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研究生: 彭羽均
Peng, Yu-Jun
論文名稱: 環狀LTIIb-B5的結構研究
The structural study of cyclic LTIIb-B5
指導教授: 蘇士哲
Sue, Shih-Che
口試委員: 陳金榜
Chen, Chin-Pan
林珮君
Lin, Pei-Chun
羅惟正
Lo, Wei-Cheng
學位類別: 碩士
Master
系所名稱: 生命科學暨醫學院 - 生物資訊與結構生物研究所
Institute of Bioinformatics and Structural Biology
論文出版年: 2022
畢業學年度: 110
語文別: 中文
論文頁數: 74
中文關鍵詞: 內含肽環狀蛋白黏膜佐劑五聚體神經節糖苷反式剪接第II型熱不穩定腸毒素
外文關鍵詞: cyclic protein, pentamer, trans-splicing, type II heat-labile enterotoxin, LTIIb
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  • 內含肽(Intein)具有連接肽骨架的能力,這樣的作用機制能夠延伸運用在環化多肽和蛋白質。根據過去的文獻提及環化的蛋白質具有較優異的抗熱性且在水溶液中表現得非常穩定,因此內含肽介導的分子內反應成為蛋白質工程中的常用且熱門的策略。在本篇的研究中,我們欲透過內含肽環化策略來形成環狀的第II型熱不穩定腸毒素B次單元,簡稱LTIIb-B5。為了產生出我們欲探討的環狀LTIIb-B5,我們使用了重組蛋白中的內含肽其剪接化學鍵的功能,藉此設計出有效的環狀蛋白黏膜佐劑。接著進行Wildtype和環狀LTIIb-B5的結構差異性比較,本篇研究使用的實驗方法包括MALDI-TOF-MS、分析型超高速離心(AUC)、核磁共振技術(NMR)以及Bio-SAXS和X射線繞射。在數個實驗中我們都證實環狀LTIIb-B5如同Wildtype具有五聚體的結構,其中在 X 射線所分析出的五聚體中能提供我們一項更為詳細的訊息:LTIIb-B5在骨架環化後結構並沒有太大的改變。重要的是環狀LTIIb-B5在高溫環境的NMR量測下具有良好耐熱性,且 1H15N 二維光譜滴定實驗顯示其與下游的醣類受體GD1a有相互作用,此作用力證據能與我們在晶體結構上所觀察到的醣類結合口袋相互佐證。
    我們期望環狀LTIIb-B5能夠改善它們在生物學上的應用,例如增加在體內的半衰期,或是提升與上下游受體的結合力,進而提高LTIIb-B5佐劑活性的強度。因此在這篇論文中,我們提供內含肽介導環化作用提升LTIIb-B5穩定性的證明,期望未來環狀LTIIb-B5有利於人體疫苗開發上及廣泛應用於相關領域中。


    Intein shows ability to ligate polypeptide backbone. The same enzyme mechanism could be extended to cyclize peptides and proteins. As the previous reports, the cyclized proteins contained increased thermo-resistance in solution. The employment of intein in protein
    engineering becomes an attractive strategy. In our study, we consider to engineer a potent mucosal protein adjuvant by using the B subunit of type II heat labile enterotoxin (LTIIb-B5) as a target. A strategy to create a cyclic LTIIb-B5 was developed by incorporating the Intein
    protein scaffold. The LTIIb-B5 was successfully cyclized during the expression. To realize the structural similarities and differences between wildtype and cyclic LTIIb-B5, the experimental methods including MALDI-TOF-MS, Analytical Ultracentrifugation, Nuclear Magnetic Resonance, Bio-SAXS and X-ray diffraction were used. The experiments consistently conclude the same conformation of P5 symmetry as identified in wildtype LTIIbB5. The X-ray structure further revealed the details of the pentameric structure, indicating no significant change caused by the backbone cyclization. Most importantly, the cyclic protein not only showed good thermal stability during the high-temperature NMR measurement, but also demonstrated the binding to its downstream ligand, GD1a. The result was supported by the similar carbohydrate binding pockets on cyclic LTIIb-B5 surface. Thus, we expect the physical property of cyclic LTIIb-B5 may improve its biological applications, such as elongating half-life in the body or better binding between the upstream and downstream receptors, thereby improving the potential of being the protein adjuvant. Here, we prove a concept of creating stable LTIIb-B5 by cyclization. The study might benefit the development of human vaccines and hopefully be used in related fields in the future.

