Molecular dynamics simulation of MTS interaction with phospholipid bilayer.

<p>A. Helical wheel representation of <i>E. coli</i> RNase E MTS (<u>M</u>embrane <u>T</u>argeting <u>S</u>equence). The 15-residue sequence corresponds to residues 568–582 of RNase E. Yellow, hydrophobic residues; blue, basic residues; green, small hydrophilic residues. Molecular dynamics simulations were made with a slightly large peptide that corresponds to residues 565–585 of RNase E. B. Snapshot from molecular dynamics simulation of the interaction of the MTS with phospholipid bilayer. The backbone of the MTS is shown in red, hydrophobic residues in yellow and charged/hydrophilic residues in pink. Water molecules have been masked. The phospholipid bilayer has been sliced transversally (aqua, acyl interior; green, glycerol moieties; brown, phosphate moieties; turquoise, ethanolamine moieties). A molecular graphics movie of the simulation is provided (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004961#pgen.1004961.s012" target="_blank">S1 Video</a>). C. Depth of insertion of the wild type MTS peptide and variants into the phospholipid bilayer. Depth (ordinate) corresponds to distance from the plane of the phospholipid bilayer. The sequence (abscissa) corresponds to the region of RNase E containing the MTS. The sequence underlined in blue corresponds to the phylogenetically conserved element (residues 568–582 of RNase E) that was shown experimentally to have the propensity to form an α-helix upon interaction with the membrane [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004961#pgen.1004961.ref006" target="_blank">6</a>]. WT = wild type sequence (black line). Sequence variants: AA, F574A/F575A (red line); E, F575E (green line); P, insertion of proline between F574 and F575 (blue line). The depth of the inserted proline is shown by the additional point on the blue line. D. Binding of fluorescein-labelled peptides corresponding to wild type MTS and AA variant (F574A/F575A) to liposomes prepared from <i>E. coli</i> lipid extracts. i) Large field image of phospholipid vesicles in the absence of peptide. ii) Vesicles in the presence of peptide. iii) Quantification of fluorescence intensity along the lines traced in ii). The higher background in the right image (AA variant) is due to unbound peptide.