Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions

• Published in: PloS one Vol. 9; no. 2; p. e87581
• Main Authors: Mercadante, Davide, Melton, Laurence D, Jameson, Geoffrey B, Williams, Martin A K
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.02.2014; Public Library of Science (PLoS)
• Subjects: Bacteria; Binding sites; Biocatalysis; Biochemical Phenomena; Biochemistry; Biology; Breathing; Carboxylic Ester Hydrolases - metabolism; Catalysis; Cell walls; Chains; Chemistry; Crystal structure; Dendroctonus ponderosae; Electrostatic properties; Electrostatics; Energy (Physics); Enzymes; Erwinia - enzymology; Free energy; Humicola; Hydrolysis; Models, Molecular; Molecular dynamics; Molecular motors; Motion; Nanotechnology; Pectin; Pectins; Physics; Polysaccharides; Protein binding; Protein transport; Proteins; Saccharides; Static Electricity; Substrate Specificity; Sugar; Thermodynamics; Translocation
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0087581

Pectin methylesterases (PMEs) hydrolyze the methylester groups that are found on the homogalacturonan (HG) chains of pectic polysaccharides in the plant cell wall. Plant and bacterial PMEs are especially interesting as the resulting de-methylesterified (carboxylated) sugar residues are found to be arranged contiguously, indicating a so-called processive nature of these enzymes. Here we report the results of continuum electrostatics calculations performed along the molecular dynamics trajectory of a PME-HG-decasaccharide complex. In particular it was observed that, when the methylester groups of the decasaccharide were arranged in order to mimic the just-formed carboxylate product of de-methylesterification, a net unidirectional sliding of the model decasaccharide was subsequently observed along the enzyme's binding groove. The changes that occurred in the electrostatic binding energy and protein dynamics during this translocation provide insights into the mechanism by which the enzyme rectifies Brownian motions to achieve processivity. The free energy that drives these molecular motors is thus demonstrated to be incorporated endogenously in the methylesterified groups of the HG chains and is not supplied exogenously.