簡易檢索 / 詳目顯示

研究生: 陳冠雯
Chen, Guan-Wen
論文名稱: 低溫電子顯微鏡解析未成熟登革類病毒的構型
Cryo-EM reveals the conformation of immature dengue virus-like particle
指導教授: 吳尚蓉
Wu, Shang-Rung
學位類別: 碩士
Master
系所名稱: 醫學院 - 口腔醫學研究所
Institute of Oral Medicine
論文出版年: 2019
畢業學年度: 107
語文別: 英文
論文頁數: 49
中文關鍵詞: 低溫冷凍電子顯微鏡登革類病毒單粒子分析三維結構重組
外文關鍵詞: Cryo-electron microscopy, dengue virus-like particle, single particles analysis, three-dimensional reconstruction
相關次數: 點閱:119下載:0
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • 登革熱屬於黃病毒科,具有四種血清型。登革病毒顆粒主要由單鏈RNA基因組、脂質雙層膜和結構蛋白質組成。其中,結構蛋白質主要包括:包膜蛋白 (E)、膜蛋白 (M)和衣殼蛋白 (C)。在病毒複製過程中,新合成的登革病毒顆粒在內質網中組裝成未成熟顆粒,未成熟顆粒的結構具有前驅膜蛋白 (pr-M),病毒釋放出細胞過程中,弗林蛋白酶除去前驅分子 (pr),形成具有感染性的成熟登革病毒。然而,弗林蛋白酶切割被認為是低效的。未成熟的登革病毒缺乏感染細胞的能力,但登革病毒感染細胞過程中,會產生高比例的不具感染性的未成熟病毒顆粒,這些顆粒會藉由依賴性增強作用進入含有Fc接受體的細胞內,增加病毒增值的機會,亦是造成感染異型登革病毒產生重症原因。我們去年與中興大學趙老師發表文章說明,成熟的登革類病毒顆粒可以中和四型血清型,加上因為不含有感染基因組,因此具安全性,是個潛在的候選疫苗。我的研究目的是使用低溫電子顯微鏡解析未成熟類登革病毒結構,結構能告訴我們顆粒成熟過程中,表面蛋白的形態變化,及抗原決定位的分佈變化。為了得到高解析度結構,我們從兩方面著手,一是找到最佳樣品製備參數,降低樣品顆粒異質性,二是我們使用高階電子顯微鏡及影像擷取系統,並使用自動化大量收集影像。目前初步結構顯示未成熟類登革病毒的表面有突起,與成熟類登革病毒表面平滑不同,經過表面蛋白的嵌入 (fitting) 發現此突起是pr組成,此外,未成熟類登革病毒的表面蛋白E與成熟類登革病毒E的排列方式都是遵從T=1的排列,此與病毒顆粒是T=3排列不同。日後期待將結構解析度再提高,更細微探討穿膜區域的變化,此外研究抗原決定位的變化,與成熟類登革病毒結構的抗原決定位做比對 (mapping),這些結構資訊將有助於應用疫苗與藥物製劑上的開發。

    Dengue fever belongs to Flaviviridae family and has four serotypes. Dengue virus particles are mainly composed of a single-stranded RNA genome, a lipid bilayer membrane, and structural proteins. Among them, structural proteins are mainly composed of envelope (E), membrane (M) and capsid (C) proteins. In the process of virus replication, newly synthesized DENVs are assembled as immature particles which have pr-M protein. The furin then cleaves away pr so that the mature DENV contains only M protein and is infectious. However, the furin cleavage is thought to be inefficient. It is believed that a completely immature DENV lacks the ability to infect cell, but cells infected with dengue virus release a high proportion of immature virions and the immature DENV could enter to the cells containing Fc receptors by dependence enhancement, increasing the chance of virus value-adding, and causing serious causes of infection with heterologous dengue virus. Our previous study showed that mature dengue viral like particle (mD2VLP) could neutralize four serotypes and was therefore suggested to be a safe vaccine candidate. My study is to solve the structure of dengue VLP in immature form (imDENV VLP) using cryo-EM. The structure of imDENV VLP could tell us the surface protein rearrangement and epitope exposure changes during maturation process. To obtain the high-resolution structure, first, we optimized the sample preparation protocol; second, we used the advanced cryo-EM and image taking system which is equipped with automatic data collection. Current imDENV VLP structure showed that there were protrusions on the imDENV VLP surface, the E lied parallelly on the surface and followed T=1 lattice arrangement which resembled the mD2VLP. In the future, we would like to improve the resolution, and map the epitopes and TM/stem regions with mature VLP. The structure information gathered could provide us the hints of vaccine development and drug design.

