BIBLIOGRAPHY Koehorst, R. B. M., Spruijt, R. B., Vergeldt, F. J. and Hemminga, M. A. (2004). Lipid Bilayer Topology <strong>of</strong> the Trans<strong>membrane</strong> α-Helix <strong>of</strong> M13 Major Coat Protein and Bilayer Polarity Pr<strong>of</strong>ile by Site-Directed Fluorescence Spectroscopy. Biophys. J. 87: 1445-1455. Kwik, J., Boyle, S., Fooksman, Margolis, L., Sheetz, M. P., and Edidin, M. (2003). Membrane Cholesterol, Lateral Mobility, and the Phosphatidylinositol 4,5-Bisphosphate-Dependent Organization <strong>of</strong> Cell Actin. PNAS USA. 100: 13964-13969. Lark, M. W., James, I. E. (2002). Novel Bone Antiresorptive Approaches. Curr. Opin. Pharmac. 2: 330- 337. Laux, T., Fukami, K., Thelen, M., Golub, T., Frey, D., and Caroni, P. (2000). GAP43, MARCKS, and CAP23 Modulate PI(4,5)P 2 at Plasmalemmal Rafts, and Regulate Cell Cortex Actin Dynamics Through a Common Mechanism. J. Cell Biol. 149: 1455-1471. Lee, A.G. (2003). Lipid-Protein <strong>Interaction</strong>s in Biological Membranes: a Structural Perspective. Biophys. Biochim. Acta 1612: 1-40. Lehtonen, J. Y. A., Holopainen, J. M., and Kinnunen, P. K. (1996). Evidence for the Formation <strong>of</strong> Microdomains in Liquid Crystalline Large Unilamellar Vesicles Caused by Hydrophobic Mismatch <strong>of</strong> the Constituent Phospholipids. Biophys. J. 70: 1753-1760. Lehtonen, J. Y. A., and Kinnunen, P. K. J. (1997). Evidence for Phospholipid Microdomain Formation in Liquid Crystalline Liposomes Reconstituted With Eschericia coli Lactose Permease. Biophys. J. 72: 1247-1257. Liu, F., Lewis, R. N. A. H., Hodges, R. S., and McElhaney, R. N. (2002). Effect <strong>of</strong> Variations in the Structure <strong>of</strong> a Polyleucine-Based α-Helical Trans<strong>membrane</strong> Peptide on its <strong>Interaction</strong>s <strong>with</strong> Phosphatidylcholine Bilayers. Biochemistry 87: 2470-82 Lentz, B. R., Barenholz, Y. and Thompson, T. E. (1976). Fluorescence Depolarization Studies <strong>of</strong> Phase Transitions and Fluidity in Phospholipid Bilayers. 2. Two-component Phosphatidylcholine Liposomes. Biochemistry 15:4529–4537. Lentz, T. L., Chaturverdi, V., and Conti-Fine, B. M. (1998). Amino Acids Within Residues 181-200 <strong>of</strong> the Nicotinic Acetylcholine Receptor Alpha1 Subunit Involved in Nicotine Binding. Biochem. Pharmacol. 55: 341-347. Lewis, B. A., and Engelman, D. M. (1983). Bacteriorhodopsin Remains Dispersed in Fluid Phospholipid Bilayers Over a Wide Range <strong>of</strong> Bilayer Thickness. J. Mol. Biol. 166:203–210. Liu, Y., Casey, L., and Pike, L. J. (1998). Compartmentalization <strong>of</strong> Phosphatidylinositol 4,5- Bisphosphate in Low-Density Membrane Domains in the Absence <strong>of</strong> Caveolin. Biochem. Biophys. Res. Commun. 245: 684-690. 197
Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. E. (2000). Molecular Cell Biology. 4 th Ed. W. H. Freeman, New York, USA Mall, S., Broadbridge, R., Sharma, R. P., Lee, A. G., and East J. M. (2000). Effects <strong>of</strong> Aromatic Residues at the Ends <strong>of</strong> Trans<strong>membrane</strong> Alpha-Helices on Helix <strong>Interaction</strong>s With Bilayers. 