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研究生: 房采薇
Fang, Tsai-Wei
論文名稱: 多價性澱粉吸附區之分子設計與功能分析
Molecular Design and Functional Analysis of Multivalent Starch Binding Domain
指導教授: 張大慈
Chang, Margaret Dah-Tsyr
口試委員: 張大慈
呂平江
吳東昆
孫玉珠
許文輝
學位類別: 碩士
Master
系所名稱: 生命科學暨醫學院 - 分子與細胞生物研究所
Institute of Molecular and Cellular Biology
論文出版年: 2011
畢業學年度: 99
語文別: 英文
論文頁數: 122
中文關鍵詞: 米根黴菌澱粉吸附區
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  • 米根黴菌(Rhizopus oryzae)之葡糖澱粉水解酵素(glucoamylase, GA)為含有579個胺基酸之醣類水解酶,其結構包括澱粉吸附區(starch-binding domain, RoSBD)、酵素催化區及一段高度醣基化的連接片段。醣類吸附模組(carbohydrate-binding module, CBM)對於不溶性多醣之水解具重要調節功能,本研究以隸屬醣類吸附模組家族二十一的RoSBD為材料進行研究。CBM之結構和免疫球蛋白具有高度相似性,並與多種具有辨識致病菌能力之凝集素同富含高度β-strand 之二級結構,顯示CBM可能與免疫球蛋白具演化相關性及功能類似性。另外,於CBM家族中亦發現部分成員具有和細胞表面醣蛋白結合的功能,進一步觀察此類CBM,發現其結構多由數個CBM串接,形成多價性蛋白構型。多價性蛋白與其配體之結合力遠大於單價性蛋白,現今常利用此觀念將標的蛋白與具有多聚體能力之蛋白(Multivalent protein binder)以分子工程方式結合表現,以提升標的蛋白作用能力。本研究將具雙聚能力之抗體Fc部位及具三聚能力之膠原蛋白類似胜肽(CLP)個別與RoSBD結合,成功於大腸桿菌表現及利用親和性管柱層析純化穩定的新穎重組蛋白質,並以非變性凝膠電泳分析、超高速離心、及分子篩層析法確認多價體蛋白質特性。以depletion isotherm assay 及Isothermal Titration Calorimetry (ITC)方法檢測,發現多價性RoSBD對於長鏈醣類之結合能力大幅提升,且其對於固態和液態之配體可能具有不同的結合機制。本研究除深入了解醣類吸附模組的特性及功能,亦進一步運用重組蛋白質工程創造新穎的多價性蛋白,未來將有機會應用於病原體的偵測或成為一種創新的殺菌劑。


    List of Contents 中文摘要 I Abstract II Acknowledgement III List of Contents IV List of Figures VI List of Tables VIII List of Appendix IX Abbreviation X Chapter 1 Introduction 1 Chapter 2 Materials and Methods 21 2-1 Strains and expression plasmids 21 2-2 Culture media composition 21 2-3 Isolation of RNA 22 2-4 First-strand cDNA synthesis 22 2-5 Plasmid construction 23 2-6 Preparation of competent cells 24 2-7 Transformation of E. coli 25 2-8 Confirmation of colonies by in situ PCR 25 2-9 Mini-preparation of plasmid 26 2-10 Recovery of DNA fragment 26 2-11 Restriction enzyme digestion 27 2-12 Ligation 27 2-13 Yeast transformation 27 2-14 Small scale expression of polymeric RoSBDs in E. coli 28 2-15 Expression of RoSBDL*-mouse IgG1-Fc in P. pastoris 28 2-16 Purification of polymeric RoSBDs by amylose column chromatography 29 2-17 Buffer exchange and determination of protein concentration 30 2-18 Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) 30 2-19 Western blotting analysis 31 2-20 Native PAGE 31 2-21 Cross-linking analysis 32 2-22 Analytical ultracentrifugation 32 2-23 Size exclusion chromatography 32 2-24 Saturation binding assay 33 2-25 Thermodynamic measurement of binding to soluble glycans by isothermal titration calorimetry (ITC) 33 Chapter 3 Results 34 3-1 Polymeric RoSBD 34 3-2 Construction of pET23a-Rosbd-(g4s)3 35 3-3 Construction of pET23a-Rosbd-(g4s)3-fc and pPICZαA-Rosbd-l*-fc 35 3-4 Small scale expression of RoSBD-(G4S)3-Fc in E. coli 