Processive Pectin Methylesterases: The Role of Electrostatic Potential, Breathing Motions and Bond Cleavage in the Rectification of Brownian Motions
Figure 5
Porcupine plots of the HXM decasaccharide in complex with Ec-PME in the time windows 15 ns to 30 ns (A and C) and 30 ns to 50 ns (B and D).
Arrows point in the direction of the motion calculated for the glycosidic bonds linking consecutive monosaccharide residues along the decasaccharide HG chain. In C and D only motions along the direction of the sliding are reported. The length of the arrows is proportional to the amplitude of the motion, which reaches a maximum of ∼10 Å for the glycosidic bond linking the pair of loosely held residues in subsites +4 and +5. Note the large component of vertical motion, consistent with the opening of the binding cleft and the loosening of binding of the HXM oligomer. Note also that the final docking of the whole oligomer with the restoration of the alternating monosaccharide residue orientations and the de-methylesterification reaction are not sampled in these molecular mechanics studies.
