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In order to understand the dimeric effects leading to membrane damage, extensive …
Biology Articles » Biochemistry » Lipid Biochemistry » Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect » Figures
Figure 1.PG-1 β-sheet arrangements. Topological diagrams for the PG-1 dimers in the (a) antiparallel and (b) parallel β-sheet arrangements. Both dimers are in an NCCN packing mode. Blue and white beads represent the positively charged (Arg) and hydrophobic residues, respectively, and the polar residue (Tyr) and Gly residues are denoted by green beads. Solid lines indicate the disulfide bonds between Cys residues, and dotted lines indicate the backbone hydrogen bond (H-bond). The first and the last residues for each monomer are indicated by the residue number.
Figure 2.Backbone hydrogen bond. Fractions of intermolecular and intramolecular backbone hydrogen bonds (H-bonds), QH-bond, as a function of the time, t, (a) for the antiparallel (A1 & A2 – 1 st & 2 nd rows) and parallel (P1 & P2 – 3 rd & 4th rows) β-sheets at the amphipathic interface of the lipid bilayer, and (b) for the antiparallel (A1) and parallel (P1) β-sheets in water. The red lines denote the fraction of intermolecular H-bond at the dimer interface, and the light and dark blue lines denote the fractions of intramolecular H-bond within each β-hairpin monomer.
Figure 3.Backbone dihedral angle. Backbone dihedral angle distributions (a) for the antiparallel (A1 & A2) and parallel (P1 & P2) β-sheets at the amphipathic interface of the lipid bilayer, and (b) for the antiparallel (A1) and parallel (P1) β-sheets in water. Dihedral angles (φ, ψ) are calculated only for the residues in the β-strands (residues 4 to 8 and 13 to 17 of each β-hairpin).
Figure 4.Peptide order parameter. (a) The probability distribution of the angle between the backbone carbonyl bond, C=O, in the β-strands and the normal to the lipid bilayer surface for the antiparallel (A1 (solid line) & A2 (dotted line)) and parallel (P1 (solid line) & P2 (dotted line)) β-sheets. (b) The probability distribution of the peptide order parameter, SC=O, for the antiparallel (A1 (solid line) & A2 (dotted line)) and parallel (P1 (solid line) & P2 (dotted line)) β-sheets. The numbers in the bracket denote the initial values of SC=O in the starting points.
Figure 5.Lipid interaction energy. Interaction energy of the PG-1 β-sheets with lipids (light gray bars), and interaction energy of the Arg residues with lipids (dark gray bars). The interaction energy is calculated separately for each monomer in the PG-1 β-sheet.
Figure 6.Lipid accessible surface area. Lipid accessible surface areas for the PG-1 β-sheets (light gray bars) and the Arg residues (dark gray bars). The lipid accessible surface area is calculated separately for each monomer in the PG-1 β-sheet.
Figure 7.Plane order parameter. Plane order parameter of the bilayer surface, SPOP, at the top leaflet (solid bars) and at the bottom leaflet (gray bars) of the lipid bilayer. The PG-1 β-sheet is located at the top leaflet of the lipid bilayer.
Figure 8.Solvent distribution. Probability distribution functions (P) for different component groups of lipid (PChol (choline – black lines), PPO4 (phosphate – red lines), PGlyc (glycerol – green lines), PCarb (carbonyls – yellow lines), and PCH3 (methyl – blue lines)), and for other solvents (Pwater (water – dashed black lines), PNa (sodium ion – dashed gray lines), and PCl (chloride ion – gray lines)) as a function of distance from the bilayer center for different PG-1 dimers on the lipid bilayer composed of POPC.
Figure 9.Lipid order parameter. Deuterium order parameters, SCD, for the oleoyl (left column) and palmitoyl (right) chains of the lipids at the top leaflet (peptide-containing) (upper panel) and the bottom leaflet (lower) of the lipid bilayer composed of POPC for the antiparallel β-sheets (A1 (solid circles) & A2 (open circles)) and the parallel β-sheets (P1 (solid triangles) & P2 (open triangles)).
Figure 10.PG-1 β-sheet conformations. Cartoons of PG-1 β-sheets in stereo view, representing the final peptide conformation on the lipid bilayer for the antiparallel ((a) A1 and (b) A2) and parallel ((c) P1 and (d) P2) β-sheets. In the cartoons, hydrophobic residues and disulfide bonded Cys residues are shown in white, a polar residue (Tyr) and Gly are shown in green, and positively charged residues (Arg) are shown in blue. Disulfide bonds are highlighted in yellow. For clarity, only the top leaflet of the lipid bilayer is shown, and phosphate atoms are denoted as red beads.
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