    摘要 I Abstract II 謝誌 III 目錄 IV 第一章、緒論 1 §1-1 內含肽與蛋白質之剪接(Intein and Protein splicing) 1 §1-2 分離式內含肽與反式剪接(Split intein and Protein Trans-Splicing, PTS)3 §1-3 內含肽剪接之生物技術應用 4 1-3.1 無標籤蛋白純化 5 1-3.2 In vitro 蛋白質半合成 7 1-3.3 分段同位素標記(Segmental isotopic labelling) 10 1-3.4 生物傳感器(Biosensor)製造 11 §1-4 內含肽介導蛋白質和肽鏈的環化 12 1-4.1 EPL半合成法環化的應用 14 1-4.2 SICLOPPS環化的應用 14 §1-5 第II型熱不穩定腸毒素B次單元(B subunits of type II heatlabile enterotoxin,LTIIb-B5) 15 1-5.1 與細胞膜上受體-神經節糖苷GD1a的結合 16 1-5.2 LTIIb-B5和下游受體結合的探討 17 第二章、環狀 LTIIb-B5之設計與探討 19 §2-1 環狀蛋白設計與實驗回顧 19 §2-2 實驗方向 24 第三章、材料與方法 29 §3-1 蛋白質表現及純化 29 3-1.1 蛋白質表現 29 3-1.2 蛋白質純化 30 §3-2 基質輔助雷射脫附游離-飛行時間質譜(MALDI-TOF-MS) 34 §3-3 分析型超高速離心(Analytical ultracentrifugation,AUC) 35 3-3.1 沉降速度(Sedimentation Velocity,SV) 35 3-3.2 沉降平衡(Sedimentation Equilibrium,SE) 37 §3-4 核磁共振技術 38 3-4.1 NMR 15N-labeled 樣品製備 38 3-4.2 NMR1H15N 二維光譜滴定實驗 38 §3-5 生物分子小角度及廣角度散射(Biological small- and wide-angle X-ray scattering,BioSAXS) 39 3-5.1 SAXS 實驗前準備 39 3-5.2 實驗流程 39 §3-6 蛋白質結晶學 (Protein Crystallography) 41 3-6.1 晶體樣品製備 41 3-6.2 實驗流程 41 第四章、實驗結果及討論 43 §4-1 Cyc-B5結構初步的探討 43 §4-2 Cyc-B5晶體的結構探討 45 4-2.1 整體結構 46 4-2.2 單一次單元結構 47 4-2.3 次單元間的作用 50 4-2.4 環化區域的確認 52 4-2.5 結合口袋(binding pocket)的探討 54 §4-3 Cyc-B5水溶液中的結構探討 58 4-3.1 SAXS 擬合結構探討 58 4-3.2 SAXS 與晶體的 Cyc-B5結構探討 62 4-3.3 NMR 1H15N HSQC 二維光譜分析 64 4-3.4 NMR 1H15N HSQC 二維光譜滴定實驗 67 第五章、實驗結論 71 參考文獻 i

    1. Wang, H.; Wang, L.; Zhong, B.; Dai, Z., Protein Splicing of Inteins: A Powerful Tool in
    Synthetic Biology. Frontiers in Bioengineering and Biotechnology 2022, 10.
    2. Shah, N. H.; Muir, T. W., Inteins: Nature's Gift to Protein Chemists. Chem Sci 2014, 5 (1), 446-
    461.
    3. Shih, C. K.; Wagner, R.; Feinstein, S.; Kanik-Ennulat, C.; Neff, N., A dominant trifluoperazine
    resistance gene from Saccharomyces cerevisiae has homology with F0F1 ATP synthase and confers
    calcium-sensitive growth. Mol Cell Biol 1988, 8 (8), 3094-103.
    4. Hirata, R.; Ohsumk, Y.; Nakano, A.; Kawasaki, H.; Suzuki, K.; Anraku, Y., Molecular structure
    of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from
    vacuolar membranes of Saccharomyces cerevisiae. Journal of Biological Chemistry 1990, 265 (12),
    6726-6733.
