Analysis of the Interaction Interfaces of the N-Terminal Domain from Pseudomonas aeruginosa MutL
Figure 7
PaNTD mixed solvent MD analysis.
Three-dimensional density distribution of iPrOH in ATP bound and unbound PaNTD is showed from a frontal A), and backside B) view. I: Dimerization interface; II: DNA binding patch; III: putative interaction surface. Figure rendering was made using VMD, with an isosurface representation and density isovalue of 20. C) Quantification of protein-iPrOH contacts between protein Cα and all iPrOH C1 was made using g_mindist with a cut-off of 0.15 nm. Cα contacts with iPrOH atom C1 along the MD were calculated. Dimerization interface (L1–45 and ATP lid) as determined with sequence alignment is indicated with black horizontal bars. Residues predicted to bind DNA (residues 259–276 and 307–330) (* and red bars) using the DNAbinR server and E. coli MutS-MutL interface mapped by Winkler et al. [45] are indicated (EcNTD r. 131–135; PaNTD r. 135–138) (• and green bar). Finally, a putative interaction interface (residues 209–230 and 245–252) (# and blue bars) was determined as high iPrOH density area. The calculated mean contact for all residues is indicates with a black line across the chart and the areas beneath this threshold were shadowed with light grey to facilitate the identification of high iPrOH density residues.