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研究生:黃瀚賜
研究生(外文):Huang, Han-Tze
論文名稱:澱粉吸附區與醣類交互作用之模型
論文名稱(外文):An Interaction Model between Glycans and Starch Binding Domain of Rhizopus oryzae Glucoamylase
指導教授:張大慈
指導教授(外文):Chang, Dah-Tsyr
學位類別:碩士
校院名稱:國立清華大學
系所名稱:分子與細胞生物研究所
學門:生命科學學門
學類:生物科技學類
論文種類:學術論文
論文出版年:2012
畢業學年度:100
語文別:英文
論文頁數:118
中文關鍵詞:葡萄糖澱粉酵素澱粉吸附區醣類吸附模組
外文關鍵詞:glucoamylasestarch binding domaincarbohydrate binding module
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米根黴菌 (Rhizopus oryzae) 葡萄糖澱粉酵素 (glucoamylase) 為579個胺基酸組成的醣類水解酶,其整體結構包含胺基端澱粉吸附區 (starch-binding domain, RoSBD)、羧基端酵素催化區及一段高度醣基化的連接片段。RoSBD隸屬於醣類吸附模組 (carbohydrate-binding module, CBM) 家族二十一,對天然澱粉與可溶性多醣具有強結合力。核磁共振與晶體繞射解析證明RoSBD具有兩個配體結合位:第一個結合位由色胺酸47、酪胺酸83、酪胺酸93、及酪胺酸94組成,第二個結合位由酪胺酸32、苯丙胺酸58組成;兩個RoSBD各提供一個不同的配體結合位與單一醣分子結合。一般而言,串接的醣類吸附模組對醣類的結合力較強;因此本研究設計以一段短胜肽鏈串接兩個RoSBD,並探討其對醣類的結合力值變化。利用恆溫滴定熱量計 (isothermal titration calorimetry, ITC) 測量雙聚體RoSBD與多種不同醣類的結合力。ITC實驗結果顯示雙聚體RoSBD對多種不同醣類的結合力都高於單體RoSBD。除此之外,本研究亦將RoSBD的主要配體結合胺基酸突變成丙胺酸,根據測量突變蛋白質對不同醣類之結合力變化配合RoSBD之三級結構,可預測雙聚體RoSBD和不同醣類之結合模式。對於短鏈或環形醣類而言,以結晶繞射解析的結果去分析,雙聚體中兩個RoSBD分子各提供一個不同的配體結合位與醣分子結合。若以恆溫滴定熱量計的數據去分析,在雙聚體RoSBD之N端的酪胺酸32對於短鏈醣類的結合是很重要的,然而在雙聚體RoSBD之C端的酪胺酸32對於環形醣的結合是很重要的;而對於長鍊醣類而言,酪胺酸32扮演著極為重要的角色,推測雙聚體中兩個RoSBD分子的皆以酪胺酸32與長鏈醣分子結合,兩個RoSBD分子形成面對面之模型。本研究發現RoSBD會和不同種類的醣類有不同的結合模型。了解RoSBD和醣類的結合模式,能更深入探討醣類吸附模組與不同醣類結合的分子機制。
The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD) belongs to carbohydrate binding module (CBM) family 21 with high binding affinities toward raw starches, and contains two ligand binding sites at opposite position (Site I: Trp47, Tyr83 and Tyr94; Site II: Tyr32, Phe58). Three dimensional structure reveals that two RoSBD molecules hold the same sugar ligand by different binding sites. Natural CBMs in tandem repeat show higher ligand-binding affinity than single CBM does, yet whether two cooperative RoSBDs enhance ligand binding properties remains to be investigated. In this study, dimeric RoSBD was constructed with a short peptide linker between two RoSBD units. Isothermal titration calorimetry (ITC) data indicated that dimeric RoSBD processed higher affinities toward a series of glycans than monomeric RoSBD. Moreover, site-directed mutagenesis of major ligand binding residues Y32 and W47 on each domain of dimeric RoSBD revealed determining factors by ITC analysis. In addition, in silico structure modeling was carried out by quantitative measurement of binding affinity between wild-type/mutant dimeric RoSBD and soluble starch by ITC and published X-ray crystallography data. For short glycans such as maltoheptaose (Glc7), or cyclic ligand β-cyclodextrin (βCD), two RoSBD molecules might hold on the same sugar ligand by different binding sites based on X-ray crystallography data to predict. However, according to ITC data, Y32 on the N-terminal RoSBD played a crucial role in Glc7 binding and Y32 on the C-terminal RoSBD was important for βCD binding. For long chain glycans, Y32 in both two RoSBD molecules played a crucial role in ligand binding, indicated that two binding site II of dimeric RoSBD bound to a same glycan to form RoSBD/RoSBD interface. In conclusion, RoSBD might bind to various glycans in different interaction models. The interaction model between RoSBD and glycans will greatly increase our understanding in the molecular mechanisms of CBM functions.
List of Content