    5. Gramespacher, J. A.; Stevens, A. J.; Thompson, R. E.; Muir, T. W., Improved protein splicing
    using embedded split inteins. Protein Science 2018, 27 (3), 614-619.
    6. Xu, M. Q.; Southworth, M. W.; Mersha, F. B.; Hornstra, L. J.; Perler, F. B., In vitro protein
    splicing of purified precursor and the identification of a branched intermediate. Cell 1993, 75 (7),
    1371-7.
    7. Shemella, P.; Pereira, B.; Zhang, Y.; Van Roey, P.; Belfort, G.; Garde, S.; Nayak, S. K.,
    Mechanism for Intein C-Terminal Cleavage: A Proposal from Quantum Mechanical Calculations.
    Biophysical Journal 2007, 92 (3), 847-853.
    8. Wood, D. W.; Camarero, J. A., Intein applications: from protein purification and labeling to
    metabolic control methods. J Biol Chem 2014, 289 (21), 14512-9.
    9. Southworth, M. W.; Amaya, K.; Evans, T. C.; Xu, M. Q.; Perler, F. B., Purification of proteins
    fused to either the amino or carboxy terminus of the Mycobacterium xenopi gyrase A intein.
    Biotechniques 1999, 27 (1), 110-4, 116, 118-20.
    10. Wood, D. W.; Wu, W.; Belfort, G.; Derbyshire, V.; Belfort, M., A genetic system yields selfcleaving inteins for bioseparations. Nature Biotechnology 1999, 17 (9), 889-892.
    11. Dawson, P. E.; Muir, T. W.; Clark-Lewis, I.; Kent, S. B., Synthesis of proteins by native
    chemical ligation. Science 1994, 266 (5186), 776-9.
    12. Muir, T. W.; Sondhi, D.; Cole, P. A., Expressed protein ligation: a general method for protein
    engineering. Proc Natl Acad Sci U S A 1998, 95 (12), 6705-10.
    13. Züger, S.; Iwai, H., Intein-based biosynthetic incorporation of unlabeled protein tags into
    isotopically labeled proteins for NMR studies. Nat Biotechnol 2005, 23 (6), 736-40.
    14. Jeon, H.; Lee, E.; Kim, D.; Lee, M.; Ryu, J.; Kang, C.; Kim, S.; Kwon, Y., Cell-Based Biosensors
    Based on Intein-Mediated Protein Engineering for Detection of Biologically Active Signaling
    Molecules. Analytical Chemistry 2018, 90 (16), 9779-9786.
    15. Scott Charles, P.; Abel-Santos, E.; Wall, M.; Wahnon Daphne, C.; Benkovic Stephen, J.,
    Production of cyclic peptides and proteins in vivo. Proceedings of the National Academy of Sciences
    1999, 96 (24), 13638-13643.
    16. Camarero, J. A.; Pavel, J.; Muir, T. W., Chemical Synthesis of a Circular Protein Domain:
    Evidence for Folding-Assisted Cyclization. Angewandte Chemie International Edition 1998, 37 (3),
    347-349.
    17. Jackson, D. Y.; Burnier, J. P.; Wells, J. A., Enzymic Cyclization of Linear Peptide Esters Using
    Subtiligase. Journal of the American Chemical Society 1995, 117 (2), 819-820.
    18. Camarero, J. A.; Muir, T. W., Biosynthesis of a Head-to-Tail Cyclized Protein with Improved
    Biological Activity. Journal of the American Chemical Society 1999, 121 (23), 5597-5598.
    19. Tavassoli, A.; Lu, Q.; Gam, J.; Pan, H.; Benkovic, S. J.; Cohen, S. N., Inhibition of HIV Budding
    by a Genetically Selected Cyclic Peptide Targeting the Gag−TSG101 Interaction. ACS Chemical Biology
    2008, 3 (12), 757-764
    20. Smith, H. W.; Halls, S., Studies on Escherichia coli enterotoxin. The Journal of Pathology and
    Bacteriology 1967, 93 (2), 531-543.
    21. Duan, Q.; Xia, P.; Nandre, R.; Zhang, W.; Zhu, G., Review of Newly Identified Functions
    Associated With the Heat-Labile Toxin of Enterotoxigenic Escherichia coli. Frontiers in Cellular and
    Infection Microbiology 2019, 9.
