請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/58026
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 吳世雄(Shih-Hsiung Wu) | |
dc.contributor.author | Chih-Ta Chien | en |
dc.contributor.author | 簡志達 | zh_TW |
dc.date.accessioned | 2021-06-16T08:04:46Z | - |
dc.date.available | 2014-07-16 | |
dc.date.copyright | 2014-07-16 | |
dc.date.issued | 2014 | |
dc.date.submitted | 2014-06-27 | |
dc.identifier.citation | 1. Cummings, R. D., and Liu, F. T. (2009) Galectins. in Essentials of Glycobiology (Varki, A., Cummings, R. D., Esko, J. D., Freeze, H. H., Stanley, P., Bertozzi, C. R., Hart, G. W., and Etzler, M. E. eds.), 2nd Ed., Cold Spring Harbor (NY). pp
2. Hernandez, J. D., and Baum, L. G. (2002) Ah, sweet mystery of death! Galectins and control of cell fate. Glycobiology 12, 127R-136R 3. St-Pierre, Y., Campion, C. G., and Grosset, A. A. (2012) A distinctive role for galectin-7 in cancer ? Frontiers in bioscience : a journal and virtual library 17, 438-450 4. Yang, R. Y., Rabinovich, G. A., and Liu, F. T. (2008) Galectins: structure, function and therapeutic potential. Expert reviews in molecular medicine 10, e17 5. Vespa, G. N., Lewis, L. A., Kozak, K. R., Moran, M., Nguyen, J. T., Baum, L. G., and Miceli, M. C. (1999) Galectin-1 specifically modulates TCR signals to enhance TCR apoptosis but inhibit IL-2 production and proliferation. Journal of immunology 162, 799-806 6. Santucci, L., Fiorucci, S., Cammilleri, F., Servillo, G., Federici, B., and Morelli, A. (2000) Galectin-1 exerts immunomodulatory and protective effects on concanavalin A-induced hepatitis in mice. Hepatology 31, 399-406 7. Garin, M. I., Chu, C. C., Golshayan, D., Cernuda-Morollon, E., Wait, R., and Lechler, R. I. (2007) Galectin-1: a key effector of regulation mediated by CD4+CD25+ T cells. Blood 109, 2058-2065 8. Lagana, A., Goetz, J. G., Cheung, P., Raz, A., Dennis, J. W., and Nabi, I. R. (2006) Galectin binding to Mgat5-modified N-glycans regulates fibronectin matrix remodeling in tumor cells. Molecular and cellular biology 26, 3181-3193 9. Stillman, B. N., Hsu, D. K., Pang, M., Brewer, C. F., Johnson, P., Liu, F. T., and Baum, L. G. (2006) Galectin-3 and galectin-1 bind distinct cell surface glycoprotein receptors to induce T cell death. Journal of immunology 176, 778-789 10. Hoyer, K. K., Pang, M., Gui, D., Shintaku, I. P., Kuwabara, I., Liu, F. T., Said, J. W., Baum, L. G., and Teitell, M. A. (2004) An anti-apoptotic role for galectin-3 in diffuse large B-cell lymphomas. The American journal of pathology 164, 893-902 11. Bernerd, F., Sarasin, A., and Magnaldo, T. (1999) Galectin-7 overexpression is associated with the apoptotic process in UVB-induced sunburn keratinocytes. Proceedings of the National Academy of Sciences of the United States of America 96, 11329-11334 12. Banh, A., Zhang, J., Cao, H., Bouley, D. M., Kwok, S., Kong, C., Giaccia, A. J., Koong, A. C., and Le, Q. T. (2011) Tumor galectin-1 mediates tumor growth and metastasis through regulation of T-cell apoptosis. Cancer research 71, 4423-4431 13. Takenaka, Y., Fukumori, T., and Raz, A. (2004) Galectin-3 and metastasis. Glycoconjugate journal 19, 543-549 14. Nobumoto, A., Nagahara, K., Oomizu, S., Katoh, S., Nishi, N., Takeshita, K., Niki, T., Tominaga, A., Yamauchi, A., and Hirashima, M. (2008) Galectin-9 suppresses tumor metastasis by blocking adhesion to endothelium and extracellular matrices. Glycobiology 18, 735-744 15. Thijssen, V. L., Poirier, F., Baum, L. G., and Griffioen, A. W. (2007) Galectins in the tumor endothelium: opportunities for combined cancer therapy. Blood 110, 2819-2827 16. Iurisci, I., Tinari, N., Natoli, C., Angelucci, D., Cianchetti, E., and Iacobelli, S. (2000) Concentrations of galectin-3 in the sera of normal controls and cancer patients. Clinical cancer research : an official journal of