Biophysical studies of membrane proteins/peptides. Interaction with ...

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BIBLIOGRAPHY Phosphatidylinositol 4,5-bisphosphate: An Electrostatic Model and Experimental Results. Biophys. J. 74: 731-744. Devaux, P. F., and Morris, R. (2004). Transmembrane Asymmetry and Lateral Domains in Biological Membranes. Traffic 5: 241-246. Dong, M., Bagetto, L. G., Falson, P., Le Maire, M., and Penin, F. (1997). CompleteRemoval and Exchange of Sodium Dodecyl Sulfate Bound to Soluble and Membrane Proteins and Restoration of Their Activities, Using Ceramic Hydroxypatite Chromatography. Anal. Biochem. 247: 333-341. Dröse, S. and Altendorf, K. (1997). Bafilomycins and Concanamycins as Inhibitors of V-ATPases and P- ATPases. J. Exp. Biol. 200, 1-8. Dumas, F., Sperotto, M. M., Lebrun, M.-C., Tocanne, J.-F., and Mouritsen, O. G. (1997). Molecular Sorting of Lipids by Bacteriorhodopsin in Dilauroylphosphatidylcholine/Distearoylphophatidylcholine Lipid Bilayers. Biophys. J. 73: 1940-1953. Dumas, F., Lebrun, C., and Tocanne, J-F. (1999). Is the Protein/Lipid Hydrophobic Matching Principle Relevant to Membrane Organization and Function. FEBS Lett. 458: 271-277. Dunnil, P. (1968). The Use of Helical Net-Diagrams to Represent Protein Structures. Biophys. J. 8: 865- 875 East, J. M., and Lee, A. G. (1982). Lipid Selectivity of the Calcium and Magnesium Ion Dependent Adenosinetriphosphatase, Studied With Fluorescence Quenching by a Brominated Phospholipid. Biochemistry 21: 4144-4151. Eisenberg, D., Weiss, R. M., Terwillinger, T. C. (1982). The Helical Hydrophobic Moment: A Measure of the Amphiphilicity of Helix. Nature 299: 371-374. Epand, R. M. (1993) Introduction. in The Amphipatic Helix. Ed. Epand, R. M. CRC Press, Boca-Raton, U.S.A. Epand, R. M., Vuong, P., Yip, C. M., Maekawa, S., and Epand, R. F. (2004). Cholesterol-Dependent Partitioning of PtdIns(4,5)P 2 into Membrane Domains by the N-terminal Fragment of NAP-22 (Neuronal Axonal Myristoylated Membrane Protein of 22 kDa). Biochem. J. 379: 527-532. Epand, R. M. (2005) The Role of Proteins in the Formation of Domains in Membranes. In In “Protein- Lipid Interactions: New Approaches and Emerging Concepts.” (Eds. Mateo, C. R., Gómez, J., Villalaín, J., Ros, J. M. G.) Springer-Verlag. Berlin, Germany. Epand, R. F., Sayer, B. G., and Epand, R. M. (2005). Induction of Raft-Like Domains by a Myristoilated NAP-22 Peptide and its Tyr Mutant. FEBS J. 272: 1792-1803. 193
Farsad, K., Ringstad, N., Takei, K., Floyd, S. R., Rose, K., and De Camilli, P. (2001). Generation of High Curvature Membranes Mediated by Direct Endophilin Bilayer Interactions. J. Cell Biol. 155: 193-200. Fattal, D. R., and Ben-Shaul, A. (1993). A Molecular Model for Lipid-Protein Interaction in Membranes: The Role of Hydrophobic Mismatch. Biophys.J. 65: 1795-1809. Finbow, M. E., and Harrison, M. A. (1997). The Vacuolar H + -ATPase: A Universal Proton Pump of Eukaryotes. Biochem. J. 324: 697-712. Ford, M.G.J., Mills, I.G., Peter, B.J., Vallis, Y., Praefcke, G.J.K., Evans, P.R. and McMahon, H.T. (2002) Curvature of Clathrin-Coated Pits Driven by Epsin. Nature 419: 361-366. Gagliardi, S., Nadler, G., Consolandi, E., Parini, C., Morvan, M., Legave, M. N., Belfiore, P., Zocchetti, A., Clarke, G. D., James, I., Nambi, P., Gowen, M., and Farina, C. (1998a). 5-(5,6-Dichloro-2-indolyl)-2- methoxy-2,4-pentadienamides: Novel and Selective Inhibitors of the Vacuolar H + -ATPase of Osteoclasts with Bone Antiresorptive Activity. J. Med. Chem. 41: 1568-1573. Gagliardi, S., Gatti, P. A., Belfiore, P., Zochetti, A., Clarke, G. D., and Farina, C. (1998b). Synthesis and Structure-Activity Relationships of Bafilomycin A 1 Derivatives as Inhibitors of Vacuolar H + -ATPase. J. Med. Chem. 41: 1883-1893. Gallop, J. L., and McMahon, H. T. (2005). BAR Domains and Membrane Curvature: Bringing your Curves to the BAR. Biochem. Soc. Symp. 72: 223-31. Gallop, J. L., Jao, C. C., Kent, H. M., Butler, P. J. G., Evans, P. R., Langen, R., and McMahon, H. T. (2006). Mechanism of Endophilin N-BAR Domain-Mediated Membrane Curvature. EMBO J. 25: 2898- 2910. Garavito, R. M., and Rosenbusch, J. P. (1980). Three Dimensional Crystals of an Integral Membrane Protein: An Initial X-Ray Analysis. J. Cell. Biol. 86: 327-329. Ge, K., and Prendergast, G. C. (2000). Bin2, a Functionally Nonredundant Member of the BAR Adaptor Gene Family. Genomics 67: 210-220. Gennis, RB (1989). Biomembranes: Molecular Structure and Function. Springer-Verlag, New York, USA. Ghambir, A., Hangyás-Milhályné, G., Zaitseva, I., Cafiso, D. S., Wang, J., Murray, D., Pentyala, S. N., Smith, S. O., and McLaughlin, S. (2004). Electrostatic Sequestration of PIP 2 on Phospholipid Membranes by Basic/Aromatic Regions of Proteins. Biophys. J. 86: 2188-2207. Gil, T., Ipsen, J. H., Mouritsen, O. G. , Sabra, M. C., Sperotto, M. M., and Zuckermann, M. J. (1998). Theoretical Analysis of Protein Organization in Lipid Membranes. Biochim. Biophys. Acta 1376: 245- 266. 194
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UNIVERSIDADE TÉCNICA DE LISBOA INS
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Fernandes, F., Loura, L. M. S., Fed
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Ao Pedro e Hugo, amigos de longa da
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2.2. - Peptides as models 2.3. - Am
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ABBREVIATIONS AND SYMBOL LIST ABBRE
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RESUMO RESUMO As biomembranas são
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SINOPSE SINOPSE Nas últimas duas d
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SINOPSE podem fornecer informação
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SINOPSE aceitantes. Dadores mais pr