39: 2071-2078. Mall, S., East, J. M., and Lee, A. G. (2002). Trans<strong>membrane</strong> α-Helices. in Current Topics in Membranes 52: 339-371 Marsh, D. (1990). Lipid-Protein <strong>Interaction</strong>s in Membranes. FEBS Lett. 268: 271-375. Marsh, D. (1996). Peptide Models for Membrane Channels. Biochem, J. 315: 345-361. Marsh, D., Horváth, L. I., Swamy, M. J., Mantripragada, S., and Kleinschmidt, J. H. (2002). <strong>Interaction</strong>s <strong>of</strong> Membrane-Spanning Proteins With Peripheral and Lipid-Anchored Membrane Proteins: Perspectives From Protein-Lipid <strong>Interaction</strong>s. Mol. Memb. Biol. 19: 247-255. Martin, T. F. J. (2001). PI(4,5)P 2 Regulation <strong>of</strong> Surface Membrane Traffic. Curr. Opin. Cell Biol. 13: 493- 499. Mascaretti, O. (2003). Bacteria Versus Antibacterial Agents: An Integrated Approach. ASM Press, Washington D. C. Masuda, M., Takeda, S., Sone, M., Ohki, T., Mori, H., Kamioka, Y., and Mochizuki, N. (2006). Endophilin BAR Domain Drives Membrane Curvature By Two Newly Identified Structure-Based Mechanisms. EMBO J. 25: 2889-2897. Mateo, C. R., de Almeida, R. F. M., Loura, L. M. S., and Prieto, M. (2006). From Lipid Phases to Membrane Protein Organization: Fluorescence Methodologies in the Study <strong>of</strong> Lipid-Protein <strong>Interaction</strong>s. in “Protein-Lipid <strong>Interaction</strong>s: New Approaches and Emerging Concepts.” (Eds. Mateo, C. R., Gómez, J., Villalaín, J., Ros, J. M. G.) Springer-Verlag. Berlin, Germany. McIntosh, T. J., Vidal, A., and Simon, S. A. (2002). The Energetics <strong>of</strong> Peptide-Lipid <strong>Interaction</strong>s: Modulation by Interfacial Dipoles and Cholesterol. in Current Topics in Membranes 52: 205-253. McLaughlin, S., Wang, J., Gambhir, A., and Murray, D. (2002). PIP 2 and Proteins: <strong>Interaction</strong>s, Organization, and Information Flow. Annu. Rev. Biophys. Struct. 31: 151-175. McMahon, H. T., and Gallop, J. L. (2005). Membrane Curvature and Mechanisms <strong>of</strong> Dynamic Cell Membrane Remodeling. Nature 438: 590-596. Meijer, A. B., Spruijt, R. B., Wolfs, C. J. A. M., and Hemminga, M. A. (2001). Membrane-Anchoring <strong>Interaction</strong>s <strong>of</strong> M13 Major Coat Protein. Biochemistry 40: 8815-8820. 198
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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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PROTEIN-PROTEIN AND PROTEIN-LIPID I
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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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FRET Study of Protein-Lipid Selecti
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FRET Study of Protein-Lipid Selecti
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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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5274 Biochemistry, Vol. 45, No. 16,
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5276 Biochemistry, Vol. 45, No. 16,
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5278 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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1780 F. Fernandes et al. / Biochimi
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1782 F. Fernandes et al. / Biochimi
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1784 F. Fernandes et al. / Biochimi
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1786 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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FIGURE 4A FIGURE 4B 132
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FIGURE 6A FIGURE 6B 134
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136
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dynamin. Soon after, the same group
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140
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142
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- Page 216 and 217: BIBLIOGRAPHY IX BIBLIOGRAPHY Albert
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- 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
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