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研究生:許育晟
研究生(外文):Yu-Cheng Hsu
論文名稱:幹細胞之調控蛋白質分子和DNA的三維構形和生化功能分析-初期研究
論文名稱(外文):A Preliminary Study- Analysis of Three-Conformation and Biochemical Function of the Stem Cell Regulatory Protein & DNA
指導教授:王清正
指導教授(外文):Ching-Cheng Wang
學位類別:碩士
校院名稱:國立成功大學
系所名稱:製造工程研究所碩博士班
學門:工程學門
學類:機械工程學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:英文
論文頁數:81
中文關鍵詞:生化功能幹細胞調控蛋白質三維構形
外文關鍵詞:three- conformationstem cells regulatory proteinbiochemical function
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人體的正常發育包括質和量的變化,前者指的是細胞分化,後者指的是細胞增殖。發育過程從生殖細胞開始,經受精奠定新生命的基礎,而後透過細胞分裂和型態發生等複雜的變化,發育成一個新的個體。基因表現指的是指位於染色體結構上的去氧核糖核酸上所賀載的遺傳訊息與蛋白質一系列相互作用的結果。而細胞分化和細胞增殖是一種連續的基因表現調節過程。基因表現是指從特定的去氧核糖核酸基因序列到合成特定蛋白質一連串的步驟。
已知細胞分化和增殖是細胞發育過程中,隨著時間,基因層層排列並逐漸表現不同的細胞分化型態。既然細胞的分化和增殖結果是去氧核糖核酸上的基因決定,決定序列上哪些基因功能開啟或關閉,其關鍵就是去氧核糖核酸上的轉錄因子。而這些能附著於去氧核糖核酸上的轉錄因子,在彼此結合的三度構形中,就牽涉到核酸和轉錄因子之間的化學作用力。因為任何生物體內化學或物理變化,都牽涉到能量變化。其中當然包括在細胞分化或增殖過程中,雙股去氧核糖核酸和轉錄因子間化學鍵結的不斷地破壞和形成。
更由於目前國內外對蛋白質功能研究尚在發展階段,從工程的角度來觀看整個細胞分化和增殖的相關研究寥寥無幾。因此,實有必要以結構力學的方式,對蛋白質三維構形,作一個綜合整理分析,藉以釐清其中的重要變因及通則。藉以能量的觀點,來計算細胞的去氧核糖核酸和蛋白質靜態鍵結的能量變化結果,以提供我們對控制細胞分化和增殖過程的另一個思考角度。故本論文的初期研究重點是將目前研究文獻整個參與幹細胞分化和增殖過程的關鍵蛋白質整理歸納,並從分子層次上,由核酸和蛋白質相互結合的空間三維構形來分析幹細胞分化和增殖,並希望進一步配合化學鍵、立體位向、或特定能階之選擇性激發,以調控生物化性之研究。所以,本研究將利用三度空間構形分析軟體,輔以靜態鍵結能量,從分子的層次來分析參與幹細胞分化與增殖過程的蛋白質,提出調控幹原細胞增殖與分化的充分且必要的條件。
The normal human growth includes the qualitative and quantitative differences, the former means to the cell differentiation, and the latter means to the cell proliferation. From the fertilization, the germ cells grow to a new individual by cell proliferation and differentiation. Gene expression means to the result of a series of interactions between proteins and codes on DNA of the chromosome. Cell differentiation and proliferation are a series of process of gene expression regulation.
As time goes on, genes increasingly express various cell types in order in cell proliferation and differentiation. Since genes on DNA determine the results of cell differentiation and proliferation. Genes on DNA determine to turn on or off by transcription factors. However, the conformations of these transcription factors attached to DNA involve in chemical interactions between DNA and transcription factors, because any biochemical reactions in vivo involve in energy change. Of course, the chemical bond continuously form and destroy between double helices of DNA and transcription factors.
Owing to the researches in proteins’ functions are increasingly developing in the world, the related researches are rare to analyze the entire differentiation and proliferation. Therefore, it is necessary to analyze the entire 3-D conformations of proteins so that we can recognize clearly the important factors and general principles. By the analysis of energy, to calculate the energy difference from beginning maybe offer to another opinion of controlling cell proliferation and differentiation. In this thesis, we preliminary focus on the 3-D conformation of proteins participating in cell differentiation and proliferation in level of the molecular, and further we will search for bond-selective, region-selective or mode-selective means to modify and manipulate biochemical reactivity in engineering. We further use the 3-D software of molecular level and minimum static energy to analyze the three-dimension conformation, then, find out the sufficient and necessary conditions to explain the process of differentiation and proliferation.
MANDARIN ABSTRACT……………………………………………Ⅰ
ENGLISH ABSTRACT………………………………………………Ⅱ
MANDARIN ACKNOWLEDGEMENTS……………………………...Ⅳ
TABLE OF CONTENTS………………………………………………Ⅴ
LIST OF TABLES……………………………………………………Ⅸ
LIST OF FIGURES…………………………………………………….Ⅹ
CHAPTER 1.INTRODUCTION………………………………………..1
CHAPTER 2. METHODOLOGY………………………………………4
CHAPTER 3. THE HUMAN STEM CELLS AND GERM CELLS……7
3.1 The Stem Cells……………………………………………………………..7
3.2 Early Development of Tissues and Cell Types…………………………….9
3.3 Cells into Tissues & Tissues into Organs…………………………………10
3.4 Body Plan and Rudimentary Tissues Form Early Embryonic
Development……………………………………………………………..10
3.5 Cell-Type Specification in Animals………………………………………11
3.6 The Germ Cells and Methylation…………………………………………12

