Figure 3

Residue-dependent RMS fluctuations of the apoform MD simulations with PqsD in its monomeric and dimer state. The fluctuations of the residues of PqsD in its monomer form (MD code A) are coloured in green, whereas for the PqsD in its dimer state (MD code B) chain A and B are shown in blue and red respectively. Domains putatively involved in the catalysis as identified by comparative analysis with homologous KAS-III enzymes are labelled with their abbreviations (dotted orange box indicates helix H14): adenosine binding site - aBS, palindromic “substrate-loop” - sL, helix H8-H9 loop - h8-9, hairpin-loop - hL, helix H12 - h12, “oxyanion-loop” – oL. Notably, also for all other MD simulations the largest RMS fluctuations were found in these areas (see also Additional file 1: Figure SI8).