研究生: |
林尚錡 |
---|---|
論文名稱: |
Detecting Transient Binding in HATH Domain of HDGF by NMR Paramagnetic Relaxation Enhancement |
指導教授: |
蘇士哲
Sue, Shin-Che |
口試委員: | |
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: | 2010 |
畢業學年度: | 98 |
語文別: | 英文 |
論文頁數: | 57 |
中文關鍵詞: | 肝癌衍生生長因子 、電子順磁的弛緩增強 、核磁共振 、瞬間作用 |
外文關鍵詞: | hHDGF, PRE, NMR, transient binding |
相關次數: | 點閱:4 下載:0 |
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A new protein growth factor, Hepatoma-derived growth factor (HDGF), was discovered from medium of hepatoma cell line and was identified in a broad range of tissues. Exogenously supplied HDGF enables to enter cells and be transported into nucleus. The process further promotes mitogenic process and enhances cell proliferation. The N-terminal conserved HATH domain is provided to be responsible for HDGF internalization through binding to membrane surface heparan sulfate (HS). There are well-known examples of dimerized growth factors with active function, i.e. fibroblast growth factor, thus we are interested in identifying the intermolecular interaction between HATH domains under the HS-presence or absence conditions. In the study, we examined the interaction by adopting paramagnetic relaxation enhancement (PRE) method. It provides a straightforward measurement to determine the distance between the paramagnetic nitroxide center and the affected nuclei by site-directed spin labeling on cysteine residue (Cys12). PRE profile established from 1H-15N HSQC measurements was not fully equal to the theoretically calculated PRE result derived from the determined structural coordinate. Differences happen in regions of N- and C-terminus, loop2 and loop3, where higher relaxation enhancement was observed in experiment. Examination from the sample mixture of 15N-labeled HATH and nitroxide spin labeling HATH dissected the effect derived from intermolecular interaction, where significant intermolecular PRE effect is observed in the regions of conflict, such as N- and C-terminus, loop2 and loop3, indicating domain contact through the particular areas. Meanwhile the presence of heparin polysaccharide even enhanced the PRE effect. Our result implies the possibility of presence of transient interaction between HATHs in solution, although no biochemical study ever reported a stable dimer. Considering the result of heparin fragment longer than 10-12 residues, twice the size of a heparin-binding site in one HATH domain, effectively blocking the HATH mediated internalization, the domain transient binding might regulate HATH dimer formation for HS binding and, in addition, manipulate the domain orientation lining on a polysaccharide chain.
肝癌衍生生長因子 (HDGF) 從肝癌細胞株的培養液被發現而且已在許多組織中被發現。細胞外提供的 HDGF 能夠被胞吞進入細胞質中,且可被運送到細胞核內進一步促進細胞的增生,位於蛋白質 N 端的 HATH domain 能藉由結合細胞膜上的硫酸乙酰肝素 (heparan sulfate) 來進行胞吞作用,使得 HDGF 能夠進入細胞。先前已經知道許多生長因子能以形成二聚體的方式作用,例如: 纖維細胞生長因子 (FGF),因此我們研究在 HATH domain 在水溶液下是否具有形成二聚體的能力。在研究中我們使用電子順磁的弛緩增強 (PRE) 方法來觀測這個作用。藉由在原有的半胱氨酸 12 的位置接上電子順磁分子 (spin label),來測量順磁中心及觀察原子核間的距離。結果發現,在 1H-15N HSQC 光譜下的 PRE 實驗,計算出的結果不完全與理論計算的結果一致,其中 PRE 的效應在N端、C端、loop2 和 loop3 的區域,實驗值明顯高於理論值。在實驗利用混合15N-labeled HATH 和 nitroxide spin labeling HATH 可以進一步區分出分子間的作用。藉由此實驗,我們瞭解實驗值與理論值不吻合的原因來自 HATH domain 具有分子間的作用,同時肝素分子會進一步加強了這個 PRE 效應。雖然目前沒有生化方法測量到穩定的二聚體,但從較靈敏的 PRE 計算,我們的結果顯示水溶液中HATH domain 具有瞬間作用的能力。目前已知道 heparin 片段超過10-12 residues, 能有效的阻止 HATH 進入細胞的作用,這個大小剛好是 HATH domain Heparin 結合區的兩倍大小,這個 HATH 分子間結合的能力指出了與 heparin 結合時形成二聚體的可能。
1. Nakamura, H., Izumoto, Y., Kambe, H., Kuroda, T., Mori, T., Kawamura, K., Yamamoto, H., and Kishimoto, T. (1994) Molecular cloning of complementary DNA for a novel human hepatoma-derived growth factor. Its homology with high mobility group-1 protein, J Biol Chem 269, 25143-25149.
2. Izumoto, Y., Kuroda, T., Harada, H., Kishimoto, T., and Nakamura, H. (1997) Hepatoma-derived growth factor belongs to a gene family in mice showing significant homology in the amino terminus, Biochem Biophys Res Commun 238, 26-32.