37 3-5 Purification of RoSBD-(G4S)3-Fc by amylose column chromatography 38 3-6 Characterization of multimeric forms of RoSBD-(G4S)3-Fc 39 3-7 Expression and characterization of RoSBD-L*-Fc in P. pastoris GS115 40 3-8 Depletion isotherm of RoSBD-(G4S)3-Fc 41 3-9 Quantitative measurement of binding affinity between dimeric RoSBD and soluble glycans 42 3-10 Construction of Rosbd-(g4s)3-clp 43 3-11 Small-scale expression of RoSBD-(G4S)3-CLP in E. coli BL21 CodonPlus (DE3) 45 3-12 Purification of RoSBD-(G4S)3-CLP by amylose column chromatography 46 3-13 Characterization of multimeric forms of RoSBD-(G4S)3-CLP 47 3-14 Depletion isotherm of RoSBD-(G4S)3-CLP 48 3-15 Quantitative measurement of binding affinity between trimeric RoSBD and soluble glycans 49 3-16 Construction of pET23a-Rosbd-(g4s)3-cs 50 3-17 Small scale expression of RoSBD-(G4S)3-CS in E. coli BL21 CodonPlus (DE3) 51 3-18 Purification of RoSBD-(G4S)3-CS by amylose column chromatography 51 Chapter 4 Discussion 54 4-1 Summary 54 4-2 Linker 56 4-3 Binder 57 4-4 Interaction of polymeric RoSBD with sugars 58 4-5 Role of RoSBD in immune system 61 Figures 64 Tables 99 Appendix 108 Reference 116

    1. Guillen, D., S. Sanchez, and R. Rodriguez-Sanoja, Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 85(5): p. 1241-9.
    2. Cantarel, B.L., et al., The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res, 2009. 37(Database issue): p. D233-8.
    3. Barral, P., et al., An olive pollen protein with allergenic activity, Ole e 10, defines a novel family of carbohydrate-binding modules and is potentially implicated in pollen germination. Biochem J, 2005. 390(Pt 1): p. 77-84.
    4. Vaaje-Kolstad, G., et al., The non-catalytic chitin-binding protein CBP21 from Serratia marcescens is essential for chitin degradation. J Biol Chem, 2005. 280(31): p. 28492-7.
    5. Rodriguez-Sanoja, R., N. Oviedo, and S. Sanchez, Microbial starch-binding domain. Curr Opin Microbiol, 2005. 8(3): p. 260-7.
    6. Ji, Q., et al., Reduction of starch granule size by expression of an engineered tandem starch-binding domain in potato plants. Plant Biotechnol J, 2004. 2(3): p. 251-60.
    7. Blake, A.W., et al., Understanding the biological rationale for the diversity of cellulose-directed carbohydrate-binding modules in prokaryotic enzymes. J Biol Chem, 2006. 281(39): p. 29321-9.
    8. Ficko-Blean, E. and A.B. Boraston, N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH. J Mol Biol, 2009. 390(2): p. 208-20.
    9. van Bueren, A.L., et al., Family 6 carbohydrate binding modules recognize the non-reducing end of beta-1,3-linked glucans by presenting a unique ligand binding surface. J Biol Chem, 2005. 280(1): p. 530-7.
