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研究生:蘇國良
研究生(外文):Kuo-Liang Su
論文名稱:決定人類抗酶抑制子二聚體結構的關鍵因子
論文名稱(外文):Critical Factors Determining the Dimeric Structure Formation of Human Antizyme Inhibitor
指導教授:洪慧芝洪慧芝引用關係
學位類別:博士
校院名稱:國立中興大學
系所名稱:生命科學系所
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:90
中文關鍵詞:鳥胺酸脫羧酶抗酶抗酶抑制子多元胺分析級超高速離心機四級結構
外文關鍵詞:ornithine decarboxylaseAntizymeantizyme inhibitorpolyamineanalytical ultracentrifugationquaternary structure
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Chinese Abstract中文摘要
人類鳥胺酸脫羧酶(ornithine decarboxylase,ODC,EC 4.1.1.17)為依賴5’-磷酸吡多醛 (pyrodoxal 5’-phosphate,PLP)輔酶之酵素,主要催化體內多元胺合成起始與速率決定步驟的酵素。此酵素以二聚體型式存在,需兩個鳥胺酸脫羧酶的單體活性中心聚合形成同源二聚體。抗酶(antizyme,AZ)可以跟鳥胺酸脫羧酶結合,形成異源二聚體,使鳥胺酸脫羧酶被26S蛋白解體降解,並不需要先跟泛素結合。人類抗酶抑制子(human antizyme inhibitor,AZI)以單體存在,與鳥胺酸脫羧酶屬高度同源的蛋白但不具有酵素活性,抗酶抑制子與抗酶的結合能力大於鳥胺酸脫羧酶,因此可以回復鳥胺酸脫羧酶的活性。我們的研究目標是經由探討鳥胺酸脫羧酶與抗酶抑制子的四級結構來確認重要的胺基酸位置。透過鳥胺酸脫羧酶與抗酶抑制子的序列比對,找出形成二聚體胺基酸位置的不同,將抗酶抑制子序列(S277、S331、E332及D389)改成鳥胺酸脫羧酶的序列(R277、Y331、D332及Y389),這些突變種利用分析級超高速離心機來分析沉降係數大小分布。從沉降係數及連續性大小分布分析可以得到野生種鳥胺酸脫羧酶是以二聚體分布。而從自我單體二聚體結合分析得到解離常數為0.18 μM。相對的野生種抗酶抑制子呈現單體存在而解離常數為84.0 μM。AZI-S331Y突變種呈現在單體及二聚體平衡中,解離常數為40.7 μM明顯比野生種低。AZI-S331Y-D389Y、AZI-S331Y-D389Y-S277R及AZI-S331Y-D389Y-S277R-E332D均為二聚體分布其解離常數分別為2.7 μM、1.3 μM及0.10 μM,很接近於野生種鳥胺酸脫羧酶。然而各種抗酶抑制子突變種如果沒有S331Y這個點突變,解離常數跟野生種抗酶抑制子並沒有差異。我們的研究成果發現胺基酸331這個位置是鳥胺酸脫羧酶及抗酶抑制子形成二聚體最主要的關鍵因子。
English Abstract
Human ornithine decarboxylase (ODC; EC 4.1.1.17) is a pyrodoxal 5’-phosphate (PLP) dependent enzyme that catalyzes the first and rate-limiting step in polyamine biosynthesis. The enzyme is an obligate homodimer, and the two identical active sites are formed at the dimer interface between the monomers. Antizyme (AZ) interacts with ODC to form heterodimer that is then degraded by 26S proteasome without ubiquitin binding. Human antizyme inhibitor (AZI) is highly homologous to ODC but lacks enzymatic activity, and it exists as a monomer. AZI has higher affinity toward AZ than ODC and that may rescue ODC enzyme activity. In this study, we aim to identify the essential amino acid residues governing the quaternary structure formation for ODC and AZI. Based on the multiple sequence alignments of ODC and AZI, the non-conserved amino acid residues in the putative dimer-interface of AZI (S277, S331, E332 and D389) were changed to the amino acid residues of ODC (R277, Y331, D332 and Y389, respectively). Analytical ultracentrifugation were used to obtain the size-distribution of these AZI mutants. Sedimentation velocity and continuous size distribution analysis demonstrated that the wild-type ODC (ODC-wt) is a dimer with a disassociation constant (Kd) of 0.18 μM. In contrast, the wild-type AZI (AZI-wt) displayed as a monomer with a Kd of 84.0 μM. The AZI-S331Y mutant displayed a monomer-dimer equilibrium with a Kd of 40.7 μM showing a lower Kd than that of AZI-wt. The double mutant, AZI-S331Y-D389Y, triple mutant, AZI-S331Y-D389Y-S277R and quadruple mutant, AZI-S331Y-D389Y-S277R-E332D displayed as a dimer with a Kd value of 2.7 μM, 1.3 μM and 0.10 μM, respectively, close to that of ODC-wt. The AZI-mutants without S331Y showed similar Kd values to that of AZI-wt. Our findings indicated that the residue 331 play a key role determining the dimer formation of ODC and AZI.
CONTENTS