the American Association for Cancer Research 6, 1389-1393 17. St-Pierre, C., Ouellet, M., Giguere, D., Ohtake, R., Roy, R., Sato, S., and Tremblay, M. J. (2012) Galectin-1-specific inhibitors as a new class of compounds to treat HIV-1 infection. Antimicrobial agents and chemotherapy 56, 154-162 18. Fort, S., Kim, H. S., and Hindsgaul, O. (2006) Screening for galectin-3 inhibitors from synthetic lacto-N-biose libraries using microscale affinity chromatography coupled to mass spectrometry. The Journal of organic chemistry 71, 7146-7154 19. Cumpstey, I., Carlsson, S., Leffler, H., and Nilsson, U. J. (2005) Synthesis of a phenyl thio-beta-D-galactopyranoside library from 1,5-difluoro-2,4-dinitrobenzene: discovery of efficient and selective monosaccharide inhibitors of galectin-7. Organic & biomolecular chemistry 3, 1922-1932 20. Thurston, T. L., Wandel, M. P., von Muhlinen, N., Foeglein, A., and Randow, F. (2012) Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature 482, 414-418 21. Kim, B. W., Hong, S. B., Kim, J. H., Kwon do, H., and Song, H. K. (2013) Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. Nature communications 4, 1613 22. Hirabayashi, J., Hashidate, T., Arata, Y., Nishi, N., Nakamura, T., Hirashima, M., Urashima, T., Oka, T., Futai, M., Muller, W. E., Yagi, F., and Kasai, K. (2002) Oligosaccharide specificity of galectins: a search by frontal affinity chromatography. Biochimica et biophysica acta 1572, 232-254 23. Sorme, P., Kahl-Knutson, B., Wellmar, U., Nilsson, U. J., and Leffler, H. (2003) Fluorescence polarization to study galectin-ligand interactions. Methods in enzymology 362, 504-512 24. Sorme, P., Kahl-Knutsson, B., Huflejt, M., Nilsson, U. J., and Leffler, H. (2004) Fluorescence polarization as an analytical tool to evaluate galectin-ligand interactions. Analytical biochemistry 334, 36-47 25. Lopez-Lucendo, M. F., Solis, D., Andre, S., Hirabayashi, J., Kasai, K., Kaltner, H., Gabius, H. J., and Romero, A. (2004) Growth-regulatory human galectin-1: crystallographic characterisation of the structural changes induced by single-site mutations and their impact on the thermodynamics of ligand binding. Journal of molecular biology 343, 957-970 26. Leonidas, D. D., Vatzaki, E. H., Vorum, H., Celis, J. E., Madsen, P., and Acharya, K. R. (1998) Structural basis for the recognition of carbohydrates by human galectin-7. Biochemistry 37, 13930-13940 27. Nesmelova, I. V., Ermakova, E., Daragan, V. A., Pang, M., Menendez, M., Lagartera, L., Solis, D., Baum, L. G., and Mayo, K. H. (2010) Lactose binding to galectin-1 modulates structural dynamics, increases conformational entropy, and occurs with apparent negative cooperativity. Journal of molecular biology 397, 1209-1230 28. Diehl, C., Genheden, S., Modig, K., Ryde, U., and Akke, M. (2009) Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3. Journal of biomolecular NMR 45, 157-169 29. Ermakova, E., Miller, M. C., Nesmelova, I. V., Lopez-Merino, L., Berbis, M. A., Nesmelov, Y., Tkachev, Y. V., Lagartera, L., Daragan, V. A., Andre, S., Canada, F. J., Jimenez-Barbero, J., Solis, D., Gabius, H. J., and Mayo, K. H. (2013) Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity. Glycobiology 23, 508-523 30. Bernado, P., Mylonas, E., Petoukhov, M. V., Blackledge, M., and Svergun, D. I. (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the American Chemical Society 129, 5656-5664 31. