研究生: |
江雅綾 Chiang, Ya Ling |
---|---|
論文名稱: |
用原子力顯微鏡觀察細菌蛋白MinE在雲母和雙層膜上的自組裝 Atomic Force Mcroscopy Charaterization of Fibrils Formed by Bacteria protein MinE on Mica and a Supported lipid bilayer |
指導教授: |
黃英碩
Hwang, Ing Shouh |
口試委員: |
張嘉升
陳祺 Wolfgang B. Fischer (費伍岡) 史有伶 邱顯智 楊志文 |
學位類別: |
博士 Doctor |
系所名稱: |
工學院 - 材料科學工程學系 Materials Science and Engineering |
論文出版年: | 2016 |
畢業學年度: | 104 |
語文別: | 英文 |
論文頁數: | 76 |
中文關鍵詞: | 原子力顯微鏡 |
外文關鍵詞: | Atomic Force Mcroscopy |
相關次數: | 點閱:4 下載:0 |
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生物系統中的蛋白、胜肽分子大部分都需要經過特殊的摺疊或自組裝之後才能發揮其應有的功能,然而這些生物分子的自組裝機制及過程到目前為止都還不是非常了解。在論文中,我們使用了最近被發現具有類β-蛋白澱粉的MinE蛋白質,用高靈敏度的頻率調制原子力顯微鏡觀察其全長以及其N端胺基酸序列1-31在雲母及單層雙層脂肪膜上的自組裝,MinE在大腸桿菌細胞分裂過程中扮演重要角色,而β-蛋白澱粉則在自然界中廣泛存在,大致可分為具功能性以及不具功能性β-蛋白澱粉,不具功能性的β-蛋白澱粉蛋白堆積在人體中會導致疾病,堆積在腦部會導致神經方面的疾病,例如愛滋海默症,而正常具功能性的β-蛋白澱粉則具高穩定性,通常扮演細胞骨架的功能。
從實驗中我們發現MinE其N端胺基酸序列1-31的合成胜肽在雲母上會自組裝成長的纖維狀巨分子,且因為頻率調制原子力顯微鏡的高靈敏度可以解出纖維狀巨分子是由一束四到六條較細的原纖維組成。纖維狀巨分子的型態會因為溶液中不同的鹽離子及蔗糖濃度而呈現直線、捲曲以及圓的型態,顯示溶液的環境對胜肽及蛋白質的自組裝有ㄧ定的影響,另外我們也觀察到MinE其N端在溶液中自組裝的動態行為,我們更進一步發現胜肽在雲母鋪附的雙層膜上也會自組裝成長的纖維狀巨分子,觀察結果顯示當雙層膜及雲母同時存在,胜肽自組裝的纖維結構只在雙層膜上出現,在雲母上則不會形成,顯示胜肽對雙層膜有高親合力。而在MinE全長的實驗中,MinE全長在雲母上的自組裝並沒有表現出特殊的可辨識的結構,當與在雲母上鋪附的雙層膜作用時則會在雙層膜的邊緣形成短的纖維化巨分子,與在雲母上的行為有所差異,也與MinE N端的表現不同。此篇論文對MinE這個具重要功能的蛋白用原子力顯微鏡做了詳盡的探討。
The placement of cell division site in model bacteria E.coli is tightly regulated by Min system. In E. Coli, Min system blocks the polar position for cell division, MinC, D and E are three members in Min system. Among the Min system, MinE can form a ring-like structure (the MinE-ring) in E. coli and oscillates with MinCD. MinE includes 88 amino acids and contains three domains: the N-terminal membrane targeting domain (MinE2-12), the anti-MinCD domain (MinE13-31) and the C-terminal dimerization domain (MinE32-88). In this study, we study the self-assembly behavior of MinE and MinE1-31 on mica and on supported lipid bilayer prepared from E-coli phospholipids extraction.
To investigate the self-assembly behavior of MinE and MinE1-31, we utilize highly sensitive Frequency Modulation Atomic Force Microscopy (FM-AFM). FM-AFM applies a small force over the surface, thereby causes little deformation on soft and fragile biological samples. The results indicated that the features of both MinE and MinE1-31 filaments on supported lipid bilayer were very different from those assembling on mica. On mica, N-terminal MinE1-31 fragments self-assembled into filamentous bundles that contained 4~6 prorofilaments. However, the number of protofilament within filamentous bundles varied when appiled MinE1-31 on support lipid bilayer. For full length MinE, although the self-assembled structure shown on mica is amorphous, MinE was able to arrange into short protein filaments that decorated around edges of the membrane patches. We can conclude that MinEexhibits spatial preference to membrane edge but MinE1-31 does not. The results also hint that C-terminal MinE plays the main role in MinE membrane edge binding activity. Thesefindings may be cruicial to the MinE-ring formation in the midcell.