    中文摘要 I Abstract II Acknowledgement III Catalogues IV Figure List VII Table List VIII Abbreviations IX 1. Introduction 1 1.1 Dengue virus 1 1.2 Dengue virus vaccine development 2 1.3 Dengue virus structure 3 1.4 The flavivirus life cycles 4 1.5 Dengue virus-like particles (DENV VLPs) 4 1.6 Transmission electron microscopy (TEM) 5 1.7 Cryo-Electron Microscopy (Cryo-EM) 6 1.8 Single-particles analysis 7 2. Rationale and Aim 8 3. Materials and methods 9 3.1 The specimen preparation and purification 9 3.1.1 Immature dengue virus-like particles preparation 9 3.1.2 VLP secretion titer by Ag-capture ELISA 10 3.1.3 Concentrate the immature DENV VLPs 10 3.1.4 20% sucrose/potassium cushion purification 11 3.1.5 5-25% discontinuous/continuous gradient purification 11 3.1.6 Ag-capture ELISA determination 12 3.1.7 Pool peak fractions 13 3.1.8 Concentrate each fraction by using Ultra centrifugal filters 13 3.2 Transmission Electron Microscopy facility 14 3.3 Negative stain approach 15 3.4 Cryo-electron microscopy (Cryo-EM) technology 15 3.5 Three-dimensional reconstruction of immature DENV VLP 16 4. Results 17 4.1 TEM revealed the heterogeneity in the sample production 17 4.2 Three-dimension reconstruction of immature DENV VLPs 17 4.2.1 2D images analysis 17 4.2.2 3D structure of immature DENV VLPs 18 5. Discussion 19 5.1 Sample heterogeneity 19 5.2 Strategy of improving high resolution of the structure 20 5.3 Organization of immature dengue VLP 20 5.4 Our imDENV VLP might have loose structure which is important for immunology study 22 6. Conclusion 24 7. References 25 8. Figures 29 9. Tables 38 10. Appendix 40