    10. Shoseyov, O., Z. Shani, and I. Levy, Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev, 2006. 70(2): p. 283-95.
    11. Sorimachi, K., et al., Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin. Structure, 1997. 5(5): p. 647-61.
    12. Liu, Y.N., et al., Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase. Biochem J, 2007. 403(1): p. 21-30.
    13. Tung, J.Y., et al., Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path. Biochem J, 2008. 416(1): p. 27-36.
    14. Boraston, A.B., et al., A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J Biol Chem, 2006. 281(1): p. 587-98.
    15. Kamitori, S., et al., Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution. J Mol Biol, 2002. 318(2): p. 443-53.
    16. Mikami, B., et al., Crystal structure of pullulanase: evidence for parallel binding of oligosaccharides in the active site. J Mol Biol, 2006. 359(3): p. 690-707.
    17. Polekhina, G., et al., Structural basis for glycogen recognition by AMP-activated protein kinase. Structure, 2005. 13(10): p. 1453-62.
    18. Koropatkin, N.M. and T.J. Smith, SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure, 2010. 18(2): p. 200-15.
    19. Sauer, J., et al., Glucoamylase: structure/function relationships, and protein engineering. Biochim Biophys Acta, 2000. 1543(2): p. 275-293.
    20. Norouzian, D., et al., Fungal glucoamylases. Biotechnol Adv, 2006. 24(1): p. 80-5.
    21. Coutinho, P.M. and P.J. Reilly, Structure-function relationships in the catalytic and starch binding domains of glucoamylase. Protein Eng, 1994. 7(3): p. 393-400.
    22. Marin-Navarro, J. and J. Polaina, Glucoamylases: structural and biotechnological aspects. Appl Microbiol Biotechnol. 89(5): p. 1267-73.
    23. Manjunath, P., B.C. Shenoy, and M.R. Raghavendra Rao, Fungal glucoamylases. J Appl Biochem, 1983. 5(4-5): p. 235-60.
    24. Coutinho, P.M. and P.J. Reilly, Glucoamylase structural, functional, and evolutionary relationships. Proteins, 1997. 29(3): p. 334-47.
    25. Mertens, J.A. and C.D. Skory, Isolation and characterization of two genes that encode active glucoamylase without a starch binding domain from Rhizopus oryzae. Curr Microbiol, 2007. 54(6): p. 462-6.
    26. Goto, M., et al., Functional analysis of O-linked oligosaccharides in threonine/serine-rich region of Aspergillus glucoamylase by expression in mannosyltransferase-disruptants of yeast. Eur J Biochem, 1999. 260(3): p. 596-602.
    27. Chou, W.I., et al., The family 21 carbohydrate-binding module of glucoamylase from Rhizopus oryzae consists of two sites playing distinct roles in ligand binding. Biochem J, 2006. 396(3): p. 469-77.
    28. Palopoli, N., et al., Starch-synthase III family encodes a tandem of three starch-binding domains. Proteins, 2006. 65(1): p. 27-31.
    29. Hashimoto, H., Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci, 2006. 63(24): p. 2954-67.
    30. Boraston, A.B., et al., Co-operative binding of triplicate carbohydrate-binding modules from a thermophilic xylanase. Mol Microbiol, 2002. 43(1): p. 187-94.
    31. van Bueren, A.L., et al., Identification and structural basis of binding to host lung glycogen by streptococcal virulence factors. Nat Struct Mol Biol, 2007. 14(1): p. 76-84.
    32. White, M.R., et al., Enhancement of antiviral activity of collectin trimers through cross-linking and mutagenesis of the carbohydrate recognition domain. J Innate Immun. 2(3): p. 267-79.
    33. Shelburne, S.A., 3rd, et al., Molecular characterization of group A Streptococcus maltodextrin catabolism and its role in pharyngitis. Mol Microbiol, 2008. 69(2): p. 436-52.
    34. Gregg, K.J., et al., Divergent modes of glycan recognition by a new family of carbohydrate-binding modules. J Biol Chem, 2008. 283(18): p. 12604-13.