1. Lutkenhaus and J, Addinall S (1997) Bacterial cell division and the Z ring. Annual review of biochemistry 66: 93-116.
2. Adams DW, Wu LJ, Errington J (2014) Cell cycle regulation by the bacterial nucleoid. Current opinion in microbiology 22: 94-101.
3. Hu Z, Lutkenhaus J (2001) Topological Regulation of Cell Division in< i> E. coli</i>: Spatiotemporal Oscillation of MinD Requires Stimulation of Its ATPase by MinE and Phospholipid. Molecular cell 7: 1337-1343.
4. Shih Y-L, Rothfield L (2006) The bacterial cytoskeleton. Microbiology and Molecular Biology Reviews 70: 729-754.
5. Raskin DM, de Boer PA (1997) The MinE ring: an FtsZ-independent cell structure required for selection of the correct division site in E. coli. Cell 91: 685-694.
6. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Physical review letters 56: 930.
7. Morris VJ, Kirby AR, Gunning AP (2010) Atomic force microscopy for biologists: Imperial College Press London.
8. BONNELL D (2001) Scanning probe microscopy and spectroscopy: theory, techniques, and applications: Wiley-vch.
9. Sugimoto Y, Pou P, Abe M, Jelinek P, Pérez R, et al. (2007) Chemical identification of individual surface atoms by atomic force microscopy. Nature 446: 64-67.
10. Jalili N, Laxminarayana K (2004) A review of atomic force microscopy imaging systems: application to molecular metrology and biological sciences. Mechatronics 14: 907-945.
11. Giessibl FJ (2003) Advances in atomic force microscopy. Reviews of modern physics 75: 949.
12. Martin Y, Williams CC, Wickramasinghe HK (1987) Atomic force microscope–force mapping and profiling on a sub 100‐Å scale. Journal of Applied Physics 61: 4723-4729.
13. Albrecht T, Grütter P, Horne D, Rugar D (1991) Frequency modulation detection using high‐Q cantilevers for enhanced force microscope sensitivity. Journal of Applied Physics 69: 668-673.
14. Giessibl FJ (1995) Atomic resolution of the silicon (111)-(7x7) surface by atomic force microscopy. Science 267: 68-71.
15. Sugawara Y, Ohta M, Ueyama H, Morita S (1995) Defect motion on an InP (110) surface observed with noncontact atomic force microscopy. Science 270: 1646-1648.
16. Fukuma T, Mostaert AS, Serpell LC, Jarvis SP (2008) Revealing molecular-level surface structure of amyloid fibrils in liquid by means of frequency modulation atomic force microscopy. Nanotechnology 19: 384010.
17. Fukuma T, Higgins MJ, Jarvis SP (2007) Direct imaging of lipid-ion network formation under physiological conditions by frequency modulation atomic force microscopy. Physical review letters 98: 106101.
18. Fukuma T, Kobayashi K, Matsushige K, Yamada H (2005) True atomic resolution in liquid by frequency-modulation atomic force microscopy. Applied Physics Letters 87: 034101.
19. Giessibl FJ (1997) Forces and frequency shifts in atomic-resolution dynamic-force microscopy. Physical Review B 56: 16010.
20. Yang CW, Hwang IS, Chen YF, Chang CS, Tsai DP (2007) Imaging of soft matter with tapping-mode atomic force microscopy and non-contact-mode atomic force microscopy. Nanotechnology 18.
21. Grütter P, Zimmermann‐Edling W, Brodbeck D (1992) Tip artifacts of microfabricated force sensors for atomic force microscopy. Applied Physics Letters 60: 2741-2743.
22. Chen Y, Cai J, Liu M, Zeng G, Feng Q, et al. (2004) Research on double‐probe, double‐and triple‐tip effects during atomic force microscopy scanning. Scanning 26: 155-161.
23. Margolin W (2005) FtsZ and the division of prokaryotic cells and organelles. Nature Reviews Molecular Cell Biology 6: 862-871.