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. Journal of biomolecular NMR 6, 277-293 32. Sancho, J. (2013) The stability of 2-state, 3-state and more-state proteins from simple spectroscopic techniques... plus the structure of the equilibrium intermediates at the same time. Archives of biochemistry and biophysics 531, 4-13 33. Hendler, R. W., and Shrager, R. I. (1994) Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners. Journal of biochemical and biophysical methods 28, 1-33 34. Sato, K., Nishina, Y., and Shiga, K. (2013) Decomposition of the fluorescence spectra of two FAD molecules in electron-transferring flavoprotein from Megasphaera elsdenii. Journal of biochemistry 154, 61-66 35. Tresset, G., Le Coeur, C., Bryche, J. F., Tatou, M., Zeghal, M., Charpilienne, A., Poncet, D., Constantin, D., and Bressanelli, S. (2013) Norovirus capsid proteins self-assemble through biphasic kinetics via long-lived stave-like intermediates. Journal of the American Chemical Society 135, 15373-15381 36. Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725 37. Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., and Lindahl, E. (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845-854 38. Yoshida, H., Yamashita, S., Teraoka, M., Itoh, A., Nakakita, S., Nishi, N., and Kamitori, S. (2012) X-ray structure of a protease-resistant mutant form of human galectin-8 with two carbohydrate recognition domains. The FEBS journal 279, 3937-3951 39. Krautler, V., Van Gunsteren, W. F., and Hunenberger, P. H. (2001) A fast SHAKE: Algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of computational chemistry 22, 501-508 40. Englander, S. W., and Kallenbach, N. R. (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Quarterly reviews of biophysics 16, 521-655 41. Andersson, F. I., Werrell, E. F., McMorran, L., Crone, W. J., Das, C., Hsu, S. T., and Jackson, S. E. (2011) The effect of Parkinson's-disease-associated mutations on the deubiquitinating enzyme UCH-L1. Journal of molecular biology 407, 261-272 42. Schanda, P., Kupce, E., and Brutscher, B. (2005) SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. Journal of biomolecular NMR 33, 199-211 43. Englander, S. W., Mayne, L., Bai, Y., and Sosnick, T. R. (1997) Hydrogen exchange: the modern legacy of Linderstrom-Lang. Protein science : a publication of the Protein Society 6, 1101-1109 44. Goujon, M., McWilliam, H., Li, W. Z., Valentin, F., Squizzato, S., Paern, J., and Lopez, R. (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic acids research 38, W695-W699 45. Schneidman-Duhovny, D., Hammel, M., and Sali, A. (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic acids research 38, W540-544 46. Schneidman-Duhovny, D., Hammel, M., Tainer, J. A., and Sali, A. (2013) Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophysical journal 105, 962-974 47. Nesmelova, I. V., Berbis, M. A., Miller, M. C., Canada, F. J., Andre, S., Jimenez-Barbero, J., Gabius, H. J., and Mayo, K. H. (2012) 1H, 13C, and 15N backbone and side-chain chemical shift assignments for the 31 kDa human galectin-7 (p53-induced gene 1) homodimer, a pro-apoptotic lectin. Biomolecular NMR assignments 6, 127-129 48. Nesmelova, I. V., Pang, M., Baum, L. G., and Mayo, K. H. (2008) 1H, 13C, and 15N backbone and side-chain chemical shift assignments for the 29 kDa human galectin-1 protein dimer. Biomolecular NMR assignments 2, 203-205 49. Bahrami, A., Assadi, A. H., Markley, J. L., and Eghbalnia, H. R. (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS computational biology 5, e1000307 50. Rachel, H., and Chang-Chun, L. (2013) Recent advances toward the development of inhibitors to attenuate tumor metastasis via the interruption of lectin-ligand interactions. Advances in carbohydrate chemistry and biochemistry 69, 125-207 51. Vivian, J. T., and Callis, P. R. (2001) Mechanisms of tryptophan fluorescence shifts in proteins. Biophysical journal 80, 2093-2109 52. Fang, Y. (2006) Label-free cell-based assays with optical biosensors in drug discovery. Assay and drug development technologies 4, 583-595 53. Abdiche, Y., Malashock, D., Pinkerton, A., and Pons, J. (2008) Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet. Analytical biochemistry 377, 209-217 