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OUTLINE OUTLINE The last two decade
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OUTLINE membranes with a distributi
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OUTLINE BAR domains (tubulation of
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ion diffusion, as the energy requir
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acid. If no more groups are linked
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sphingomyelin, the most abundant sp
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signal for neighbouring cells to ph
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functional role in process such as
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in the L α phase, while lateral di
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1.7. Lateral heterogeneity in lipid
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the vesicle through bilayer deforma
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Figure I.9 - Depiction of the sever
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Figure I.11 - Experimentally obtain
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drying into a film and ressuspensio
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deactivating agents. Zwitterionic d
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amphipatic helices (see Section 2.3
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size corresponding to the hydrophob
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changes abruptly in the interfacial
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thickness of the bilayer (Section 1
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some α-helical membrane proteins a
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The formation of a lipid population
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homogeneous distribution of lipids
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Figure I.20 - Relative binding cons
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2.9. Lipid phase preferential parti
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In Figure I.21, theoretical simulat
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PROTEIN-PROTEIN AND PROTEIN-LIPID I
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2430 Biophysical Journal Volume 85
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2432 Fernandes et al. Coat protein
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2434 Fernandes et al. leads to an a
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2436 Fernandes et al. FIGURE 4 (A)
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2438 Fernandes et al. section of th
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2440 Fernandes et al. tein oligomer
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QUANTIFICATION OF PROTEIN-LIPID SEL
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FRET Study of Protein-Lipid Selecti
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BINDING OF INHIBITORS TO A PUTATIVE
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BINDING OF INHIBITORS TO A PUTATIVE
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INTERACTION OF THE INDOLE CLASS OF
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5272 Biochemistry, Vol. 45, No. 16,
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BINDING ASSAYS OF INHIBITORS TOWARD
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1778 F. Fernandes et al. / Biochimi
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apparently the most significant as
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110
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Introduction Quinolones are broad-s
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[9-12]. Having this into considerat
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any case, very similar, probably wi
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placement of the protein around the
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⎛ II t ⎛ R ⎞ 0 ρ () t = exp
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APPENDIX - Derivation of the FRET r
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2 2w J ( t) = '2 R − R + w / 1
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[14] L. Plançon, M. Chami, L. Lete
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acceptors) (Eqs. 4-6) (⋅-⋅-⋅)
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FIGURE 1A FIGURE 1B 130
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136
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dynamin. Soon after, the same group
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Page 172 and 173: Introduction Control of membrane re
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Page 184 and 185: Figure Legends Fig.1: N-terminal am
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Page 202 and 203: zoxadiazol (NBD)-PC were obtained f
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Page 206 and 207: CONCLUSIONS VII CONCLUSIONS Chapter
Page 208 and 209: CONCLUSIONS constants recovered by
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Page 212 and 213: CONCLUSIONS Chapter VI - Clustering
Page 214 and 215: FINAL CONSIDERATIONS AND PROSPECTS
Page 216 and 217: BIBLIOGRAPHY IX BIBLIOGRAPHY Albert
Page 220 and 221: BIBLIOGRAPHY Glaubitz, C., Grobner,
Page 222 and 223: BIBLIOGRAPHY Koehorst, R. B. M., Sp
Page 224 and 225: BIBLIOGRAPHY Mishra, V. K., Palguna
Page 226 and 227: BIBLIOGRAPHY Pluschke, G., Hirota,
Page 228 and 229: BIBLIOGRAPHY Sperotto, M. M., and M
Page 230: BIBLIOGRAPHY Williamson, I. M., Alv
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