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

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acid. If no more groups are linked to the molecule, the resulting compound is phospatidic acid (PA), the simplest phosphoglycerolipid. In general, the phosphate group is linked to an alcohol, and together, the phosphate group and the bound alcohol shape the polar headgroup section of the molecule. Phosphoglycerolipids are classified according to the nature of the alcohol moiety in the headgroup. The most common alcohols found in phospholipids are serine, ethanolamine, choline, glycerol, and inositol (Figure I.2). The corresponding phosphoglycerolipids are named phosphatidylserine (PS), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidylinositol (PI). The latter can also be phosphorylated at three different positions in the inositol ring resulting in seven different combinations that correspond to seven different species as will be discussed in chapter VI. Table I.1 - Nomenclature of relevant acyl-chains Short notation Name 14:0 Myristoyl 14:1 (9-cis) Myristoleoyl 16:0 Palmitoyl 16:1 (9-cis) Palmitoleoyl 18:0 Stearoyl 18:1 (9-cis) Oleoyl 18:2 (9,12 cis) Linoleoyl 18:3 (6,9,12–cis) γ-Linolenoyl 18:3 (9,12,15–cis) α-Linolenoyl 20:0 Arachidoyl 20:4 (5,8,11,14–cis) Arachidonoyl 22:0 Behenoyl 22:1 (13-cis) Erucoyl The phosphate group in phosphoglycerolipids is always negatively charged, and the net charge of the molecule is dictated by the charge of the alcohol moiety. Thus PA, PG, PS, PI, and phosphorylated PI are negatively charged, while PC and PE present a net neutral charge due to the positively charged amine in choline and ethanolamine. PC is the most abundant phosphoglycerolipid in the plasma membrane, whereas PE is in general the major component in bacterial membranes. 4
INTRODUCTION: BIOMEMBRANES Figure I.2 – a) Schematic representation of the phosphoglycerolipid structure. b) Most common alcohols found in the headgroups of phosphoglycerolipids. From Berg et al., 2002). c) Structure of a phosphatidylcholine - 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC). The acyl-chains found in each class of phosphoglycerolipids is also different. PC’s are mainly composed of short saturated chains (16 to 18 carbons) or 18:1 and 18:2 unsaturated chains. PE’s have a large fraction of polyunsaturated chains, in particular 20:4 (arachidonoyl). Charged phosphoglycerolipids also present a significant content of unsaturated acyl-chains (Sackmann, 1995). Other types of glycerolipids are found in biomembranes, namely the plasmalogens, in which one of the acyl-chains is bound to glycerol by a vinyl ether linkage. Plasmalogens constitute about 20 % of the total content of phosphoglycerides in humans, although their abundance varies dramatically among tissues and species. Human brain and heart tissues are particularly enriched in this class of lipids (Lodish et al., 2000). Cardiolipin is a dimer lipid since it contains four acyl chains. It constitutes about 20 % of the inner mitochondrial membrane and is also found in the membrane of plant chloroplasts and of certain bacterias. 1.2.1.2. Sphingolipids Sphingolipids are based on sphingosine instead of glycerol. Sphingosine is an aminoalcohol with a long unsaturated hydrocarbon chain. A long fatty-acid is attached to sphingosine by an amide bound. This basic structure is a ceramide, which is involved in cell death and is an essential component of skin (Mouritsen, 2005). The linkage of a choline to the terminal hydroxyl group of sphingosine in ceramide leads to 5
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
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Page 36 and 37: signal for neighbouring cells to ph
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Page 56 and 57: size corresponding to the hydrophob
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Page 75 and 76: 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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