24. Shih YL, Zheng M (2013) Spatial control of the cell division site by the Min system in Escherichia coli. Environmental microbiology 15: 3229-3239.
25. De Boer P, Crossley RE, Rothfield LI (1988) Isolation and properties of minB, a complex genetic locus involved in correct placement of the division site in Escherichia coli. Journal of bacteriology 170: 2106-2112.
26. Raskin DM, de Boer PA (1999) MinDE-dependent pole-to-pole oscillation of division inhibitor MinC in Escherichia coli. Journal of bacteriology 181: 6419-6424.
27. De Boer P, Crossley RE, Rothfield LI (1992) Roles of MinC and MinD in the site-specific septation block mediated by the MinCDE system of Escherichia coli. Journal of bacteriology 174: 63-70.
28. de Boer PA, Crossley RE, Rothfield LI (1989) A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli. Cell 56: 641-649.
29. Zheng M, Chiang YL, Lee HL, Kong LR, Hsu ST, et al. (2014) Self-Assembly of MinE on the Membrane Underlies Formation of the MinE Ring to Sustain Function of the Escherichia coli Min System. J Biol Chem 289: 21252-21266.
30. Shih YL, Huang KF, Lai HM, Liao JH, Lee CS, et al. (2011) The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature. PLoS One 6: e21425.
31. Hsieh CW, Lin TY, Lai HM, Lin CC, Hsieh TS, et al. (2010) Direct MinE-membrane interaction contributes to the proper localization of MinDE in E. coli. Mol Microbiol 75: 499-512.
32. Chiang Y-L, Chang Y-C, Chiang I-C, Mak H-M, Hwang S, et al. (2015) Atomic Force Microscopy Characterization of Protein Fibrils Formed by the Amyloidogenic Region of the Bacterial Protein MinE on Mica and a Supported Lipid Bilayer. PLoS One 10: e0142506.
33. Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, et al. (2012) Geometry sensing by self-organized protein patterns. Proceedings of the National Academy of Sciences 109: 15283-15288.
34. Zheng M, Chiang Y-L, Lee H-L, Kong L-R, Hsu S-TD, et al. (2014) Self-Assembly of MinE on the Membrane Underlies Formation of the MinE-Ring to Sustain Function of the E. coli Min System. Journal of Biological Chemistry: jbc. M114. 571976.
35. Cooper GM, Hausman RE (2000) The cell: Sinauer Associates Sunderland.
36. Makin OS, Sikorski P, Serpell LC (2006) Diffraction to study protein and peptide assemblies. Current opinion in chemical biology 10: 417-422.
37. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75: 333-366.
38. Hane F, Drolle E, Gaikwad R, Faught E, Leonenko Z (2011) Amyloid-β aggregation on model lipid membranes: an atomic force microscopy study. Journal of Alzheimer's Disease 26: 485-494.
39. Selivanova O, Galzitskaya O (2012) Structural polymorphism and possible pathways of amyloid fibril formation on the example of insulin protein. Biochemistry (Moscow) 77: 1237-1247.
40. Fowler DM, Koulov AV, Balch WE, Kelly JW (2007) Functional amyloid–from bacteria to humans. Trends in biochemical sciences 32: 217-224.
41. Lührs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, et al. (2005) 3D structure of Alzheimer's amyloid-β (1–42) fibrils. Proceedings of the National Academy of Sciences of the United States of America 102: 17342-17347.
42. Stromer T, Serpell LC (2005) Structure and morphology of the Alzheimer's amyloid fibril. Microscopy research and technique 67: 210-217.
43. Wegmann S, Medalsy ID, Mandelkow E, Müller DJ (2013) The fuzzy coat of pathological human Tau fibrils is a two-layered polyelectrolyte brush. Proceedings of the National Academy of Sciences 110: E313-E321.
44. Wegmann S, Jung YJ, Chinnathambi S, Mandelkow E-M, Mandelkow E, et al. (2010) Human Tau isoforms assemble into ribbon-like fibrils that display polymorphic structure and stability. Journal of Biological Chemistry 285: 27302-27313.
45. Quist A, Doudevski I, Lin H, Azimova R, Ng D, et al. (2005) Amyloid ion channels: a common structural link for protein-misfolding disease. Proc Natl Acad Sci U S A 102: 10427-10432.