3. Ikegame, K., Yamamoto, M., Kishima, Y., Enomoto, H., Yoshida, K., Suemura, M., Kishimoto, T., and Nakamura, H. (1999) A new member of a hepatoma-derived growth factor gene family can translocate to the nucleus, Biochem Biophys Res Commun 266, 81-87.
4. Dietz, F., Franken, S., Yoshida, K., Nakamura, H., Kappler, J., and Gieselmann, V. (2002) The family of hepatoma-derived growth factor proteins: characterization of a new member HRP-4 and classification of its subfamilies, Biochem J 366, 491-500.
5. Ge, H., Si, Y., and Roeder, R. G. (1998) Isolation of cDNAs encoding novel transcription coactivators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation, EMBO J 17, 6723-6729.
6. Lukasik, S. M., Cierpicki, T., Borloz, M., Grembecka, J., Everett, A., and Bushweller, J. H. (2006) High resolution structure of the HDGF PWWP domain: a potential DNA binding domain, Protein Sci 15, 314-323.
7. Stec, I., Nagl, S. B., van Ommen, G. J., and den Dunnen, J. T. (2000) The PWWP domain: a potential protein-protein interaction domain in nuclear proteins influencing differentiation?, FEBS Lett 473, 1-5.
8. Zhou, S. J., Xu, S. F., Zhang, H. Q., and Liu, Z. D. (2007) [Expression of HDGF and its implication in stage I non-small cell lung cancer], Zhonghua Zhong Liu Za Zhi 29, 927-930.
9. Abouzied, M. M., Baader, S. L., Dietz, F., Kappler, J., Gieselmann, V., and Franken, S. (2004) Expression patterns and different subcellular localization of the growth factors HDGF (hepatoma-derived growth factor) and HRP-3 (HDGF-related protein-3) suggest functions in addition to their mitogenic activity, Biochem J 378, 169-176.
10. Everett, A. D., Lobe, D. R., Matsumura, M. E., Nakamura, H., and McNamara, C. A. (2000) Hepatoma-derived growth factor stimulates smooth muscle cell growth and is expressed in vascular development, J Clin Invest 105, 567-575.
11. Oliver, J. A., and Al-Awqati, Q. (1998) An endothelial growth factor involved in rat renal development, J Clin Invest 102, 1208-1219.
12. Enomoto, H., Yoshida, K., Kishima, Y., Kinoshita, T., Yamamoto, M., Everett, A. D., Miyajima, A., and Nakamura, H. (2002) Hepatoma-derived growth factor is highly expressed in developing liver and promotes fetal hepatocyte proliferation, Hepatology 36, 1519-1527.
13. Everett, A. D., Narron, J. V., Stoops, T., Nakamura, H., and Tucker, A. (2004) Hepatoma-derived growth factor is a pulmonary endothelial cell-expressed angiogenic factor, Am J Physiol Lung Cell Mol Physiol 286, L1194-1201.
14. Mori, M., Morishita, H., Nakamura, H., Matsuoka, H., Yoshida, K., Kishima, Y., Zhou, Z., Kida, H., Funakoshi, T., Goya, S., Yoshida, M., Kumagai, T., Tachibana, I., Yamamoto, Y., Kawase, I., and Hayashi, S. (2004) Hepatoma-derived growth factor is involved in lung remodeling by stimulating epithelial growth, Am J Respir Cell Mol Biol 30, 459-469.
15. Everett, A. D., and Bushweller, J. (2003) Hepatoma derived growth factor is a nuclear targeted mitogen, Curr Drug Targets 4, 367-371.
16. El-Rifai, W., Frierson, H. F., Jr., Harper, J. C., Powell, S. M., and Knuutila, S. (2001) Expression profiling of gastric adenocarcinoma using cDNA array, Int J Cancer 92, 832-838.
17. Yamamoto, S., Tomita, Y., Hoshida, Y., Takiguchi, S., Fujiwara, Y., Yasuda, T., Doki, Y., Yoshida, K., Aozasa, K., Nakamura, H., and Monden, M. (2006) Expression of hepatoma-derived growth factor is correlated with lymph node metastasis and prognosis of gastric carcinoma, Clin Cancer Res 12, 117-122.
18. Yoshida, K., Nakamura, H., Okuda, Y., Enomoto, H., Kishima, Y., Uyama, H., Ito, H., Hirasawa, T., Inagaki, S., and Kawase, I. (2003) Expression of hepatoma-derived growth factor in hepatocarcinogenesis, J Gastroenterol Hepatol 18, 1293-1301.
19. Hu, T. H., Huang, C. C., Liu, L. F., Lin, P. R., Liu, S. Y., Chang, H. W., Changchien, C. S., Lee, C. M., Chuang, J. H., and Tai, M. H. (2003) Expression of hepatoma-derived growth factor in hepatocellular carcinoma, Cancer 98, 1444-1456.
20. Zhou, Z., Yamamoto, Y., Sugai, F., Yoshida, K., Kishima, Y., Sumi, H., Nakamura, H., and Sakoda, S. (2004) Hepatoma-derived growth factor is a neurotrophic factor harbored in the nucleus, J Biol Chem 279, 27320-27326.