    22. Haan, L. d.; Hirst, T. R., Cholera toxin: A paradigm for multi-functional engagement of cellular
    mechanisms (Review). Molecular Membrane Biology 2004, 21 (2), 77-92.
    23. Zalem, D.; Juhás, M.; Terrinoni, M.; King-Lyons, N.; Lebens, M.; Varrot, A.; Connell, T. D.;
    Teneberg, S., Characterization of the ganglioside recognition profile of Escherichia coli heat-labile
    enterotoxin LT-IIc. Glycobiology 2022, 32 (5), 391-403.
    24. Connell, T. D., Cholera toxin, LT-I, LT-IIa and LT-IIb: the critical role of ganglioside binding in
    immunomodulation by Type I and Type II heat-labile enterotoxins. Expert Review of Vaccines 2007, 6
    (5), 821-834.
    25. Tatsumoto, M.; Koga, M.; Gilbert, M.; Odaka, M.; Hirata, K.; Kuwabara, S.; Yuki, N., Spectrum
    of neurological diseases associated with antibodies to minor gangliosides GM1b and GalNAc-GD1a.
    Journal of Neuroimmunology 2006, 177 (1), 201-208.
    26. Hajishengallis, G.; Tapping Richard, I.; Martin Michael, H.; Nawar, H.; Lyle Elizabeth, A.;
    Russell Michael, W.; Connell Terry, D., Toll-Like Receptor 2 Mediates Cellular Activation by the B
    Subunits of Type II Heat-Labile Enterotoxins. Infection and Immunity 2005, 73 (3), 1343-1349.
    27. Clark Richard, J.; Fischer, H.; Dempster, L.; Daly Norelle, L.; Rosengren, K. J.; Nevin Simon, T.;
    Meunier Frederic, A.; Adams David, J.; Craik David, J., Engineering stable peptide toxins by means of
    backbone cyclization: Stabilization of the α-conotoxin MII. Proceedings of the National Academy of
    Sciences 2005, 102 (39), 13767-13772.
    28. Clark, R. J.; Craik, D. J., Invited reviewnative chemical ligation applied to the synthesis and
    bioengineering of circular peptides and proteins. Peptide Science 2010, 94 (4), 414-422.
    29. Clark, R. J.; Akcan, M.; Kaas, Q.; Daly, N. L.; Craik, D. J., Cyclization of conotoxins to improve
    their biopharmaceutical properties. Toxicon 2012, 59 (4), 446-455.
    30. Harford, S.; Dykes, C. W.; Hobden, A. N.; Read, M. J.; Halliday, I. J., Inactivation of the
    Escherichia coli heat-labile enterotoxin by in vitro mutagenesis of the A-subunit gene. European
    Journal of Biochemistry 1989, 183 (2), 311-316.
    31. Norton Elizabeth, B.; Lawson Louise, B.; Mahdi, Z.; Freytag Lucy, C.; Clements John, D.;
    Payne, S. M., The A Subunit of Escherichia coli Heat-Labile Enterotoxin Functions as a Mucosal
    Adjuvant and Promotes IgG2a, IgA, and Th17 Responses to Vaccine Antigens. Infection and Immunity
    2012, 80 (7), 2426-2435.
    32. De Haan, L.; Verweij, W. R.; Feil, I. K.; Holtrop, M.; Hol, W. G. J.; Agsteribbe, E.; Wilschut, J.,
    Role of GM1 binding in the mucosal immunogenicity and adjuvant activity of the Escherichia coli
    heat-labile enterotoxin and its B subunit. Immunology 1998, 94 (3), 424-430.
    33. van Rosmalen, M.; Krom, M.; Merkx, M., Tuning the Flexibility of Glycine-Serine Linkers To
    Allow Rational Design of Multidomain Proteins. Biochemistry 2017, 56 (50), 6565-6574.
    34. Mahmoudi Gomari, M.; Saraygord-Afshari, N.; Farsimadan, M.; Rostami, N.; Aghamiri, S.;
    Farajollahi, M. M., Opportunities and challenges of the tag-assisted protein purification techniques:
    Applications in the pharmaceutical industry. Biotechnology Advances 2020, 45, 107653.