46. Fink AL (2005) Natively unfolded proteins. Current opinion in structural biology 15: 35-41.
47. Forman CJ, Nickson AA, Anthony-Cahill SJ, Baldwin AJ, Kaggwa G, et al. (2012) The morphology of decorated amyloid fibers is controlled by the conformation and position of the displayed protein. ACS nano 6: 1332-1346.
48. Drolle E, Hane F, Lee B, Leonenko Z (2014) Atomic force microscopy to study molecular mechanisms of amyloid fibril formation and toxicity in Alzheimer's disease. Drug Metabolism Reviews 46: 207-223.
49. Milhiet P-E, Yamamoto D, Berthoumieu O, Dosset P, Le Grimellec C, et al. (2010) Deciphering the structure, growth and assembly of amyloid-like fibrils using high-speed atomic force microscopy. Plos One 5: e13240.
50. Zhang S, Andreasen M, Nielsen JT, Liu L, Nielsen EH, et al. (2013) Coexistence of ribbon and helical fibrils originating from hIAPP20–29 revealed by quantitative nanomechanical atomic force microscopy. Proceedings of the National Academy of Sciences 110: 2798-2803.
51. Jarvis S, Mostaert A (2012) The functional fold: amyloid structures in nature: CRC Press.
52. Chapman MR, Robinson LS, Pinkner JS, Roth R, Heuser J, et al. (2002) Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 295: 851-855.
53. Barnhart MM, Chapman MR (2006) Curli biogenesis and function. Annual review of microbiology 60: 131.
54. Cherny I, Rockah L, Levy-Nissenbaum O, Gophna U, Ron EZ, et al. (2005) The Formation of< i> Escherichia coli</i> Curli Amyloid Fibrils is Mediated by Prion-like Peptide Repeats. Journal of molecular biology 352: 245-252.
55. Gebbink MF, Claessen D, Bouma B, Dijkhuizen L, Wösten HA (2005) Amyloids—a functional coat for microorganisms. Nature Reviews Microbiology 3: 333-341.
56. Claessen D, Rink R, de Jong W, Siebring J, de Vreugd P, et al. (2003) A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils. Genes & development 17: 1714-1726.
57. Shorter J, Lindquist S (2005) Prions as adaptive conduits of memory and inheritance. Nature Reviews Genetics 6: 435-450.
58. Dos Reis S, Coulary-Salin B, Forge V, Lascu I, Bégueret J, et al. (2002) The HET-s prion protein of the filamentous fungus Podospora anserina aggregates in vitro into amyloid-like fibrils. Journal of Biological Chemistry 277: 5703-5706.
59. Balguerie A, Reis SD, Ritter C, Chaignepain S, Coulary‐Salin B, et al. (2003) Domain organization and structure–function relationship of the HET‐s prion protein of Podospora anserina. The EMBO journal 22: 2071-2081.
60. Ritter C, Maddelein M-L, Siemer AB, Lührs T, Ernst M, et al. (2005) Correlation of structural elements and infectivity of the HET-s prion. Nature 435: 844-848.
61. Uptain SM, Lindquist S (2002) Prions as protein-based genetic elements. Annual Reviews in Microbiology 56: 703-741.
62. Baxa U, Cheng N, Winkler DC, Chiu TK, Davies DR, et al. (2005) Filaments of the Ure2p prion protein have a cross-β core structure. Journal of structural biology 150: 170-179.
63. King C-Y, Tittmann P, Gross H, Gebert R, Aebi M, et al. (1997) Prion-inducing domain 2–114 of yeast Sup35 protein transforms in vitro into amyloid-like filaments. Proceedings of the National Academy of Sciences 94: 6618-6622.
64. True HL, Berlin I, Lindquist SL (2004) Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. Nature 431: 184-187.
65. Mackay JP, Matthews JM, Winefield RD, Mackay LG, Haverkamp RG, et al. (2001) The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures. Structure 9: 83-91.
66. Butko P, Buford JP, Goodwin JS, Stroud PA, McCormick CL, et al. (2001) Spectroscopic evidence for amyloid-like interfacial self-assembly of hydrophobin Sc3. Biochemical and biophysical research communications 280: 212-215.
67. de Vocht ML, Reviakine I, Wösten HA, Brisson A, Wessels JG, et al. (2000) Structural and functional role of the disulfide bridges in the hydrophobin SC3. Journal of Biological Chemistry 275: 28428-28432.