中文摘要 I
Abstract II
Acknowledgement......................................................................................................IV
Table of Contents V
List of Figures VII
List of Tables IX
List of Appendix X
Abbreviations XI

Chapter 1 Introduction 1
1.1 Carbohydrates 1
1.2 Starch 1
1.3 Glucoamylase 2
1.4 Carbohydrate binding module (CBM) 4
1.5 Starch binding domain (SBD) 9
1.6 Single chain antibody variable region fragment 13
1.7 Research motivation 15

Chapter 2 Materials and Methods 17
2.1 Microbial strains, media and plasmid 17
2.2 Construction of plasmid 17
2.3 Site-directed mutagenesis 18
2.4 Competent cell preparation 19
2.5 Escherichia coli heat-shock transformation 19
2.6 Confirmation of colonies by in situ PCR 20
2.7 Mini-preparation of plasmid 20
2.8 Recovery of DNA fragment 21
2.9 Restriction enzyme digestion and Ligation 21
2.10 Small scale expression of wild-type and mutant dimeric RoSBDs in E. coli 22
2.11 Purification of wild-type and mutant dimeric RoSBDs by amylose column chromatography 22
2.12 Buffer exchange and determination of protein concentration 23
2.13 Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) 24
2.14 Saturation binding assay 24
2.15 Thermodynamic measurement of binding to soluble glycans by isothermal titration calorimetry (ITC) 25
2.16 Feature-incorporated alignment (FIA)-based homology modeling 25

Chapter 3 Results 26
3.1 Characterization of dimeric RoSBD 26
3.2 Construction of pET23a-Rosbd-(g4s)1-Rosbd 26
3.3 Small scale expression of dimeric RoSBD 27
3.4 Purification of RoSBD-(G4S)3-RoSBD by amylose column chromatography 28
3.5 Quantitative measurement of binding affinity between RoSBD-(G4S)3- RoSBD and soluble glycans 29
3.6 Construction of RoSBD-(G4S)3-RoSBD mutants 31
3.7 Small scale expression of RoSBD-(G4S)3-RoSBD mutants 33
3.8 Purification of RoSBD-(G4S)3-RoSBD mutants by amylose column
chromatography 34
3.9 Quantitative measurement of binding affinity between RoSBD-(G4S)3- RoSBD mutants and soluble glycans 35
3.10 Depletion isotherm of wild-type/mutant RoSBD-(G4S)3-RoSBDs………...40
3.11 Large scale purification of RoSBD-(G4S)3-RoSBD………………………...41

Chapter 4 Discussion 43
4.1 Predicted RoSBD-(G4S)3-RoSBD structure 43
4.2 Structure comparison between SBD and tandem repeat CBMs……… .46
4.3 Role of CBMs in immune system…………………………………………….48

