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

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some α-helical membrane proteins are dependent on the membrane thickness (East and Lee, 1982). Most likely, the most common distortion available for α-helical membrane proteins as a response to positive hydrophobic mismatch is a change of tilt of the TM helices relative to the bilayer normal. This mechanism allows for an easy modulation of the length along the bilayer normal occupied by the hydrophobic domains of the protein. Indeed, tilting has been observed and measured for various TM proteins (Harzer and Bechinger, 2000). Rotation of amino acid residues at the end of TM α-helices was also proposed as another distortion mechanism available for membrane proteins as this results in changes in the effective hydrophobic thickness of the protein (Lee, 2003). However, the ability of proteins and lipids to adapt to situations of hydrophobic mismatch is limited, and drastic changes in the membrane distribution of these elements is possible. In cases of severe hydrophobic mismatch, the TM orientation of TM helices might not be maintained anymore and transitions to non-TM orientations are possible (Ren et al., 1997; Ren et al., 1999) as well as decrease of partition to bilayers (Figure I.16). Aggregation of TM domains is another possibility in hydrophobic mismatch as this reduces the lipid-protein interface, minimizing stress. Protein aggregation will be discussed in greater detail in section 2.11. A B Figure I.16 – Possible adaptations to hydrophobic mismatch between a TM peptide and the lipid bilayer. A – Response to positive hydrophobic mismatch (a): acyl-chain ordering (b), peptide backbone deformation (c), peptide oligomerization (d), peptide tilt (e), non-TM orientation or absence of binding to the bilayer (f). B – Response to negative hydrophobic mismatch (a): acyl-chain disordering (b), peptide backbone deformation (c), peptide oligomerization (d), non-lamellar phase formation (e), non-TM orientation or absence of binding to the bilayer (f). (Adapted from de Planque and Killian, 2003). 34
INTRODUCTION: LIPID-PROTEIN INTERACTIONS In the presence of lipids with tendency to establish nonlamellar structures, cubic and nonlamellar lipid phases can be formed in the interface with the protein as a response to hydrophobic mismatch. Nonlamellar arrangements of lipids change the curvature of the bilayer in the vicinity of the protein and allow for a better fitting of the hydrophobic sections of both proteins and lipids (Killian, 2003). Peptide backbone deformation, such as transition from α-helix to π-helix (helices with a wider helical pitch), could be a possible mechanism for adjustment to situations of hydrophobic mismatch. However, several studies have confirmed that the α-helical structure is insensitive to hydrophobic mismatch and this strategy to minimize hydrophobic mismatch is unlikely (de Planque and Killian, 2003). Nevertheless a recent study suggests that TM α-helices may flex in the lipid bilayer in order to submerge most of the hydrophobic domain inside the bilayer core (Yeagle et al., 2007). The hydrophobic matching principle might be a mechanism by which the activity of some membrane proteins can be modulated. Thickness variations induced either internally or externally can trigger some proteins in or out of an active status. This has already been observed for some ion pumps such as Ca 2+ -ATPase and Na + ,K + -ATPase that exhibit maximum activity in bilayers with a specific number of carbon atoms (Lee, 2003). 2.7. Transmembrane protein-lipid interface As already stated, the lipids on the vicinity of the protein can either stretch or compress their acyl-chains in response to hydrophobic mismatch. In pure lipids this often results in the observation of two different lipid populations in protein-lipid systems. One of these is very similar to the lipid in the absence of the protein (but not necessarily identical), and its contribution to the total lipid population is inversely dependent on protein concentration. The other population is more significant at higher protein/peptide concentrations, frequently presenting a different gel-fluid phase transition temperature (smaller T m for bilayers thinner than the protein and higher T m for thicker bilayers) as well as a smaller cooperativity for this transition (Liu et al., 2002; Morein et al., 2002). These two components are expected to correspond to free and protein-associated lipids, respectively. 35
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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
Page 11 and 12: ABBREVIATIONS AND SYMBOL LIST ABBRE
Page 13: RESUMO RESUMO As biomembranas são
Page 17 and 18: SINOPSE SINOPSE Nas últimas duas d
Page 19 and 20: SINOPSE podem fornecer informação
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Page 23 and 24: OUTLINE OUTLINE The last two decade
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Page 30 and 31: ion diffusion, as the energy requir
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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
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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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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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