    35. Shih, O.; Liao, K.-F.; Yeh, Y.-Q.; Su, C.-J.; Wang, C.-A.; Chang, J.-W.; Wu, W.-R.; Liang, C.-C.;
    Lin, C.-Y.; Lee, T.-H.; Chang, C.-H.; Chiang, L.-C.; Chang, C.-F.; Liu, D.-G.; Lee, M.-H.; Liu, C.-Y.; Hsu, T.-
    W.; Mansel, B.; Ho, M.-C.; Shu, C.-Y.; Lee, F.; Yen, E.; Lin, T.-C.; Jeng, U., Performance of the new
    biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon Source. Journal
    of Applied Crystallography 2022, 55 (2), 340-352.
    36. Bernadó, P.; Svergun, D. I., Structural analysis of intrinsically disordered proteins by smallangle X-ray scattering. Molecular BioSystems 2012, 8 (1), 151-167.
    37. Ouedraogo, R.; Daumas, A.; Capo, C.; Mege, J.-L.; Textoris, J., Whole-cell MALDI-TOF Mass
    Spectrometry is an Accurate and Rapid Method to Analyze Different Modes of Macrophage
    Activation. Journal of visualized experiments : JoVE 2013, 82.
    38. Lebowitz, J.; Lewis, M. S.; Schuck, P., Modern analytical ultracentrifugation in protein
    science: A tutorial review. Protein Science 2002, 11 (9), 2067-2079.
    39. Cole, J. L.; Lary, J. W.; T, P. M.; Laue, T. M., Analytical ultracentrifugation: sedimentation
    velocity and sedimentation equilibrium. Methods Cell Biol 2008, 84, 143-79.
    40. Edwards, G. B.; Muthurajan, U. M.; Bowerman, S.; Luger, K., Analytical Ultracentrifugation
    (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of
    Biological Macromolecules. Current Protocols in Molecular Biology 2020, 133 (1), e131.
    41. Wohlleben, W., Validity range of centrifuges for the regulation of nanomaterials: from
    classification to as-tested coronas. J Nanopart Res 2012, 14 (12), 1300.
    42. Dessau, M. A.; Modis, Y., Protein crystallization for X-ray crystallography. J Vis Exp 2011,
    (47).
    43. Callaway, E., The revolution will not be crystallized: a new method sweeps through structural
    biology. Nature 2015, 525 (7568), 172-174.
    44. Murzin, A. G., OB(oligonucleotide/oligosaccharide binding)-fold: common structural and
    functional solution for non-homologous sequences. Embo j 1993, 12 (3), 861-7.
    45. Connell, T. D.; Holmes, R. K., Mutational analysis of the ganglioside-binding activity of the
    type II Escherichia coli heat-labile enterotoxin LT-IIb. Mol Microbiol 1995, 16 (1), 21-31.
    46. Connell, T. D.; Holmes, R. K., Molecular genetic analysis of ganglioside GD1b-binding activity
    of Escherichia coli type IIa heat-labile enterotoxin by use of random and site-directed mutagenesis.
    Infect Immun 1992, 60 (1), 63-70.
    47. Bell, C. E.; Eisenberg, D., Crystal structure of diphtheria toxin bound to nicotinamide adenine
    dinucleotide. Biochemistry 1996, 35 (4), 1137-49.
    48. Dafforn, T. R., So how do you know you have a macromolecular complex? Acta Crystallogr D
    Biol Crystallogr 2007, 63 (Pt 1), 17-25.
    49. Korasick, D. A.; Tanner, J. J., Determination of protein oligomeric structure from small-angle
    X-ray scattering. Protein Science 2018, 27 (4), 814-824.
    50. Petoukhov, M. V.; Svergun, D. I., Global Rigid Body Modeling of Macromolecular Complexes
    against Small-Angle Scattering Data. Biophysical Journal 2005, 89 (2), 1237-1250.
    51. Svergun, D.; Barberato, C.; Koch, M. H. J., CRYSOL - a Program to Evaluate X-ray Solution
    Scattering of Biological Macromolecules from Atomic Coordinates. Journal of Applied
    Crystallography 1995, 28 (6), 768-773.

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