54. Ramstad, T., Hadden, C. E., Martin, G. E., Speaker, S. M., Teagarden, D. L., and Thamann, T. J. (2005) Determination by NMR of the binding constant for the molecular complex between alprostadil and alpha-cyclodextrin. Implications for a freeze-dried formulation. International journal of pharmaceutics 296, 55-63 55. Plevin, M. J., Bryce, D. L., and Boisbouvier, J. (2010) Direct detection of CH/pi interactions in proteins. Nature chemistry 2, 466-471 56. Meynier, C., Guerlesquin, F., and Roche, P. (2009) Computational studies of human galectin-1: role of conserved tryptophan residue in stacking interaction with carbohydrate ligands. Journal of biomolecular structure & dynamics 27, 49-58 57. Saraboji, K., Hakansson, M., Genheden, S., Diehl, C., Qvist, J., Weininger, U., Nilsson, U. J., Leffler, H., Ryde, U., Akke, M., and Logan, D. T. (2012) The carbohydrate-binding site in galectin-3 is preorganized to recognize a sugarlike framework of oxygens: ultra-high-resolution structures and water dynamics. Biochemistry 51, 296-306 58. Hwang, T. L., van Zijl, P. C., and Mori, S. (1998) Accurate quantitation of water-amide proton exchange rates using the phase-modulated CLEAN chemical EXchange (CLEANEX-PM) approach with a Fast-HSQC (FHSQC) detection scheme. Journal of biomolecular NMR 11, 221-226 | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/58026 | - |
dc.description.abstract | 半乳糖凝集素是一個特定辨識半乳糖衍生物的凝集素家族。它們表現在細胞質、細胞核、以及胞外,並且擁有各式不同的生物功能。研究顯示半乳糖凝集素跟細胞間作用、細胞基質吸附、跨膜信號息息相關。目前已經發現十五種半乳糖凝集素,它們的序列相似度並不高,對於乳糖的結合能力也非常不同,但三維結構,無論是骨架或支鏈結構幾乎一模一樣。即使是直接接觸配體的支鏈結構也都難以用肉眼分辨,所以基質辨識的機制很難從晶體結構解釋。我們使用三種不需要額外螢光標記的技術(自身螢光、干涉儀、核磁共振)來量測半乳糖凝集素與乳糖的結合強度,如此可以避免螢光標記所造成的誤差, 增加數值的可信度。為了要解釋半乳糖凝集素是如何辨識基質以及它的選擇性,我們系統性的研究半乳糖凝集素一號、七號、及八號在結合乳糖後對於動態及折疊穩定性的影響。我們使用的工具包括分子動力模擬、圓二色光譜儀、螢光光譜儀、以及核磁共振光譜儀。我們使用核磁共振光譜儀來監測氫氘交換的速率,藉由觀察乳糖結合後交換速率的改變,我們可以獲得原子級解析度的結構及穩定性的資訊。與乳糖結合不僅影響直接接觸的殘基,一些與結合位置較遠的氨基酸也有明顯的改變。螢光及圓二色光譜加上奇異值分解的輔助來偵測平衡狀態下半乳糖凝集素的摺疊穩定性。半乳糖凝集素一號、七號、八號氮端區段、及八號碳端區段有非常不同的折疊特性:一號及八號氮端區段是兩態摺疊機制而七號及八號碳端是三態摺疊機制。這樣不同的特性或許可以解釋它們對於基質有不同的結合能力及選擇性。我們的實驗結果對於設計高專一性及高結合性的藥物將會有很大的幫助。 | zh_TW |
dc.description.abstract | Galectins are a family of lectins that interact with β-galactosides, express in cytosol, nucleus, and extracellular matrix, and confer a broad range of functions including cell-cell interaction, cell-matrix adhesion and transmembrane signaling. Despite their low sequence homology, their three-dimensional structures are essentially identical. The binding affinity of galectins to lactose and other β-galactosides vary significantly. However, it is difficult to rationalize the molecular recognition mechanisms of different galectins based on their crystal structures of the apo- and holo-forms, which exhibit minimal conformational changes even for the side-chains that are involved in ligand binding. In order to better understand the origin of substrate binding affinity and selectivity, we systematically investigate the differential effects of lactose binding on human galectin-1, -7, and -8 in terms of their internal dynamics and folding stabilities using molecular dynamics (MD) simulation, far-UV circular dichroism (CD), intrinsic fluorescence and nuclear magnetic resonance (NMR) spectroscopy. NMR hydrogen-deuterium exchange (HDX) data suggest that lactose binding not only perturbs the structures and dynamics of the residues that are directly involved ligand binding but also results in long-range perturbations at the dimer interface for galectin-1 and -7. This is consistent with the differences in fast internal dynamics in MD simulations and 15N spin relaxation dynamics, as well as the folding stabilities of galectin-1, -7, -8 in response to lactose binding. Such differential responses to ligand binding for different galectins may be implicated in modulating the binding affinity and selectivity, and hence could potentially be exploited for designs of better inhibitors with higher specificity. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T08:04:46Z (GMT). No. of bitstreams: 1 ntu-103-R01223183-1.pdf: 19223890 bytes, checksum: 1418fd1892a145887f9a43a0ff021d81 (MD5) Previous issue date: 2014 | en |
