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

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ion diffusion, as the energy required to move a hydrated ion through it, is extremely high (for a monovalent ion with 2 Å radius, it takes about 40 Kcal/mol to transfer it into the membrane core – Gennis, 1989). Figure I.1 – a) Electron micrograph of a section from the plasma membrane of a erythrocyte membrane. b) Schematic depiction of a lamellar arrangement of a lipid bilayer. Polar headgroups face outwards and shield the interior hydrophobic tails (from Lodish et al., 2000). The bilayer can be regarded as a two-dimensional solvent that provides the hydrophobic anchor to membrane proteins in biomembranes. This two-dimensional fluid character of the lipid bilayer is central to lipid-lipid, lipid-protein and proteinprotein interactions. It is responsible for an increase of the efficiency of membranebound enzymes whose substrates are located in the plane of the bilayer. The average time for a reactant to reach a target site depends drastically on the dimensionality. Reactions that require collisions of three bodies are very rare in three dimensions, but can be very effective in two dimensions (Hardt, 1979; Sackmann, 1995). The biomembrane is not only a physical barrier between the inside and outside of the cell or between intracellular compartments and the cytosol. As the cell needs to get nutrients in and out, the membrane must accommodate this. Some membrane-bound 2
INTRODUCTION: BIOMEMBRANES proteins are responsible by the regulation of the transport of ions and molecules across the membrane. Thus, the biomembrane is actually a selective barrier. To this effect, the distributions of both lipids and proteins exhibit asymmetry in each side of the bilayer. Another consequence of the fluid character of the lipid bilayer is its high flexibility that allows for an easy adaptation to exterior perturbations. In biomembranes, the lipid bilayer also interacts with the cytoskeleton. This interaction is responsible for the mechanical stability of cells that combined with the flexibility of the lipid bilayer confers the biomembrane with unique mechanical properties. 1.2. Molecular composition of biomembranes 1.2.1. Lipid composition Biomembranes are typically composed by four classes of lipids: glycerolipids, sphingolipids, glycolipids and sterols. Their common characteristic is the amphipatic character which determines the lipid bilayer structure. 1.2.1.1. Glycerolipids The hydrophobic section of glycerolipids is composed of linear hydrocarbon chains esterified to sn-1 and sn-2 (stereospecific numbers) positions of a glycerol moiety. These hydrocarbon chains exhibit great diversity of length (commonly from 14 to 24 carbon atoms) and unsaturation (from 0 to 4) in biomembranes. A list of some of the most common acyl-chains and their nomenclature is shown in Table I.1. A short notation normally used for describing them is based on the number of carbons and double bonds. Thus 18:1 stands for an acyl-chain with 18 carbons in the hydrocarbon chain and one double bond. In nature, virtually all double bonds in fatty-acids present a cis configuration and generally the longer the hydrocarbon chain, the more double bounds are present. The cis configuration has drastic consequences in the packing of lipids (Berg et al., 2002) as will be discussed later. The number of carbons in the hydrophobic chain is nearly always even. In biomembranes, lipids generally contain two different acyl-chains and frequently one of them is unsaturated (Mouritsen, 2005). The predominant class of lipids in biomembranes are the phosphoglycerolipids. These molecules are glycerolipids in which the sn-3 position is esterified to phosphoric 3
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 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
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Page 50 and 51: drying into a film and ressuspensio
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Page 54 and 55: amphipatic helices (see Section 2.3
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Page 58 and 59: changes abruptly in the interfacial
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Page 62 and 63: some α-helical membrane proteins a
Page 64 and 65: The formation of a lipid population
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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: PROTEIN-PROTEIN AND PROTEIN-LIPID I
Page 79: 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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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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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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