(3.230.76.48) 您好!臺灣時間:2021/04/13 16:12
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果

詳目顯示:::

我願授權國圖
: 
twitterline
研究生:張哲銘
研究生(外文):Che-Ming Chang
論文名稱(外文):Molecular Dynamics Simulation of the Molecular Mechanism of Membrane Fusion
指導教授:蔡惠旭
學位類別:碩士
校院名稱:國立中央大學
系所名稱:化學學系
學門:自然科學學門
學類:化學學類
論文種類:學術論文
論文出版年:2013
畢業學年度:101
語文別:英文
論文頁數:73
中文關鍵詞:微胞融合囊泡融合鈣離子能量圖融合機制
外文關鍵詞:micelle fusionvesicle fusioncalciumenergy landscapefusion mechanism
相關次數:
  • 被引用被引用:0
  • 點閱點閱:166
  • 評分評分:系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
細胞膜融合在生物系統中扮演了非常重要的角色,例如細胞間的物質傳遞;不過其基本的融合機制卻尚未完全瞭解。在本篇論文中,我們使用全原子分子動態模擬來探討由鈣離子誘導POPE組成的微胞(Micelle)及囊泡(Vesicle)自發性融合的反應機制。研究結果顯示鈣離子具有較好的催化能力來加速POPE微胞的融合,相對的,在含鈉離子或鎂離子的系統中,我們並未觀察到微胞發生融合或是彼此互相靠近的現象。鈣離子在催化膜融合的過程中扮演以下幾種角色:(1). 鈣離子會使微胞的表面變得更具疏水性,引發兩個微胞互相靠近;(2). 鈣離子可以同時吸附在兩顆微胞之間,將兩顆微胞限制在一定的距離;(3). 鈣離子會使微胞變的較不穩定,增加生成pre-stalk state的機率。細胞膜融合的過程依序生成的步驟分別為pre-stalk、stalk、hemi-fused以及fused state。Pre-stalk 是整個融合過程的速率決定步驟,其特徵是將疏水性的磷脂質長碳鏈暴露至微胞表面或水層上。而stalk state是由疏水性的長碳鏈在兩顆微胞之間聚集形成一個具有疏水性核心的結構,其生成的過程中會伴隨著排水現象的發生。而在大尺寸的囊泡模擬中,我們也觀察到stalk state的結構中不只含有外層磷脂質,同時也含有些微的內層磷脂質;而hemi-fused state的橫膈膜只由內層磷脂質所組成。除此之外,模擬結果中也發現多個穩定的hemi-fused state。在本篇研究中,我們從能量、結構以及動力學等不同的角度來觀察細胞膜融合的分子機制。
Although membrane fusion plays key roles in many biological functions, its underlying molecular mechanism remains poorly understood. We employed all-atom molecular dynamics simulations to investigate the fusion mechanism, catalyzed by Ca2+ ions, of two highly hydrated 1-palmitoyl-2-oleoyl-sn-3-phosphoethanolamine (POPE) micelles and vesicels. Our simulations revealed that Ca2+ ions are capable of catalyzing the fusion of POPE micelles; in contrast, we did not observe close contact of the two micelles in the presence of only Na+ or Mg2+ ions. The Ca2+ ions play a key role in catalyzing the micelle fusion in three aspects: creating a more-hydrophobic surface on the micelles, binding two micelles together, and enhancing the formation of the pre-stalk state. Effective fusion proceeds through sequential formation of pre-stalk, stalk, hemifused-like, and fused states. The pre-stalk state is a state featuring solvent-exposed lipid tails; its formation is the rate-limiting step. The stalk state is a state where a localized hydrophobic core is formed connecting two micelles; its formation occurs in conjunction with a dehydration process between two micelles. Our large-scale simulations of vesicle fusion show the stalk formation is mainly dominated by the outer lipids, but it also involves with the inner lipids. On the other hand, the formation of hemi-fused state is dominated by the inner lipids to a diaphragm. Moreover, more than one stable hemi-fused state can be formed. This study provides insight into the molecular mechanism of membrane fusion from the points of view of energetics, structure, and dynamics.