    35. Boraston, A.B., E. Ficko-Blean, and M. Healey, Carbohydrate recognition by a large sialidase toxin from Clostridium perfringens. Biochemistry, 2007. 46(40): p. 11352-60.
    36. Abbott, D.W., J.M. Eirin-Lopez, and A.B. Boraston, Insight into ligand diversity and novel biological roles for family 32 carbohydrate-binding modules. Mol Biol Evol, 2008. 25(1): p. 155-67.
    37. Alderwick, L.J., et al., The C-terminal domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC is a lectin-like carbohydrate binding module. PLoS Pathog. 7(2): p. e1001299.
    38. van Kooyk, Y. and G.A. Rabinovich, Protein-glycan interactions in the control of innate and adaptive immune responses. Nat Immunol, 2008. 9(6): p. 593-601.
    39. Balzarini, J., Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy. Nat Rev Microbiol, 2007. 5(8): p. 583-97.
    40. Dodd, R.B. and K. Drickamer, Lectin-like proteins in model organisms: implications for evolution of carbohydrate-binding activity. Glycobiology, 2001. 11(5): p. 71R-9R.
    41. Dam, T.K. and C.F. Brewer, Lectins as pattern recognition molecules: the effects of epitope density in innate immunity. Glycobiology. 20(3): p. 270-9.
    42. Boyd, M.R., et al., Discovery of cyanovirin-N, a novel human immunodeficiency virus-inactivating protein that binds viral surface envelope glycoprotein gp120: potential applications to microbicide development. Antimicrob Agents Chemother, 1997. 41(7): p. 1521-30.
    43. Mori, T., et al., Isolation and characterization of griffithsin, a novel HIV-inactivating protein, from the red alga Griffithsia sp. J Biol Chem, 2005. 280(10): p. 9345-53.
    44. Balzarini, J., Inhibition of HIV entry by carbohydrate-binding proteins. Antiviral Res, 2006. 71(2-3): p. 237-47.
    45. Mo, H., et al., Carbohydrate binding properties of banana (Musa acuminata) lectin I. Novel recognition of internal alpha1,3-linked glucosyl residues. Eur J Biochem, 2001. 268(9): p. 2609-15.
    46. Balzarini, J., et al., Marked depletion of glycosylation sites in HIV-1 gp120 under selection pressure by the mannose-specific plant lectins of Hippeastrum hybrid and Galanthus nivalis. Mol Pharmacol, 2005. 67(5): p. 1556-65.
    47. Tanaka, H., et al., Mechanism by which the lectin actinohivin blocks HIV infection of target cells. Proc Natl Acad Sci U S A, 2009. 106(37): p. 15633-8.
    48. Swanson, M.D., et al., A lectin isolated from bananas is a potent inhibitor of HIV replication. J Biol Chem. 285(12): p. 8646-55.
    49. Balestrieri, E., et al., Inhibition of cell-to-cell transmission of human T-cell lymphotropic virus type 1 in vitro by carbohydrate-binding agents. Antimicrob Agents Chemother, 2008. 52(8): p. 2771-9.
    50. Moulaei, T., et al., Monomerization of viral entry inhibitor griffithsin elucidates the relationship between multivalent binding to carbohydrates and anti-HIV activity. Structure, 2010. 18(9): p. 1104-15.
    51. Meagher, J.L., et al., Crystal structure of banana lectin reveals a novel second sugar binding site. Glycobiology, 2005. 15(10): p. 1033-42.
    52. Ghazarian, H., B. Idoni, and S.B. Oppenheimer, A glycobiology review: carbohydrates, lectins and implications in cancer therapeutics. Acta Histochem. 113(3): p. 236-47.
    53. Sharon, N. and H. Lis, History of lectins: from hemagglutinins to biological recognition molecules. Glycobiology, 2004. 14(11): p. 53R-62R.
    54. Loris, R., Principles of structures of animal and plant lectins. Biochim Biophys Acta, 2002. 1572(2-3): p. 198-208.
    55. Ohlson, S., Designing transient binding drugs: a new concept for drug discovery. Drug Discov Today, 2008. 13(9-10): p. 433-9.
