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

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[14] L. Plançon, M. Chami, L. Letellier, Reconstitution of FhuA, an Escherichia coli outer membrane protein, into liposomes, J. Biol. Chem. 272 (1997) 16868-16872. [15] J. Knol, K. Sjollema, B. Poolman, Detergent- mediated reconstitution of membrane proteins. Biochemistry 37 (1998) 16410-16415. [16] A. D. Bangham M. M. Standish, J. C. Watkins, Diffusion of univalent ions across the lamellae of swollen phospholipids, J. Mol. Biol. 13 (1965) 238-252. [17] W. Im, B. Roux, Ions and counterions in a biological channel: A molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1M KCl aqueous salt solution. Journal of Molecular biology, 319 (2002) 1177-1197. [18] E. M. Nestorovich, C. Danelon, M. Winterhalter, S. M. Bezrukov, Designed to penetrate: timeresolved interaction of single antibiotic molecules with bacterial pores. Proc. Nat. Acad. Sci. USA, 99 (2002) 9789-9794. [19] J. R. Lakowicz, Principles of fluorescence spectroscopy. Chapter 13, 443-475. Springer Science, 3 rd edition, New York, 2006. [20] L. Davenport, R. E. Dale, R. E. Bisby, R. B. Cundall, Transverse location of the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene in model lipid bilayer membrane systems by resonance energy transfer, Biochemistry 24 (1985) 4097-4108. [21] D. W. Martin, Active unit of solubilized sarcoplasmic reticulum calcium adenosinetriphophatase: an active enzyme centrifugation analysis, Biochemistry 22 (1983) 2276 – 2282. [22] J. L. Vazquez, M. T. Montero, S. Merino, O. Domenech, M. Berlanga, M. Vinas, J. Hernandez- Borrel, Location and Nature of the Surface Membrane Binding Site of Ciprofloxacin: A Fluorescence Study, Langmuir. 17 (2001) 1009-1014. [23] J. F. Nagle, S. Tristam-Nagle, Structure of lipid bilayers, Biochim. Biophys. Acta 1469 (2000) 159-195. [24] S. W. Cowan, R. M. Garavito, J. N. Jansonius, J. A. Jenkins, R. Karlsson, N. Konig, E. F. Pai, R. A. Pauptit, P. J. Rizkallah, J. P. Rosenbusch, G. Rummel, T. Schimer, The structure of OmpF porin in a tetragonal crystal form, Structure 10 (1995) 1041-50. [25] P. Neves, E. Berkane, P. Gameiro, M. Winterhalter, B. de Castro, Interaction between quinolones antibiotics and bacterial outer membrane porin OmpF, Biophys.Chem. 113 (2005)123-128. [26] P. K. Wolber, B. S. Hudson, An analytical solution to the Förster energy transfer problem in two dimensions, Biophys. J. 28 (1979) 197–210. [27] R. C. Capeta, J. A. Poveda, L. M. S. Loura, Non-uniform membrane probe distribution in resonance energy transfer. Application to protein-lipid selectivity, J. Fluoresc. 16 (2005) 161-172. 126
BINDING OF A QUINOLONE ANTIBIOTIC TO BACTERIAL PORIN OmpF Figure Legends: Figure 1: The structure of the OmpF trimer. The positions of the two Trp residues (Trp 214 and Trp 61 ) in each monomer are shown. Views of OmpF organization: top (A) (8) (Reproduced by permission of Biophysical Journal) and perpendicular to membrane axis (B). Trimer interface in (B) is assigned by T. The image was draw with PYMOL (DeLano Scientific, San Carlos, CA, http://pymol.sourceforge.net) using PDB coordinates 1OMF1 (22). Figure 2: Chemical structure of ciprofloxacin. Figure 3: Normalized fluorescence emission spectra of OmpF (---) and absorption spectra of ciprofloxacin (▬). Figure 4: A: Positions of donors (Trp 61 and Trp 214 ) and acceptors (ciprofloxacin) in the DMPC bilayer. In the simulations, the OmpF monomer is approximated to a cylinder of radius 30 Å (see text). B: Representation of the OmpF trimer as assumed in the FRET simulations. Trp 61 is located in the trimer interface whereas Trp 214 is located in the periphery of the OmpF trimer. Figure 5: Representations of the OmpF trimer with possible ciprofloxacin binding sites specified (diagonal filling) for each of chosen binding models. A: Model I) binding site for ciprofloxacin is located near the trimer interface. Quenching of Trp 61 is complete after antibiotic binding, while the three Trp 214 are at a distance of 30 Å from ciprofloxacin. B: Model II) binding site for ciprofloxacin is located in the trimer periphery near one of the Trp 214 which is completely quenched after binding. The other Trp 214 are at a distance of 52 Å from the binding site, whereas the three Trp 61 are at a distance of 30 Å. Figure 6: Extent of energy transfer (Eq.1) for the OmpF tryptophan-Ciprofloxacin, donor acceptor FRET pair. Simulation for absence of binding (random distribution of 127
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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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Page 104 and 105: FRET Study of Protein-Lipid Selecti
Page 107 and 108: BINDING OF INHIBITORS TO A PUTATIVE
Page 109 and 110: BINDING OF INHIBITORS TO A PUTATIVE
Page 111: INTERACTION OF THE INDOLE CLASS OF
Page 114 and 115: 5272 Biochemistry, Vol. 45, No. 16,
Page 123: BINDING ASSAYS OF INHIBITORS TOWARD
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Page 140 and 141: Introduction Quinolones are broad-s
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Page 150 and 151: APPENDIX - Derivation of the FRET r
Page 152 and 153: 2 2w J ( t) = '2 R − R + w / 1
Page 156 and 157: acceptors) (Eqs. 4-6) (⋅-⋅-⋅)
Page 158 and 159: FIGURE 1A FIGURE 1B 130
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Page 166 and 167: dynamin. Soon after, the same group
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Page 172 and 173: Introduction Control of membrane re
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Page 176 and 177: Rho-DOPE (acceptor). The increase o
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Page 184 and 185: Figure Legends Fig.1: N-terminal am
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Page 188 and 189: FIG. 3A FIG. 3B 19
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Page 196 and 197: The signalling functions of PI(4,5)
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Fig. 3. Fluorescence decays of diph
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CONCLUSIONS VII CONCLUSIONS Chapter
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CONCLUSIONS constants recovered by
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CONCLUSIONS Chapter IV ‐ Binding
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CONCLUSIONS Chapter VI - Clustering
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FINAL CONSIDERATIONS AND PROSPECTS
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BIBLIOGRAPHY IX BIBLIOGRAPHY Albert
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BIBLIOGRAPHY Phosphatidylinositol 4
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BIBLIOGRAPHY Glaubitz, C., Grobner,
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BIBLIOGRAPHY Koehorst, R. B. M., Sp
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BIBLIOGRAPHY Mishra, V. K., Palguna
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BIBLIOGRAPHY Pluschke, G., Hirota,
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BIBLIOGRAPHY Sperotto, M. M., and M
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BIBLIOGRAPHY Williamson, I. M., Alv
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