酵素基因hogg1上有許多單一核甘酸突變多樣性(single nucleotide polymorphism, SNP)，其中一個在exon7上1245的位置，在大部分的人們都是呈現C base，而有一部分的人們是呈現G base，特別是亞洲人攜帶此SNP的人群比西方人多。因為這個SNP的差異，造成hOGG1移除8-oxodG的能力較低。
攜帶此SNP的基因產物在蛋白質C端上326的位置是cysteine (C)，而正常的hOGG1是serine (S)。許多文獻指出，hOGG1的C端能驅使受損DNA進入active site，而此SNP的cysteine取代原本正常的serine，造成此酵素的功能降低。另外，也有別的文獻指出hOGG1 S326C type會從單體變成雙體形式。

3D domain swapping是一種相同的蛋白質群彼此交換相同的區域而從單體形式轉換成雙體甚至是oligomer的特殊蛋白質現象，我們推敲可能的原因是326位置上的cysteine本身容易受氧化影響而跟同樣在326位置上的cysteine產生雙硫鍵，使其從單體形式變雙體形式(3D domain swapping)進而造成受損的DNA不易進入active site。

因為hOGG1的C端不易解出結晶結構，所以目前也無法得知此機致是如何運作。我們利用GROMACS這套分子動力模擬軟體去推敲此機致是如何運作。雖然我們無法利用GROMACS得知是否會產生雙硫鍵，但是我們可以根據模擬出來的結果解釋C端在hOGG1上所扮演的角色，並與之前的文獻資料相呼應。

我們的研究結果或許無法得知S326C hOGG1是不是因為3D domain swapping而造成差異，但是據我們所知，我們是第一個利用GROMACS模擬hOGG1 C端的人，我們希望可以藉此論文，協助人們研究此議題。

We are exposed to reactive oxygen species (ROS) every day. A common example of ROS is 7,8-dihydro-8-oxodeoxyguanine (8-OxodG), which can pair with an adenine base and result in mutation. In the human body, a glycosylase known as hOGG1 functions as removing the 8-oxodG in a base excision repair process that make damaged DNA regions recover normal functions.
There are many single nucleotide polymorphisms (SNP) on gene hogg1; for instance, a SNP is at the position 1245 of exon 7. The wild type hogg1 possesses a cytosine (C) base at this position but for some people, particularly Asian people, a guanine (G) base substitutes the C base. As a result, on the amino acid sequences, the product of the wild type hogg1 gene, i.e., the hOGG1 protein, possesses a serine at position 326, whereas the above-mentioned SNP mutant type possesses a cysteine at this position (that is, a S326C mutant). Some literatures proposed that the carboxyl-terminus of hOGG1 can force damaged DNA into the functional pocket of hOGG1 and the conformation of the S326C mutant is dimeric . The cysteine on position 326 lets the enzymatic activity reduced indirectly.
Three-dimensional (3D) domain swapping is a phenomenon that molecules of a protein exchanges identical domains with one another and form domain-swapped oligomers, inclusive of dimers. The cysteine on position 326 of the S326C mutant is prone to be oxidized when exposed to ROS. We proposed that the S326C mutant can form 3D domain-swapped dimer because of a disulfide bond linking the Cys326 residues from two S326C molecules (Cys326-Cys326).
Because of the high flexibility, the carboxyl-terminal structure of hOGG1 has not been determined yet. In this study, we used GROMACS, a molecular dynamics simulation software package, to simulate the carboxyl-terminal structure of hOGG1 and tried to determine whether the S326C is a case of 3D domain swapping. Although so far we are not able to make solid conclusion about whether the S326C type from dimers via 3D domain swapping, we are able to explain the function of C-terminus on hOGG1.

中文摘要………………………………………………………………………………i
ABSTRACT…………………………………………………………………………..ii
致謝...…………………………………………………………………………………iv
Contents………………………………………………………………………………v
List of Tables………………………………………………………………………..vii
List of Figures ………………………………………………………………..……..vii
I. INTRODUCTION
1.1 Reactive oxygen species (ROS)…………………………………………...1
1.1.1 7,8-dihydro-8-oxodeoxyguanine(8-OxodG) and it’s mutagenesis….….1
1.2 The human 8-oxoguanine-DNA glycosylase(hOGG1)……………………....4
1.2.1 hOGG1…………………………………………………………………….4
1.2.2 The importance of the single nucleotide polymorphism (SNP) Ser326Cys
on hOGG1……………………………………………………………...…4
1.3 Three-dimensional domain swapping………………………………………..6
1.3.1 Introduction……………………………………………………………….6
1.3.2 Common terms related with 3D domain swapping………………………..7
1.4 Motivation…………………………………………………………………….10
1.4.1 Literature Review I………………………………………………………..10
1.4.2 Literature Review II……………………………………………………….10
1.4.3 3DSwap-pred: A 3D domain swapping prediction web server…………... 11
1.3 Research goal…………………………………………………………………12
II. Materials and Methods………………………………………………………13
2.1 PDB files from the protein data bank…………………………………………13
2.2 3D-Jigsaw………………………………………………………………………15
2.3 Pymol…………………………………………………………………………...15
2.4 GROMACS 4.6.3……………………………………………………………….15
III Results and Discussions
3.1 Structural modeling with 3D-Jigsaw………………………………………..21
3.1.1 Construction of the structural models of hOGG1………………………....21
3.1.2 The role of C-terminus from 3D-Jigsaw……………………………………23
3.1.3 The Hinge Loop……………………………………………………………..25
3.2 MD simulation with GROMACS……………………………….……………...26
3.2.1 The quality of molecular dynamic simulations……………………………..26
3.2.2 The flexibility of wild type and S326C……………………………………….29
3.2.3 The flexibility of Hinge Loop…………………………………………….…..31
3.2.4 The radius of gyration………………………………………………………..33
3.2.5 On the proposed disulfide bond of Cys326…………………………………..35
3.2.6 Experiments regarding the disulfide bonds of S326C………………………38
IV Conclusion……………………………………………………………………… 40
V. Future Works…………………………………………………………………….42

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