    56. Denkberg, G., et al., Direct visualization of distinct T cell epitopes derived from a melanoma tumor-associated antigen by using human recombinant antibodies with MHC- restricted T cell receptor-like specificity. Proc Natl Acad Sci U S A, 2002. 99(14): p. 9421-6.
    57. Rheinnecker, M., et al., Multivalent antibody fragments with high functional affinity for a tumor-associated carbohydrate antigen. J Immunol, 1996. 157(7): p. 2989-97.
    58. Graversen, J.H., et al., Mutational analysis of affinity and selectivity of kringle-tetranectin interaction. Grafting novel kringle affinity ontp the trtranectin lectin scaffold. J Biol Chem, 2000. 275(48): p. 37390-6.
    59. Binz, H.K., et al., High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol, 2004. 22(5): p. 575-82.
    60. Silverman, J., et al., Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat Biotechnol, 2005. 23(12): p. 1556-61.
    61. Frank, S., et al., Stabilization of short collagen-like triple helices by protein engineering. J Mol Biol, 2001. 308(5): p. 1081-9.
    62. Lin, Y., et al., A genetically engineered anti-CD45 single-chain antibody-streptavidin fusion protein for pretargeted radioimmunotherapy of hematologic malignancies. Cancer Res, 2006. 66(7): p. 3884-92.
    63. Albrecht, H., G.L. Denardo, and S.J. Denardo, Monospecific bivalent scFv-SH: effects of linker length and location of an engineered cysteine on production, antigen binding activity and free SH accessibility. J Immunol Methods, 2006. 310(1-2): p. 100-16.
    64. Huang, C., Receptor-Fc fusion therapeutics, traps, and MIMETIBODY technology. Curr Opin Biotechnol, 2009. 20(6): p. 692-9.
    65. Sano, T., et al., Molecular engineering of streptavidin. Ann N Y Acad Sci, 1996. 799: p. 383-90.
    66. Wilson, D.S., et al., Improved method for pepsinolysis of mouse IgG(1) molecules to F(ab')(2) fragments. J Immunol Methods, 2002. 260(1-2): p. 29-36.
    67. Aybay, C., Differential binding characteristics of protein G and protein A for Fc fragments of papain-digested mouse IgG. Immunol Lett, 2003. 85(3): p. 231-5.
    68. Tartour, E., et al., Identification, in mouse macrophages and in serum, of a soluble receptor for the Fc portion of IgG (Fc gamma R) encoded by an alternatively spliced transcript of the Fc gamma RII gene. Int Immunol, 1993. 5(8): p. 859-68.
    69. Liu, J., et al., pPIC9-Fc: a vector system for the production of single-chain Fv-Fc fusions in Pichia pastoris as detection reagents in vitro. J Biochem, 2003. 134(6): p. 911-7.
    70. Tao, M.H. and S.L. Morrison, Studies of aglycosylated chimeric mouse-human IgG. Role of carbohydrate in the structure and effector functions mediated by the human IgG constant region. J Immunol, 1989. 143(8): p. 2595-601.
    71. Holliger, P. and P.J. Hudson, Engineered antibody fragments and the rise of single domains. Nat Biotechnol, 2005. 23(9): p. 1126-36.
    72. Yang, W., et al., Gly-Pro-Arg confers stability similar to Gly-Pro-Hyp in the collagen triple-helix of host-guest peptides. J Biol Chem, 1997. 272(46): p. 28837-40.
    73. Chan, V.C., et al., Positional preferences of ionizable residues in Gly-X-Y triplets of the collagen triple-helix. J Biol Chem, 1997. 272(50): p. 31441-6.
    74. Malone, J. and M.A. Sullivan, Analysis of antibody selection by phage display utilizing anti-phenobarbital antibodies. J Mol Recognit, 1996. 9(5-6): p. 738-45.