摘要 i
Abstract ii
誌謝 iii
Table of contents iv
List of figures vi
List of tables vii
Chapter 1 – Introduction 1
Chapter 2 – Computational Methods 4
2.1 Micelle Construct 4
2.2 Vesicle Construct 7
2.3 Setting of Molecular Dynamics Simulation 9
Chapter 3 – Results and Discussion of Micelle Fusion 13
3.1 Fusion Characteristics as a Function of Time of Micelle Fusion 13
3.2 Free Energy Landscape of Ca2+-Catalyzed Micelle Fusion 24
Chapter 4 –Results and Discussion of Vesicle Fusion 36
4.1 Fusion Characteristics as a Function of Time of Vesicle Fusion 36
4.2 Free Energy Landscape of Vesicle Fusion 46
Chapter 5 – Conclusions and Summary 49
Reference 50
Appendix A 57
Appendix B 58
Appendix C 59
Appendix D 61
[1] L.V. Chernomordik, M.M. Kozlov, Membrane Hemifusion: Crossing a Chasm in Two Leaps, Cell, 123 (2005) 375-382.
[2] R. Jahn, T. Lang, T.C. Südhof, Membrane Fusion, Cell, 112 (2003) 519-533.
[3] J.C. Shillcock, R. Lipowsky, Tension-induced fusion of bilayer membranes and vesicles, Nat Mater, 4 (2005) 225-228.
[4] P. Kasson, V.S. Pande, Control of membrane fusion mechanism by lipid composition: Predictions from ensemble molecular dynamics, PLOS Comput. Biol., 3 (2007) 2228-2238.
[5] A. Portis, C. Newton, W. Pangborn, D. Papahadjopoulos, Studies on the mechanism of membrane fusion: evidence for an intermembrane calcium(2+) ion-phospholipid complex, synergism with magnesium(2+) ion, and inhibition by spectrin, Biochemistry, 18 (1979) 780-790.
[6] R. Jahn, H. Grubmüller, Membrane fusion, Curr. Opin. Cell Biol., 14 (2002) 488-495.
[7] L. Yang, H.W. Huang, Observation of a Membrane Fusion Intermediate Structure, Science, 297 (2002) 1877-1879.
[8] L. Yang, H.W. Huang, A Rhombohedral Phase of Lipid Containing a Membrane Fusion Intermediate Structure, Biophys. J., 84 (2003) 1808-1817.
[9] S.-J. Marrink, A.E. Mark, Molecular View of Hexagonal Phase Formation in Phospholipid Membranes, Biophys. J., 87 (2004) 3894-3900.
[10] S.J. Marrink, A.E. Mark, The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations, J. Am. Chem. Soc., 125 (2003) 11144-11145.
[11] P.M. Kasson, N.W. Kelley, N. Singhal, M. Vrljic, A.T. Brunger, V.S. Pande, Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion, Proc. Natl. Acad. Sci., 103 (2006) 11916-11921.
[12] Y. Norizoe, K. Daoulas, M. Muller, Measuring excess free energies of self-assembled membrane structures, Faraday Discuss., 144 (2010) 369-391; discussion 445-381.
[13] Y. Kozlovsky, M.M. Kozlov, Stalk model of membrane fusion: solution of energy crisis, Biophys J, 82 (2002) 882-895.
[14] Y.G. Smirnova, S.J. Marrink, R. Lipowsky, V. Knecht, Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration, J Am Chem Soc, 132 (2010) 6710-6718.
[15] A. Grafmuller, J. Shillcock, R. Lipowsky, Pathway of membrane fusion with two tension-dependent energy barriers, Phys Rev Lett, 98 (2007) 218101.
[16] D. Mirjanian, A.N. Dickey, J.H. Hoh, T.B. Woolf, M.J. Stevens, Splaying of aliphatic tails plays a central role in barrier crossing during liposome fusion, The journal of physical chemistry. B, 114 (2010) 11061-11068.
[17] R. Schneggenburger, E. Neher, Presynaptic calcium and control of vesicle fusion, Curr. Opin. Neurobiol., 15 (2005) 266-274.
[18] J. Wilschut, N. Duzgunes, R. Fraley, D. Papahadjopoulos, Studies on the mechanism of membrane fusion: kinetics of calcium ion induced fusion of phosphatidylserine vesicles followed by a new assay for mixing of aqueous vesicle contents, Biochemistry, 19 (1980) 6011-6021.
[19] R. Ekerdt, D. Papahadjopoulos, Intermembrane contact affects calcium binding to phospholipid vesicles, Proc Natl Acad Sci U S A, 79 (1982) 2273-2277.
[20] L. Herbette, C.A. Napolitano, R.V. McDaniel, Direct determination of the calcium profile structure for dipalmitoyllecithin multilayers using neutron diffraction, Biophys. J., 46 (1984) 677-685.