Figures 51
Tables 96
References 105
Appendix 112


List of Figures

Fig. 1-1 Schematic diagram of amylose and amylopectin……………………….2
Fig. 1-2 Different modular arrangements found in glucoamylases……………..3
Fig. 1-3 Structure of glucoamylase………………………………………………..4
Fig. 1-4 CBM distribution in different proteins………………………………….5
Fig. 1-5 CBM distribution in different proteins………………………………….7
Fig. 1-6 Carbohydrate binding modules containing starch binding activities 8
Fig. 1-7 The three dimensional structure of RoSBD 10
Fig. 1-8 The overall structures of the RoSBD complexes 12
Fig. 1-9 RoSBD molecules cooperated in ligand binding 13
Fig. 1-10 Structures of antibody and single chain antibody variable region fragment 14
Fig. 3-1 Small scale expression of RoSBD-(G4S)1-RoSBD 51
Fig. 3-2 Small scale expression of RoSBD-(G4S)2-RoSBD 52
Fig. 3-3 Small scale expression of RoSBD-(G4S)3-RoSBD 53
Fig. 3-4 Verification of expression of dimeric RoSBDs by Western blot analysis 54
Fig. 3-5 Purification of RoSBD-(G4S)3-RoSBD by amylose resin………………55
Fig. 3-6 Exact pI value of native RoSBD-(G4S)3-RoSBD ……………………....56
Fig. 3-7 Molecular weight of native RoSBD-(G4S)3-RoSBD 57
Fig. 3-8 Binding affinity between RoSBD-(G4S)3-RoSBD and αCD 58
Fig. 3-9 Binding affinity between RoSBD-(G4S)3-RoSBD and βCD 59
Fig. 3-10 Binding affinity between RoSBD-(G4S)3-RoSBD and γCD 60
Fig. 3-11 Binding affinity between RoSBD-(G4S)3-RoSBD and soluble starch 61
Fig. 3-12 Binding affinity between RoSBD-(G4S)3-RoSBD and DP17 62
Fig. 3-13 Binding affinity between RoSBD-(G4S)3-RoSBD and Glc7 63
Fig. 3-14 Binding affinity between RoSBD-(G4S)3-RoSBD and Glc3 64
Fig. 3-15 Binding affinity between RoSBD-(G4S)3-RoSBD and iGlc3 65
Fig. 3-16 Small scale expression of RoSBD(Y32A)-(G4S)3-RoSBD 66
Fig. 3-17 Small scale expression of RoSBD-(G4S)3-RoSBD(Y32A) 67
Fig. 3-18 Small scale expression of RoSBD(W47A)-(G4S)3-RoSBD 68
Fig. 3-19 Small scale expression of RoSBD-(G4S)3-RoSBD(W47A) 69
Fig. 3-20 Verification of of RoSBD(Y32A)-(G4S)3-RoSBD expression by Western blot analysis 70
Fig. 3-21 Verification of of RoSBD-(G4S)3-RoSBD(Y32A) expression by Western blot analysis 71
Fig. 3-22 Verification of of RoSBD(W47A)-(G4S)3-RoSBD and RoSBD(W47A)-(G4S)3-RoSBD expression by Western blot analysis 72
Fig. 3-23 Purification of RoSBD(Y32A)-(G4S)3-RoSBD by amylose resin 73
Fig. 3-24 Purification of RoSBD-(G4S)3-RoSBD(Y32A) by amylose resin 74
Fig. 3-25 Purification of RoSBD(W47A)-(G4S)3-RoSBD by amylose resin 75
Fig. 3-26 Purification of RoSBD-(G4S)3-RoSBD(W47A) by amylose resin 76
Fig. 3-27 Binding affinity between mutant RoSBD-(G4S)3-RoSBD and soluble starch 77
Fig. 3-28 Binding affinity between mutant RoSBD-(G4S)3-RoSBD and DP17 79
Fig. 3-29 Binding affinity between mutant RoSBD-(G4S)3-RoSBD and Glc7 81
Fig. 3-30 Binding affinity between mutant RoSBD-(G4S)3-RoSBD and βCD 83
Fig. 3-31 Depletion isotherms of wild-type/mutant RoSBD-(G4S)3-RoSBDs….85
Fig. 3-32 Purification of RoSBD-(G4S)3-RoSBD by amylose resin 86
Fig. 4-1 Three dimensional structure of scFv…………...………………………87
Fig. 4-2 Putative structures of RoSBD-(G4S)3-RoSBD derived ITC data..…....88
Fig. 4-3 Predicted structures of RoSBD-(G4S)3-RoSBD by X-ray
crystallography…………………………………………………………..90
Fig. 4-4 Three dimensional structure of BhCBM25 and BhCBM26……….....91
Fig. 4-5 Three dimensional structure of the tandem CBM41s……………..….92
Fig. 4-6 Schematic diagrams of type I topology and type II topology………...93
Fig. 4-7 An immunoglobulin-like structure of carbohydrate binding proteins. .94
Fig. 4-8 Sequence alignment of immunoglobulin-like proteins………………..95











List of Tables

Table 1 Properties of dimeric RoSBDs 96
Table 2 Thermodynamic parameters of RoSBD-(G4S)3-RoSBD –glycan interaction…………………………………………………………….. ..97
Table 3 Ligand binding constants of RoSBD and RoSBD-(G4S)3-RoSBD 98
Table 4 The reduction rates of dissociation constant of RoSBD-(G4S)3-RoSBD comparing to RoSBD 99
Table 5 Thermodynamic parameters of wild-type and mutant RoSBD-(G4S)3- RoSBD binding to soluble starch, DP17, Glc7, and βCD 100
Table 6 Ligand binding constants of RoSBD-(G4S)3-RoSBD and RoSBD-(G4S)3- RoSBD mutants 102
Table 7 Binding parameters of wild-type/mutant RoSBD-(G4S)3-RoSBD to granular corn starch determined by depletion isotherms………......104


List of Appendix

Appendix I Map for pET23a(+) vector 112
Appendix II DNA fragment encoding (g4s)1-Rosbd amplified by PCR 113
Appendix III Verification of recombinant pET23a-Rosbd-(g4s)1-Rosbd 114
Appendix IV Site-directed mutagenesis of pET23a-Rosbd-(g4s)3 and pET23a- Rosbd………………………………………………………………115
Appendix V Verification of site-directed mutagenesis of pET23a-Rosbd (y32a) -(g4s)3-Rosbd and pET23a-Rosbd-(g4s)3-Rosbd(y32a) 116
Appendix VI Verification of site-directed mutagenesis of pET23a-Rosbd
(w47a)-(g4s)3-Rosbd……………………………………………….117
Appendix VII Verification of site-directed mutagenesis of pET23a-Rosbd
-(g4s)3-Rosbd(w47a) 118




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