Processive Pectin Methylesterases: The Role of Electrostatic Potential, Breathing Motions and Bond Cleavage in the Rectification of Brownian Motions
Figure 9
Representation of the interactions in the −2 subsite during the sliding of the decasaccharide along the binding groove of Ec-PME.
At the start of the simulation (crystal structure coordinates) the monosaccharide residue docked in the −2 subsite establishes hydrogen bonds between Thr109 and Ala110 backbone nitrogens (A). After the rotation of the monosaccharide residues about the glycosidic bond and the sliding of the polysaccharide along the groove, the monosaccharide residue previously docked in the subsite −1 establishes contacts with Thr109 and Ala110 in the −2 subsite. The same two sugar moieties are circled in yellow and blue respectively in both (A) and (B) to highlight changes occurring in their interactions with the protein. PME secondary structure is shown in cartoon form and colored in grey. The active site (+1 subsite) region is colored in green. Thr109, Ala110 and the HG decasaccharide are represented with cyan for carbon and red for oxygen atoms.