[21] C. Altenbach, J. Seelig, Calcium binding to phosphatidylcholine bilayers as studied by deuterium magnetic resonance. Evidence for the formation of a calcium complex with two phospholipid molecules, Biochemistry, 23 (1984) 3913-3920.
[22] R. Dluhy, D.G. Cameron, H.H. Mantsch, R. Mendelsohn, Fourier transform infrared spectroscopic studies of the effect of calcium ions on phosphatidylserine, Biochemistry, 22 (1983) 6318-6325.
[23] Z.K. Issa, C.W. Manke, B.P. Jena, J.J. Potoff, Ca2+ Bridging of Apposed Phospholipid Bilayers, J. Phys. Chem. B, 114 (2010) 13249-13254.
[24] H.H. Tsai, W.X. Lai, H.D. Lin, J.B. Lee, W.F. Juang, W.H. Tseng, Molecular dynamics simulation of cation-phospholipid clustering in phospholipid bilayers: possible role in stalk formation during membrane fusion, Biochim. Biophys. Acta, 1818 (2012) 2742-2755.
[25] M. Ross, C. Steinem, H.-J. Galla, A. Janshoff, Visualization of Chemical and Physical Properties of Calcium-Induced Domains in DPPC/DPPS Langmuir−Blodgett Layers, Langmuir, 17 (2001) 2437-2445.
[26] L. Picas, M.T. Montero, A. Morros, M.E. Cabañas, B. Seantier, P.-E. Milhiet, J. Hernández-Borrell, Calcium-Induced Formation of Subdomains in Phosphatidylethanolamine−Phosphatidylglycerol Bilayers: A Combined DSC, 31P NMR, and AFM Study, J. Phys. Chem. B, 113 (2009) 4648-4655.
[27] Z.D. Schultz, I.M. Pazos, F.K. McNeil-Watson, E.N. Lewis, I.W. Levin, Magnesium-Induced Lipid Bilayer Microdomain Reorganizations: Implications for Membrane Fusion, J. Phys. Chem. B, 113 (2009) 9932-9941.
[28] Z.D. Schultz, I.W. Levin, Lipid Microdomain Formation: Characterization by Infrared Spectroscopy and Ultrasonic Velocimetry, Biophys. J., 94 (2008) 3104-3114.
[29] H. Binder, O. Zschörnig, The effect of metal cations on the phase behavior and hydration characteristics of phospholipid membranes, Chem. Phys. Lipids, 115 (2002) 39-61.
[30] V. Knecht, S.-J. Marrink, Molecular Dynamics Simulations of Lipid Vesicle Fusion in Atomic Detail, Biophys. J., 92 (2007) 4254-4261.
[31] J.B. Klauda, R.M. Venable, J.A. Freites, J.W. O'Connor, D.J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A.D. MacKerell, R.W. Pastor, Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types, J. Phys. Chem. B, 114 (2010) 7830-7843.
[32] W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, Comparison of Simple Potential Functions for Simulating Liquid Water, J. Chem. Phys., 79 (1983) 926-935.
[33] L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, K. Schulten, NAMD2: Greater scalability for parallel molecular dynamics, J. Comp. Phys., 151 (1999) 283-312.
[34] S.E. Feller, Y.H. Zhang, R.W. Pastor, B.R. Brooks, Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method, J. Chem. Phys., 103 (1995) 4613-4621.
[35] P.J. Steinbach, B.R. Brooks, New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation, J. Comput. Chem., 15 (1994) 667-683.
[36] J.-P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comp. Phys., 23 (1977) 327-341.
[37] H.-H.G. Tsai, J.-B. Lee, S.-S. Tseng, X.-A. Pan, Y.-C. Shih, Folding and membrane insertion of amyloid-beta (25-35) peptide and its mutants: Implications for aggregation and neurotoxicity, Proteins: Structure, Function, and Bioinformatics, 78 (2010) 1909-1925.
[38] H.H. Tsai, M. Reches, C.J. Tsai, K. Gunasekaran, E. Gazit, R. Nussinov, Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder, Proc. Natl. Acad. Sci. U. S. A., 102 (2005) 8174-8179.
[39] C.-W. Tsai, N.-Y. Hsu, C.-H. Wang, C.-Y. Lu, Y. Chang, H.-H.G. Tsai, R.-C. Ruaan, Coupling Molecular Dynamics Simulations with Experiments for the Rational Design of Indolicidin-Analogous Antimicrobial Peptides, J. Mol. Biol., 392 (2009) 837-854.