21. El-Tahir, H. M., Dietz, F., Dringen, R., Schwabe, K., Strenge, K., Kelm, S., Abouzied, M. M., Gieselmann, V., and Franken, S. (2006) Expression of hepatoma-derived growth factor family members in the adult central nervous system, BMC Neurosci 7, 6.
22. Marubuchi, S., Okuda, T., Tagawa, K., Enokido, Y., Horiuchi, D., Shimokawa, R., Tamura, T., Qi, M. L., Eishi, Y., Watabe, K., Shibata, M., Nakagawa, M., and Okazawa, H. (2006) Hepatoma-derived growth factor, a new trophic factor for motor neurons, is up-regulated in the spinal cord of PQBP-1 transgenic mice before onset of degeneration, J Neurochem 99, 70-83.
23. Sue, S. C., Chen, J. Y., Lee, S. C., Wu, W. G., and Huang, T. H. (2004) Solution structure and heparin interaction of human hepatoma-derived growth factor, J Mol Biol 343, 1365-1377.
24. Abouzied, M. M., El-Tahir, H. M., Prenner, L., Haberlein, H., Gieselmann, V., and Franken, S. (2005) Hepatoma-derived growth factor. Significance of amino acid residues 81-100 in cell surface interaction and proliferative activity, J Biol Chem 280, 10945-10954.
25. Kishima, Y., Yamamoto, H., Izumoto, Y., Yoshida, K., Enomoto, H., Yamamoto, M., Kuroda, T., Ito, H., Yoshizaki, K., and Nakamura, H. (2002) Hepatoma-derived growth factor stimulates cell growth after translocation to the nucleus by nuclear localization signals, J Biol Chem 277, 10315-10322.
26. Tkachenko, E., Lutgens, E., Stan, R. V., and Simons, M. (2004) Fibroblast growth factor 2 endocytosis in endothelial cells proceed via syndecan-4-dependent activation of Rac1 and a Cdc42-dependent macropinocytic pathway, J Cell Sci 117, 3189-3199.
27. Gleizes, P. E., Noaillac-Depeyre, J., Dupont, M. A., and Gas, N. (1996) Basic fibroblast growth factor (FGF-2) is addressed to caveolae after binding to the plasma membrane of BHK cells, Eur J Cell Biol 71, 144-153.
28. Wang, C. H. (2009) PWWP/HATH domain of HDGF binds to cell surface heparin sulfate and triggers macropinocytosis to regulate fibroblast cell migration and proliferation, submitted.
29. 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, J Biomol NMR 6, 277-293.
30. Krugh, T. R., Laing, J. W., and Young, M. A. (1976) Hydrogen-bonded complexes of the ribodinucleoside monophosphates in aqueous solution. Proton magnetic resonance studies, Biochemistry 15, 1224-1228.
31. Kosen, P. A. (1989) Spin labeling of proteins, Methods Enzymol 177, 86-121.
32. Danielsson, J., Liljedahl, L., Barany-Wallje, E., Sonderby, P., Kristensen, L. H., Martinez-Yamout, M. A., Dyson, H. J., Wright, P. E., Poulsen, F. M., Maler, L., Graslund, A., and Kragelund, B. B. (2008) The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer, Biochemistry 47, 13428-13437.
33. Teilum, K., Kragelund, B. B., and Poulsen, F. M. (2002) Transient structure formation in unfolded acyl-coenzyme A-binding protein observed by site-directed spin labelling, J Mol Biol 324, 349-357.
34. Xue, Y., Podkorytov, I. S., Rao, D. K., Benjamin, N., Sun, H., and Skrynnikov, N. R. (2009) Paramagnetic relaxation enhancements in unfolded proteins: theory and application to drkN SH3 domain, Protein Sci 18, 1401-1424.
35. Lindfors, H. E., de Koning, P. E., Drijfhout, J. W., Venezia, B., and Ubbink, M. (2008) Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR, J Biomol NMR 41, 157-167.
36. Wu, K. P., and Baum, J. (2010) Detection of transient interchain interactions in the intrinsically disordered protein alpha-synuclein by NMR paramagnetic relaxation enhancement, J Am Chem Soc 132, 5546-5547.
37. Cierpicki, T., Liang, B., Tamm, L. K., and Bushweller, J. H. (2006) Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A, J Am Chem Soc 128, 6947-6951.
38. Van Horn, W. D., Beel, A. J., Kang, C., and Sanders, C. R. (2010) The impact of window functions on NMR-based paramagnetic relaxation enhancement measurements in membrane proteins, Biochim Biophys Acta 1798, 140-149.
39. Sue, S. C., Lee, W. T., Tien, S. C., Lee, S. C., Yu, J. G., Wu, W. J., Wu, W. G., and Huang, T. H. (2007) PWWP module of human hepatoma-derived growth factor forms a domain-swapped dimer with much higher affinity for heparin, J Mol Biol 367, 456-472.
40. Tang, C., Iwahara, J., and Clore, G. M. (2006) Visualization of transient encounter complexes in protein-protein association, Nature 444, 383-386.
41. Tang, C., Louis, J. M., Aniana, A., Suh, J. Y., and Clore, G. M. (2008) Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease, Nature 455, 693-696.