    75. Freitag, S., et al., Structural studies of the streptavidin binding loop. Protein Sci, 1997. 6(6): p. 1157-66.
    76. Pagel, J.M., et al., Comparison of a tetravalent single-chain antibody-streptavidin fusion protein and an antibody-streptavidin chemical conjugate for pretargeted anti-CD20 radioimmunotherapy of B-cell lymphomas. Blood, 2006. 108(1): p. 328-36.
    77. Johnson, J.A. and R.B. Clark, Multiple non-specific effects of sphingosine on adenylate cyclase and cyclic AMP accumulation in S49 lymphoma cells preclude its use as a specific inhibitor of protein kinase C. Biochem J, 1990. 268(2): p. 507-11.
    78. Andrews, P., Estimation of the molecular weights of proteins by Sephadex gel-filtration. Biochem J, 1964. 91(2): p. 222-33.
    79. Siegel, L.M. and K.J. Monty, Determination of molecular weights and frictional ratios of proteins in impure systems by use of gel filtration and density gradient centrifugation. Application to crude preparations of sulfite and hydroxylamine reductases. Biochim Biophys Acta, 1966. 112(2): p. 346-62.
    80. Huston, J.S., et al., Protein engineering of antibody binding sites: recovery of specific activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli. Proc Natl Acad Sci U S A, 1988. 85(16): p. 5879-83.
    81. Argos, P., An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J Mol Biol, 1990. 211(4): p. 943-58.
    82. Dias, F.M., et al., The N-terminal family 22 carbohydrate-binding module of xylanase 10B of Clostridium themocellum is not a thermostabilizing domain. FEMS Microbiol Lett, 2004. 238(1): p. 71-8.
    83. Riechmann, L., et al., Reshaping human antibodies for therapy. Nature, 1988. 332(6162): p. 323-7.
    84. Alt, M., R. Muller, and R.E. Kontermann, Novel tetravalent and bispecific IgG-like antibody molecules combining single-chain diabodies with the immunoglobulin gamma1 Fc or CH3 region. FEBS Lett, 1999. 454(1-2): p. 90-4.
    85. Guillen, D., et al., Alpha-amylase starch binding domains: cooperative effects of binding to starch granules of multiple tandemly arranged domains. Appl Environ Microbiol, 2007. 73(12): p. 3833-7.
    86. Kusunoki, K., et al., A kinetic expression for hydrolysis of soluble starch by glucoamylase. Biotechnol Bioeng, 1982. 24(2): p. 347-54.
    87. Morris, A., Increasing food production by embracing new technology. Vet Rec. 168(10): p. 258-60.
    88. Wittwer, S.H., Food production: technology and the resource base. Science, 1975. 188(4188): p. 578-84.
    89. Sharon, E., et al., Hierarchy and adaptivity in segmenting visual scenes. Nature, 2006. 442(7104): p. 810-3.
    90. Ahmad, N., et al., Thermodynamic binding studies of bivalent oligosaccharides to galectin-1, galectin-3, and the carbohydrate recognition domain of galectin-3. Glycobiology, 2004. 14(9): p. 817-25.
    91. Minko, T., Drug targeting to the colon with lectins and neoglycoconjugates. Adv Drug Deliv Rev, 2004. 56(4): p. 491-509.
    92. Gorelik, E., U. Galili, and A. Raz, On the role of cell surface carbohydrates and their binding proteins (lectins) in tumor metastasis. Cancer Metastasis Rev, 2001. 20(3-4): p. 245-77.
    93. Haruo Tanaka, I., Omura, Anti-HIV drug, polypeptide constituting the same, gene encoding the polypeptide and method of producing the anti-HIV drug. United States Patent Application Publication, 2008. US 20080254507A1.
    94. Freelove, A.C., et al., A novel carbohydrate-binding protein is a component of the plant cell wall-degrading complex of Piromyces equi. J Biol Chem, 2001. 276(46): p. 43010-7.

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