[40] D.P. Tieleman, D. van der Spoel, H.J.C. Berendsen, Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes:  Micellar Structure and Chain Relaxation, J. Phys. Chem. B, 104 (2000) 6380-6388.
[41] B. Lee, F.M. Richards, The interpretation of protein structures: Estimation of static accessibility, J. Mol. Biol., 55 (1971) 379-IN374.
[42] N. Galamba, Water's structure around hydrophobic solutes and the iceberg model, The journal of physical chemistry. B, 117 (2013) 2153-2159.
[43] T.M. Raschke, M. Levitt, Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them, Proc. Natl. Acad. Sci. U. S. A., 102 (2005) 6777-6782.
[44] B.A. Joughin, M.B. Yaffe, B. Tidor, Computational prediction of protein phosphopeptide-binding sites, Protein Science, 13 (2004) 146-146.
[45] R.I. MacDonald, Membrane fusion due to dehydration by polyethylene glycol, dextran, or sucrose, Biochemistry, 24 (1985) 4058-4066.
[46] J.J. Potoff, Z. Issa, C.W. Manke, B.P. Jena, Ca2+-dimethylphosphate complex formation: Providing insight into Ca2+-mediated local dehydration and membrane fusion in cells, Cell Biol. Int., 32 (2008) 361-366.
[47] A.A. Yaroslavov, A.V. Sybachin, E. Kesselman, J. Schmidt, Y. Talmon, S.A.A. Rizvi, F.M. Menger, Liposome Fusion Rates Depend upon the Conformation of Polycation Catalysts, J. Am. Chem. Soc., 133 (2011) 2881-2883.
[48] A.F. Smeijers, A.J. Markvoort, K. Pieterse, P.A.J. Hilbers, A Detailed Look at Vesicle Fusion, J. Phys. Chem. B, 110 (2006) 13212-13219.
[49] P.K. Kinnunen, Fusion of lipid bilayers: a model involving mechanistic connection to HII phase forming lipids, Chem. Phys. Lipids, 63 (1992) 251-258.
[50] S. Ohta-Iino, M. Pasenkiewicz-Gierula, Y. Takaoka, H. Miyagawa, K. Kitamura, A. Kusumi, Fast Lipid Disorientation at the Onset of Membrane Fusion Revealed by Molecular Dynamics Simulations, Biophys. J., 81 (2001) 217-224.
[51] S.J. Marrink, A.E. Mark, Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles, J. Am. Chem. Soc., 125 (2003) 15233-15242.
[52] V. Knecht, A.E. Mark, S.-J. Marrink, Phase Behavior of a Phospholipid/Fatty Acid/Water Mixture Studied in Atomic Detail, J. Am. Chem. Soc., 128 (2006) 2030-2034.
[53] X. Huang, C.J. Margulis, B.J. Berne, Dewetting-induced collapse of hydrophobic particles, Proc Natl Acad Sci U S A, 100 (2003) 11953-11958.
[54] R.D. Mountain, D. Thirumalai, Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution, J Am Chem Soc, 125 (2003) 1950-1957.
[55] Z. Yang, B. Shi, H. Lu, P. Xiu, R. Zhou, Dewetting Transitions in the Self-Assembly of Two Amyloidogenic β-Sheets and the Importance of Matching Surfaces, J. Phys. Chem. B, 115 (2011) 11137-11144.
[56] M.G. Krone, L. Hua, P. Soto, R. Zhou, B.J. Berne, J.-E. Shea, Role of Water in Mediating the Assembly of Alzheimer Amyloid-β Aβ16−22 Protofilaments, J. Am. Chem. Soc., 130 (2008) 11066-11072.
[57] G. Hummer, S. Garde, A.E. Garcia, L.R. Pratt, New perspectives on hydrophobic effects, Chem. Phys., 258 (2000) 349-370.
[58] R. Zhou, X. Huang, C.J. Margulis, B.J. Berne, Hydrophobic Collapse in Multidomain Protein Folding, Science, 305 (2004) 1605-1609.
[59] P.M. Kasson, E. Lindahl, V.S. Pande, Water Ordering at Membrane Interfaces Controls Fusion Dynamics, J. Am. Chem. Soc., 133 (2011) 3812-3815.
連結至畢業學校之論文網頁點我開啟連結
註: 此連結為研究生畢業學校所提供,不一定有電子全文可供下載,若連結有誤,請點選上方之〝勘誤回報〞功能,我們會盡快修正,謝謝!
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
系統版面圖檔 系統版面圖檔