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

More documents

Recommendations

Info

CONCLUSIONS Chapter IV ‐ Binding of a Quinolone Antibiotic to Bacterial Porin OmpF. In this case, the FRET analysis allowed us to conclude on a likely location for the binding site of CP in OmpF. Two limiting positions for the binding site were considered: i) in the trimer interface, leading to a maximum efficiency of donor quenching; ii) in the periphery of the trimer, causing minimum quenching of donor fluorescence due to FRET. For each of these two limiting conditions, intervals for binding constants were retrieved. By comparison of the binding constants retrieved with the results of an independent method that made use of changes in the absorption spectra of CP upon binding to OmpF (Neves et al., 2005), it is concluded that the binding site for CP is likely to be located away from the trimer interface and close to the periphery of OmpF. The FRET methodology developed for the analysis of the interactions between OmpF and CP is suitable to be used in the analysis of FRET data for similar systems, containing two populations of donors (or acceptors) separated by a distance larger or comparable to the Förster distance of the donor-acceptor pair used, so that the analysis is sensitive enough to be able to distinguish the contributions from these two populations. 185
Chapter V – Interaction of Helix‐0 of the N‐BAR Domain With Lipid Membranes The membrane modelling properties of N-BAR domains are generally attributed to two structural features of the BAR domain containing proteins: the concave surface of the crescent shaped dimer, that is expected to act as a scaffold for curvature and an N- terminal amphipatic helix or H0, that is expected to be deeply buried within the lipid bilayer, driving monolayer asymmetry and finally curvature. This latter strategy for curvature generation should be effective in the absence of the rest of the protein, and a peptide comprising this amphipatic helix would be expected to produce the same results. The results reproduced here clearly demonstrate that this is not the case. H0 is unable to drive significant changes in liposome morphology. Therefore we can conclude that N-BAR domains do not use their N-terminal amphipatic helices to produce bilayer curvature in the manner often proposed (Gallop and McMahon, 2005; Gallop et al., 2006; Masuda et al., 2006). Nevertheless, the results point to different roles of Helix-0 on membrane remodelling by N-BAR domains. The high water/lipid partition coefficients determined for H0 are expected to have a dramatic effect in the partition properties of the entire protein, and this alone could explain the great decreases in liposome tubulation efficiency of BAR domains without H0. A role as a mediator of interactions between dimers of BAR domains was also proposed for H0 (Gallop and McMahon, 2005), and here it is shown that H0 does indeed oligomerize into dimers in the lipid environment. Oligomerization of H0 might provide BAR domain-containing proteins with a more efficient mechanism to colocalize, and membrane curvature induction by scaffolding by proteins is only expected to be efficient at high local concentrations of scaffold proteins. 186
Page 1:
UNIVERSIDADE TÉCNICA DE LISBOA INS
Page 4 and 5:
Fernandes, F., Loura, L. M. S., Fed
Page 6 and 7:
Ao Pedro e Hugo, amigos de longa da
Page 8 and 9:
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
Page 21 and 22:
SINOPSE aceitantes. Dadores mais pr
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
Page 44 and 45:
the vesicle through bilayer deforma
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
Page 52 and 53:
deactivating agents. Zwitterionic d
Page 54 and 55:
amphipatic helices (see Section 2.3
Page 56 and 57:
size corresponding to the hydrophob
Page 58 and 59:
changes abruptly in the interfacial
Page 60 and 61:
thickness of the bilayer (Section 1
Page 62 and 63:
some α-helical membrane proteins a
Page 64 and 65:
The formation of a lipid population
Page 66 and 67:
homogeneous distribution of lipids
Page 68 and 69:
Figure I.20 - Relative binding cons
Page 70 and 71:
2.9. Lipid phase preferential parti
Page 72 and 73:
In Figure I.21, theoretical simulat
Page 75 and 76:
PROTEIN-PROTEIN AND PROTEIN-LIPID I
Page 77 and 78:
Page 79:
Page 83 and 84:
2430 Biophysical Journal Volume 85
Page 85 and 86:
2432 Fernandes et al. Coat protein
Page 87 and 88:
2434 Fernandes et al. leads to an a
Page 89 and 90:
2436 Fernandes et al. FIGURE 4 (A)
Page 91 and 92:
2438 Fernandes et al. section of th
Page 93 and 94:
2440 Fernandes et al. tein oligomer
Page 95:
QUANTIFICATION OF PROTEIN-LIPID SEL
Page 98 and 99:
FRET Study of Protein-Lipid Selecti
Page 100 and 101:
Page 102 and 103:
Page 104 and 105:
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 116 and 117:
Page 118 and 119:
Page 120 and 121:
Page 123:
BINDING ASSAYS OF INHIBITORS TOWARD
Page 126 and 127:
1778 F. Fernandes et al. / Biochimi
Page 128 and 129:
Page 130 and 131:
Page 132 and 133:
Page 134 and 135:
Page 136 and 137:
apparently the most significant as
Page 138 and 139:
110
Page 140 and 141:
Introduction Quinolones are broad-s
Page 142 and 143:
[9-12]. Having this into considerat
Page 144 and 145:
any case, very similar, probably wi
Page 146 and 147:
placement of the protein around the
Page 148 and 149:
⎛ II t ⎛ R ⎞ 0 ρ () t = exp
Page 150 and 151:
APPENDIX - Derivation of the FRET r
Page 152 and 153:
2 2w J ( t) = '2 R − R + w / 1
Page 154 and 155:
[14] L. Plançon, M. Chami, L. Lete
Page 156 and 157:
acceptors) (Eqs. 4-6) (⋅-⋅-⋅)
Page 158 and 159:
FIGURE 1A FIGURE 1B 130
Page 160 and 161: FIGURE 4A FIGURE 4B 132
Page 162 and 163: FIGURE 6A FIGURE 6B 134
Page 164 and 165: 136
Page 166 and 167: dynamin. Soon after, the same group
Page 168 and 169: 140
Page 170 and 171: 142
Page 172 and 173: Introduction Control of membrane re
Page 174 and 175: Steady-state fluorescence measureme
Page 176 and 177: Rho-DOPE (acceptor). The increase o
Page 178 and 179: where η is the viscosity of the me
Page 180 and 181: ound conformation of the BAR domain
Page 182 and 183: 19. Fernandes, F., L. M. S. Loura,
Page 184 and 185: Figure Legends Fig.1: N-terminal am
Page 186 and 187: FIG. 1A FIG.1B 17
Page 188 and 189: FIG. 3A FIG. 3B 19
Page 190 and 191: FIG.5A 21
Page 192 and 193: FIG 6. 23
Page 194 and 195: FIG. 8 A B 25
Page 196 and 197: The signalling functions of PI(4,5)
Page 198 and 199: 172
Page 200 and 201: 174
Page 202 and 203: zoxadiazol (NBD)-PC were obtained f
Page 204 and 205: Fig. 3. Fluorescence decays of diph
Page 206 and 207: CONCLUSIONS VII CONCLUSIONS Chapter
Page 208 and 209: CONCLUSIONS constants recovered by
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 218 and 219: BIBLIOGRAPHY Phosphatidylinositol 4
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
show all

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

Create successful ePaper yourself

Delete template?

Save as template?