dc.description.tableofcontents | 口試委員會審定書 #
誌謝 i 中文摘要 ii ABSTRACT iii CONTENTS iv LIST OF FIGURES viii LIST OF TABLES x LIST OF EQUATIONS xi LIST OF ABBREVIATIONS xii Chapter 1 Introduction 2 1.1 Biological functions of galectins and related cancer 3 1.2 Discovery of galectins inhibitors 4 1.3 Binding activity of galectins 4 1.4 X-ray crystallography studies of galectins 5 1.5 NMR studies of galectins 7 Chapter 2 Material and Methods 8 2.1 Protein expression and purification 8 2.1.1 Plasmid preparation 8 2.1.2 Recombinant protein expression 8 2.1.3 Recombinant protein purification 9 2.2 Small angle X-ray scattering (SAXS) 9 2.2.1 Experimental procedure 9 2.2.2 Comparison of SAXS data with known structures 10 2.2.3 Ab initio modeling 10 2.2.4 Ensemble optimization method (EOM) 10 2.3 Characterization of lactose binding affinity 11 2.3.1 Intrinsic fluorescence spectroscopy 11 2.3.2 Bio-layer interferometry 11 2.3.3 NMR titration by 15N-1H HSQC spectroscopy 12 2.3.4 Data fitting and analysis 13 2.4 Equilibrium unfolding by urea 14 2.4.1 Sample preparation 14 2.4.2 Intrinsic fluorescence spectroscopy 14 2.4.3 Far-UV circular dichroism spectroscopy 15 2.4.4 Singular value decomposition (SVD) in folding analysis 16 2.5 MD simulation 18 2.6 Hydrogen-deuterium exchange 18 Chapter 3 Results 21 3.1 Structural analysis of galectins 21 3.1.1 Sequence homology of galectins 21 3.1.2 Comparison of crystal structures of galectins 22 3.1.3 Use of SAXS to study the solution structures of galectins 22 3.2 NMR assignments of galectin-8 NTD and CTD 27 3.3 Lactose binding affinity of galectins 29 3.3.1 Intrinsic fluorescence spectroscopy 30 3.3.2 Bio-layer interferometry 32 3.3.3 NMR titration by 15N-1H HSQC NMR spectroscopy 33 3.3.4 Comparison of lactose binding affinities of galectins 37 3.4 Dynamics and folding stability of galectins 38 3.4.1 MD simulation 38 3.4.2 SVD data analysis 39 3.4.3 Intrinsic fluorescence spectroscopy 41 3.4.4 Far-UV CD spectroscopy 43 3.4.5 Hydrogen-deuterium exchange 46 3.5 Use of CLEANEX-PM to study the hydrogen exchange rates of N-acetyllactosamine derivatives in the context of inhibitor development 51 Chapter 4 Discussion 53 4.1 Solution structure of full-length galectin-8 53 4.2 Comparison of label-free biophysical characterizations of galectin-lactose interactions 54 4.3 Correlation between folding stability and lactose binding of galectins 57 Chapter 5 Conclusion 59 Chapter 6 Supplementary Information 61 6.1 Designs of primers for galectin-8 NTD and CTD 61 6.2 Sequences of galectins 61 6.2.1 Galectin-1 61 6.2.2 Galectin-7 61 6.2.3 Galectin-8 full-length 61 6.2.4 Galectin-8 NTD 62 6.2.5 Galectin-8 CTD 62 6.3 Scripts of SVD in MATLAB 62 REFERENCE 64 | |
dc.language.iso | en | |
dc.title | "人類半乳糖凝集素1, 7, 8之乳糖結合親和力結構分析" | zh_TW |
dc.title | Structural Study of Differential Lactose Binding Affinities of Human Galectin-1, -7, and -8. | en |
dc.type | Thesis | |
dc.date.schoolyear | 102-2 | |
dc.description.degree | 碩士 | |
dc.contributor.coadvisor | 徐尚德(Shang-Te Danny Hsu) | |
dc.contributor.oralexamcommittee | 林俊宏(Chun-Hung Lin) | |
dc.subject.keyword | 半乳糖凝集素,核磁共振,蛋白摺疊, | zh_TW |
dc.subject.keyword | galectin,NMR spectroscopy,protein folding, | en |
dc.relation.page | 72 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2014-06-30 | |
dc.contributor.author-college | 理學院 | zh_TW |
dc.contributor.author-dept | 化學研究所 | zh_TW |
顯示於系所單位: | 化學系 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-103-1.pdf 目前未授權公開取用 | 18.77 MB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。