Table contents
iv

Figure contents v

Abbreviations vii

Chinese Abstract 1
English Abstract 2
Introduction 3
Human ornithine decarboxylase 3
ODC and polyamines 3
ODC structure 5
ODC regulation 5
Antizyme inhibitor can rescue ODC from degradation 6
AZI increases cell proliferation 6
Specific aims 7
Material and methods 9
Chemicals and enzymes 9
Plasmids 10
Expression and purification of ODC-wt, AZI-wt, AZI mutants and AZ 10
Plasmid DNA extraction 10
Competent cell preparation 11
Transformation 11
Site-directed mutagenesis 11
Protein expression and purification 13
Buffer exchange 13
Structural studies by using analytical ultracentrifugation 14
Examination of the quaternary structural change by analytical ultracentrifugation 14
Continuous size distribution analysis 15
Self-association and hetero-association of ODC-wt, AZI-wt and AZI mutants by using analytical ultracentrifugation 16
Hetero-binding of ODC-wt, AZI-wt and AZI quadruple mutant with AZ 16
Self-association of ODC-wt, AZI-wt and AZI mutants 16
Hetero-association of ODC-wt, AZI-wt and AZI quadruple mutant with AZ 17
ODC enzyme assay 17
ODC couple reaction assay 17
ODC enzyme activity 18
Relative enzyme activity of ODC inhibited by AZ 18
Rescue of the AZ-inhibited ODC enzyme activity with AZI proteins 19
Result 20
Expression and purification of ODC-wt, AZI-wt, AZI mutants and AZ 20
Structural studies by using analytical ultracentrifugation 20
Hydrodynamic behaviors and sw of ODC-wt, AZI-wt and AZI mutants by sedimentation velocity 20
Size distribution of ODC-wt and AZI-wt proteins 21
Size distribution of AZI single mutant proteins 22
Size distribution of AZI double mutant proteins 22
Size distribution of AZI triple and quadruple mutant proteins 23
Self-association and hetero-association of ODC-wt, AZI-wt and AZI mutants by using analytical ultracentrifugation 23
Self-association of ODC-wt, AZI-wt and AZI single mutants 23
Self-association of AZI double mutants 24
Self-association of AZI triple and quadruple mutants 24
Hetero-association of ODC-wt, AZI-wt and AZI quadruple mutant 25
ODC enzyme assay 25
Enzyme activity assay 26
Relative enzyme activity of ODC inhibited by AZ 26
Rescue of the AZ-inhibited ODC enzyme activity with AZI proteins 26
Discussion 28
Structural variation of human ODC and AZI 28
Factors that determine the dimerization of AZI 28
AZI saves ODC enzyme activity 30
Functional properties of the quadruple mutant S331Y/D389Y/S277R/E332D human AZI protein 30
Conclusion 32
References 33
Tables 45
Figures 53
Appendix 79
Appendix 1 Devices and Equipments 80
Appendix 2 Preparation of medium, reagent and buffer 82
Appendix 3 Curriculum vitae of Kuo-Liang Su 88








Table contents

Table
Page
1. Amino acid residues in the dimer interface of human ODC and AZI 45
2. Sedimentation analysis of human ODC and AZI proteins 46
3. Size distribution analysis of human ODC and AZI-mutants proteins by serial integration 48
4. The dissociation constants of the human ODC and AZI-mutant proteins analyzed by a monomer-dimer rapid self-association model 51
5. The dissociation constants of the human ODC and AZI-mutant proteins analyzed by a hetro-association model 52






















Figure contents

Figure
Page
1. Human ODC homodimer structure 53
2. Role of antizyme and ODC in polyamine metabolism 54
3. Regulation of polyamine homeostasis by AZI-suggested model 55
4. The interaction of dimer interface in ODC 56
5. The amino acid sequence alignment of human ODC-wt and AZI-wt proteins 57
6. The interaction of active site in ODC 58
7. The interaction of the amino acid residues R277 in ODC 59
8. The interaction of the amino acid residues Y331 and D332 in ODC 60
9. The interaction of the amino acid residues Y389 in ODC 61
10. Crystal structure and the amino acid residues in the dimer interface for human ornithine decarboxylase (hODC) and mouse antizyme inhibitor (mAZI) 62
11. The pQE-30 vector map 63
12. AZI-wt cDNA and deduced protein sequence 64
13. ODC couple reaction mechanism 65
14. SDS-PAGE analysis of proteins 66
15. Sedimentation velocity experiments of AZI-wt 67
16. Continuous sedimentation coefficient distribution of ODC-wt, AZI-wt and AZI single mutants 69
17. Continuous sedimentation coefficient distribution of AZI double mutants 70
18. Continuous sedimentation coefficient distribution of AZI triple and quadruple mutants 71
19. Dissociation constant of the AZI-S331Y/D389Y/S277R/E332D protein analyzed by monomer-dimer rapid self-association model 72
20. Continuous sedimentation coefficient distribution for ODC-wt, AZI-wt and AZI quadruple mutant bound AZ 73
21. Hetero-association model for ODC-wt, AZI-wt and AZI quadruple mutant bound AZ 74
22. Dissociation constant of the AZI-S331Y/D389Y/S277R/E332D protein analyzed by hetero-association model 75
23. Absorbance consumption of NADH analog spectrum in couple reaction assay of ODC enzyme activity 76
24. Relative enzyme activity of ODC inhibited by AZ 77
25. Rescue of the AZ-inhibited ODC enzyme activity with AZI 78
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