CHAPTER 4. CELL PROLIFERATION AND DIFFERENTIATION
4.1 Gene Transcription, Translation, and Protein Synthesis………………….15
4.2 Cell Proliferation…………………………………………………………16
4.2.1 Definition of the Cell Proliferation…………………………………...16
4.2.2 The Cell-Division Cycle……………………………………………...17
4.2.3 The Cell-Cycle Control System Is a Protein-Kinase-Based Machine.
……………………………………………………………………...19
4.2.4 The Key Proteins of the Proliferation in the M Phase………………19
4.2.5 The Simple Process and Related Proteins of the Cell Proliferation…20
4.3 Cell Differentiation……………………………………………………...20
4.3.1 Definition of the Cell Differentiation………………………………..20
4.3.2 Different Cell Types Synthesis Different Sets of Protein…………...21
4.3.3 A Cell Can Change the Expression of Its Genes in Response to External Signals………………………………………………………………..21
4.3.4 Gene Expression Can Be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein……………………………….…….....21
4.3.5 The Simple Process and Related Proteins of the Cell Differentiation
……………………………………………………………………...22
CHAPTER 5. DNA STRUCTURAL FUNDAMENTALS
5.1 The Double Helix DNA………………………………………………….23
5.2 The Types of DNA………………………………………………………25
5.2.1 A-DNA……………………………………………………………...25
5.2.2 B-DNA……………………………………………………………...25
5.2.3 Z-DNA……………………………………………………………...25
5.3 The Backbone Torsion Angles and Correlated Flexibility………………25
5.4 Helical Parameters in DNA Three- Dimension Conformation………….26
5.5 Groove Dimensions in DNA Double Helices…………………………...27

CHAPTER 6. DNA BINDING PROTEINS AND THE COMFORMATION OF DNA-BINDING DOMAINS
6.1 DNA-Binding Proteins Can Be Categorized in Functional Terms…….28
6.2 DNA Binding Factors………………………………………………….28
6.3 Principles of Protein-DNA Recognition……………………………….29
6.3.1 Direct Readout and Indirect Readout……………………………....29
6.3.2 Proteins Can Read Outside of the DNA Helix……………………..29
6.3.3 Major Groove Interaction – the α-Helix as the Recognition Element
…………………………………………………………………….31
6.3.4 Minor Groove Recognition………………………………………...31
6.3.5 Zinc Finger and Other Recognition Modes………………………..31
6.4 The Conformation of DNA-Binding Domains…………………….…..31
6.4.1 Helix-Turn-Helix (HTH) Containing DNA-Binding Domains……32
6.4.1.1 HTH Motifs………………………………………………...…32
6.4.1.2 α/β HTH Motifs…………………………………………...32
6.4.2 Zinc-Containing DNA-Binding Domains…………………………35
6.4.2.1 Classical Zinc Fingers (Cys2His2)…………………………….35
6.4.2.2 Nuclear Hormone Receptor (Cys4Cys4)………………………35
6.4.2.3 GATA Factors (Cys2Cys2)……………………………………35
6.4.2.4 Cys6Zn2 Binuclear Cluster……………………………………36
6.4.3 Other DNA-Binding Domains That Use α-Helices to Bind DNA
6.4.3.1 MADS………………………………………………………...40
6.4.3.2 bZIP Motif……………………………………………………40
6.4.3.3 bHLH and bHLHZ Motifs……………………………………40
6.4.3.4 High Mobility Group Domain………………………………..40
6.4.4 DNA-Binding Domains That use β-Strands to Bind DNA……..44
6.4.5 β-Barrels and β-Sandwiches…………………………………..46
6.4.5.1 β-Barrels……………………………………………………..46
6.4.5.2β-Sandwiches………………………………………………..46
6.4.6 Overall Motifs……………………………………………………48

CHAPTER 7. DISCUSSIONS AND CONCLUSIONS…………...50

REFERENCES…………………………………………………….52
APPENDIX A: CELLS OF THE ADULT HUMAN BODY……...61
APPENDIX B: THE SIMPLE PROCESS OF CELL
PROLIFERATION……………………………….71
APPENDIX C: THE SIMPLE PROCESS OF CELL DIFFERENTIATION…………………………….72
APPENDIX D: THE LIST OF THREE DNA’s FEATURES…….73
APPENDIX E: DNA-BINDING PROTEINS OF HUMAN SELECTED FROM THE NDB………………………………..74
APPENDIX F: PROTEIN-DNA COMPLEXES OF HUMAN SELECTED FROM THE NDB………………….76
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