    1. Bhatt, S., et al., The global distribution and burden of dengue. Nature, 2013. 496(7446): p. 504-7.
    2. Yuan, H.Y., et al., Prediction of annual dengue incidence by hydro-climatic extremes for southern Taiwan. Int J Biometeorol, 2019. 63(2): p. 259-268.
    3. Estrada, J.L.T., et al., Spatial repellency and other effects of transfluthrin and linalool on Aedes aegypti and Aedes albopictus. J Vector Ecol, 2019. 44(1): p. 89-93.
    4. Lim, X.X., et al., Conformational changes in intact dengue virus reveal serotype-specific expansion. Nat Commun, 2017. 8: p. 14339.
    5. Astuti, E.P., et al., Paediatric dengue infection in Cirebon, Indonesia: a temporal and spatial analysis of notified dengue incidence to inform surveillance. Parasit Vectors, 2019. 12(1): p. 186.
    6. Halstead, S.B., Dengue. Lancet, 2007. 370(9599): p. 1644-52.
    7. Coller, B.A. and D.E. Clements, Dengue vaccines: progress and challenges. Curr Opin Immunol, 2011. 23(3): p. 391-8.
    8. Chien, Y.W., et al., Seroepidemiology of dengue virus infection among adults during the ending phase of a severe dengue epidemic in southern Taiwan, 2015. BMC Infect Dis, 2019. 19(1): p. 338.
    9. Kostyuchenko, V.A., et al., Immature and mature dengue serotype 1 virus structures provide insight into the maturation process. J Virol, 2013. 87(13): p. 7700-7.
    10. Zhang, X., et al., Cryo-EM structure of the mature dengue virus at 3.5-A resolution. Nat Struct Mol Biol, 2013. 20(1): p. 105-10.
    11. Fibriansah, G., et al., A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins. Nat Commun, 2015. 6: p. 6341.
    12. Kostyuchenko, V.A., et al., Near-atomic resolution cryo-electron microscopic structure of dengue serotype 4 virus. J Virol, 2014. 88(1): p. 477-82.
    13. Li, J., et al., Structural and Functional Characterization of a Cross-Reactive Dengue Virus Neutralizing Antibody that Recognizes a Cryptic Epitope. Structure, 2018. 26(1): p. 51-59 e4.
    14. Rodenhuis-Zybert, I.A., et al., Immature Dengue Virus: A Veiled Pathogen? Plos Pathogens, 2010. 6(1).
    15. Rouvinski, A., et al., Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope. Nat Commun, 2017. 8: p. 15411.
    16. Khetarpal, N. and I. Khanna, Dengue Fever: Causes, Complications, and Vaccine Strategies. J Immunol Res, 2016. 2016: p. 6803098.
    17. Halstead, S.B., Safety issues from a Phase 3 clinical trial of a live-attenuated chimeric yellow fever tetravalent dengue vaccine. Hum Vaccin Immunother, 2018. 14(9): p. 2158-2162.
    18. Heinz, F.X. and K. Stiasny, Flaviviruses and flavivirus vaccines. Vaccine, 2012. 30(29): p. 4301-6.
    19. Kuhn, R.J., et al., Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell, 2002. 108(5): p. 717-25.
    20. Pierson, T.C., et al., Structural insights into the mechanisms of antibody-mediated neutralization of flavivirus infection: implications for vaccine development. Cell Host Microbe, 2008. 4(3): p. 229-38.
    21. Prasad, V.M., et al., Structure of the immature Zika virus at 9 A resolution. Nat Struct Mol Biol, 2017. 24(2): p. 184-186.
    22. Rodenhuis-Zybert, I.A., et al., Immature dengue virus: a veiled pathogen? PLoS Pathog, 2010. 6(1): p. e1000718.
    23. Pierson, T.C. and M.S. Diamond, Degrees of maturity: the complex structure and biology of flaviviruses. Curr Opin Virol, 2012. 2(2): p. 168-75.
    24. Halstead, S.B., Neutralization and antibody-dependent enhancement of dengue viruses. Adv Virus Res, 2003. 60: p. 421-67.
    25. Fuenmayor, J., F. Godia, and L. Cervera, Production of virus-like particles for vaccines. N Biotechnol, 2017. 39(Pt B): p. 174-180.
    26. Allison, S.L., et al., Oligomeric rearrangement of tick-borne encephalitis virus envelope proteins induced by an acidic pH. J Virol, 1995. 69(2): p. 695-700.
    27. Shen, W.F., et al., Epitope resurfacing on dengue virus-like particle vaccine preparation to induce broad neutralizing antibody. Elife, 2018. 7.
    28. Bai, X.C., G. McMullan, and S.H. Scheres, How cryo-EM is revolutionizing structural biology. Trends Biochem Sci, 2015. 40(1): p. 49-57.
    29. Brenner, S. and R.W. Horne, A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta, 1959. 34: p. 103-10.
    30. De Carlo, S. and J.R. Harris, Negative staining and cryo-negative staining of macromolecules and viruses for TEM. Micron, 2011. 42(2): p. 117-31.
    31. Dubochet, J., et al., Cryo-electron microscopy of vitrified specimens. Q Rev Biophys, 1988. 21(2): p. 129-228.
    32. Callaway, E., The revolution will not be crystallized: a new method sweeps through structural biology. Nature, 2015. 525(7568): p. 172-4.
    33. Ludtke, S.J., P.R. Baldwin, and W. Chiu, EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol, 1999. 128(1): p. 82-97.
    34. Tang, G., et al., EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol, 2007. 157(1): p. 38-46.
    35. Wu, S.R., et al., Single-particle cryoelectron microscopy analysis reveals the HIV-1 spike as a tripod structure. Proc Natl Acad Sci U S A, 2010. 107(44): p. 18844-9.
    36. Wu, S.R., et al., The dynamic envelope of a fusion class II virus. Prefusion stages of semliki forest virus revealed by electron cryomicroscopy. J Biol Chem, 2007. 282(9): p. 6752-62.
    37. Yan, X., R.S. Sinkovits, and T.S. Baker, AUTO3DEM--an automated and high throughput program for image reconstruction of icosahedral particles. J Struct Biol, 2007. 157(1): p. 73-82.
    38. Wu, S.R., et al., The dynamic envelope of a fusion class II virus. E3 domain of glycoprotein E2 precursor in Semliki Forest virus provides a unique contact with the fusion protein E1. J Biol Chem, 2008. 283(39): p. 26452-60.
    39. Kimanius, D., et al., Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Elife, 2016. 5.
    40. Ge, L. and R. Schekman, The ER-Golgi intermediate compartment feeds the phagophore membrane. Autophagy, 2014. 10(1): p. 170-2.
    41. Randolph, V.B., G. Winkler, and V. Stollar, Acidotropic amines inhibit proteolytic processing of flavivirus prM protein. Virology, 1990. 174(2): p. 450-8.
    42. Zhang, Y., et al., Structure of immature West Nile virus. J Virol, 2007. 81(11): p. 6141-5.
    43. Yu, I.M., et al., Structure of the immature dengue virus at low pH primes proteolytic maturation. Science, 2008. 319(5871): p. 1834-7.
    44. Li, L., et al., The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science, 2008. 319(5871): p. 1830-4.
    45. Yu, Z. and C. Bajaj, Computational approaches for automatic structural analysis of large biomolecular complexes. IEEE/ACM Trans Comput Biol Bioinform, 2008. 5(4): p. 568-82.
    46. Zhang, Q., et al., Direct observation of multiferroic vortex domains in YMnO3. Sci Rep, 2013. 3: p. 2741.

    無法下載圖示
    校外:不公開
    電子論文及紙本論文均尚未授權公開
    QR CODE