68. Kwan A, Winefield R, Sunde M, Matthews J, Haverkamp R, et al. (2006) Structural basis for rodlet assembly in fungal hydrophobins. Proceedings of the National Academy of Sciences of the United States of America 103: 3621-3626.
69. Iconomidou VA, Vriend G, Hamodrakas SJ (2000) Amyloids protect the silkmoth oocyte and embryo. FEBS letters 479: 141-145.
70. Iconomidou VA, Chryssikos GD, Gionis V, Galanis AS, Cordopatis P, et al. (2006) Amyloid fibril formation propensity is inherent into the hexapeptide tandemly repeating sequence of the central domain of silkmoth chorion proteins of the A-family. Journal of structural biology 156: 480-488.
71. Podrabsky JE, Carpenter JF, Hand SC (2001) Survival of water stress in annual fish embryos: dehydration avoidance and egg envelope amyloid fibers. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 280: R123-R131.
72. Kenney JM, Knight D, Wise MJ, Vollrath F (2002) Amyloidogenic nature of spider silk. European Journal of Biochemistry 269: 4159-4163.
73. Fowler DM, Koulov AV, Alory-Jost C, Marks MS, Balch WE, et al. (2005) Functional amyloid formation within mammalian tissue. PLoS biology 4: e6.
74. Iglic A, Kulkarni CV (2014) Advances in Planar Lipid Bilayers and Liposomes: Elsevier.
75. Castellana ET, Cremer PS (2006) Solid supported lipid bilayers: From biophysical studies to sensor design. Surface Science Reports 61: 429-444.
76. Tamm LK, McConnell HM (1985) Supported phospholipid bilayers. Biophysical journal 47: 105-113.
77. McConnell H, Watts T, Weis R, Brian A (1986) Supported planar membranes in studies of cell-cell recognition in the immune system. Biochimica et Biophysica Acta (BBA)-Reviews on Biomembranes 864: 95-106.
78. Brian AA, McConnell HM (1984) Allogeneic stimulation of cytotoxic T cells by supported planar membranes. Proceedings of the National Academy of Sciences 81: 6159-6163.
79. Kalb E, Frey S, Tamm LK (1992) Formation of supported planar bilayers by fusion of vesicles to supported phospholipid monolayers. Biochimica et Biophysica Acta (BBA)-Biomembranes 1103: 307-316.
80. Jiang FY, Bouret Y, Kindt JT (2004) Molecular dynamics simulations of the lipid bilayer edge. Biophysical journal 87: 182-192.
81. Smith AM, Vinchurkar M, Gronbech-Jensen N, Parikh AN (2010) Order at the edge of the bilayer: Membrane remodeling at the edge of a planar supported bilayer is accompanied by a localized phase change. Journal of the American Chemical Society 132: 9320-9327.
82. Lu Y-H, Yang C-W, Hwang I-S (2012) Molecular Layer of Gaslike Domains at a Hydrophobic–Water Interface Observed by Frequency-Modulation Atomic Force Microscopy. Langmuir 28: 12691-12695.
83. Hsieh CW, Lin TY, Lai HM, Lin CC, Hsieh TS, et al. (2010) Direct MinE–membrane interaction contributes to the proper localization of MinDE in E. coli. Molecular microbiology 75: 499-512.
84. Stafford RE, Fanni T, Dennis EA (1989) Interfacial properties and critical micelle concentration of lysophospholipids. Biochemistry 28: 5113-5120.
85. Weltzien HU (1979) Cytolytic and membrane-perturbing properties of lysophosphatidylcholine. Biochimica et Biophysica Acta (BBA)-Reviews on Biomembranes 559: 259-287.
86. Vendeville A, Lariviere D, Fourmentin E (2011) An inventory of the bacterial macromolecular components and their spatial organization. FEMS Microbiol Rev 35: 395-414.
87. Minton AP (2005) Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations. J Pharm Sci 94: 1668-1675.
88. Popp D, Iwasa M, Narita A, Erickson HP, Maeda Y (2009) FtsZ condensates: an in vitro electron microscopy study. Biopolymers 91: 340-350.
89. Harries D, Rosgen J (2008) A practical guide on how osmolytes modulate macromolecular properties. METHODS IN CELL BIOLOGY: Elsevier Inc. pp. 679-735.
90. Cacace MG, Landau EM, Ramsden JJ (1997) The Hofmeister series: salt and solvent effects on interfacial phenomena. Q Rev Biophys 30: 241-277.