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

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In Figure I.21, theoretical simulations are shown that predict the wetting phenomenon. For Figure I.21c), sharing of a wetting layer by two or more proteins can give rise to colocalization and aggregation phenomena as described in detail on Section 2.11. A B B Figure I.21 – Computer simulation snapshots of a large protein embedded in a binary lipid matrix in which one of the lipids is preferentially bound to the protein. (a) – Selective binding of one of the lipid species at the protein-lipid interface. (b) – Wetting of one of the lipids around the protein. (c) – Wetting and formation of a capillary condensate between two adjacent proteins (taken from Gil et al., 1998). These types of lateral structures initiated by proteins can function in biomembranes as the signal for recruitment of other molecules to those domains. This has been proposed as the molecular mechanism behind some signalling platforms (Pérez-Gil et al., 2005). 2.11. Lipid-mediation of protein-protein interactions The principle of hydrophobic matching, and the possibility of membrane proteins to change the lipid environment around them, offer membranes a mechanism for lipidmediation of protein-protein interactions. When proteins change the order parameter of lipids around them, overlap of disturbed lipids can again lead to colocalization of proteins in the same area of the membrane or aggregation (Gil et al., 1998) (Figure I.22). The system, when moving to equilibrium, will have the tendency to decrease the extent of presented interface, and this is achievable by clustering of proteins and ultimately by protein aggregation. Of course, protein aggregation can have its energetic costs that may rise from helix-dipole moment and charge repulsion or entropic factors. 44
INTRODUCTION: LIPID-PROTEIN INTERACTIONS Figure I.22 - Schematic representation of protein-protein interactions mediated by hydrophobic mismatch. (a) – Hydrophobically matched membrane. (b, c) - Lipid-mediated protein-protein attraction by same type of hydrophobic mismatch. (d) - Lipid-mediated protein-protein repulsion by opposite type of hydrophobic mismatch (Taken from Gil et al., 1998). When more than one lipid species is present, wetting of membrane proteins also implies formation of an interface between lipids in the wetting phase and lipids in the protein-poor phase. Again the tendency to minimize the interface between these two phases can lead to coalescence or capillary condensation of wetting domains and stimulation of protein-protein interactions (Fig. I.21.c)). In this way, wetting occurs in addition to direct protein-protein (Van der Waals and electrostatic) and the above described lipid-mediated interactions, by selecting the environment in which they take place, i.e., wetting provides the mechanism for modulation of membrane protein organization (clustering and aggregation) on larger length scales (Gil et al., 1998). 45
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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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Page 23 and 24: OUTLINE OUTLINE The last two decade
Page 25 and 26: OUTLINE membranes with a distributi
Page 27: OUTLINE BAR domains (tubulation of
Page 30 and 31: ion diffusion, as the energy requir
Page 32 and 33: acid. If no more groups are linked
Page 34 and 35: sphingomyelin, the most abundant sp
Page 36 and 37: signal for neighbouring cells to ph
Page 38 and 39: functional role in process such as
Page 40 and 41: in the L α phase, while lateral di
Page 42 and 43: 1.7. Lateral heterogeneity in lipid
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Page 46 and 47: Figure I.9 - Depiction of the sever
Page 48 and 49: Figure I.11 - Experimentally obtain
Page 50 and 51: drying into a film and ressuspensio
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Page 75 and 76: PROTEIN-PROTEIN AND PROTEIN-LIPID I
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Page 83 and 84: 2430 Biophysical Journal Volume 85
Page 85 and 86: 2432 Fernandes et al. Coat protein
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Page 95: QUANTIFICATION OF PROTEIN-LIPID SEL
Page 98 and 99: FRET Study of Protein-Lipid Selecti
Page 107 and 108: BINDING OF INHIBITORS TO A PUTATIVE
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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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140
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142
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Introduction Control of membrane re
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Steady-state fluorescence measureme
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Rho-DOPE (acceptor). The increase o
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where η is the viscosity of the me
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ound conformation of the BAR domain
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19. Fernandes, F., L. M. S. Loura,
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Figure Legends Fig.1: N-terminal am
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FIG. 1A FIG.1B 17
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FIG. 3A FIG. 3B 19
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FIG.5A 21
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FIG 6. 23
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FIG. 8 A B 25
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The signalling functions of PI(4,5)
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172
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174
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zoxadiazol (NBD)-PC were obtained f
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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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