Molecular dynamics simulation of the endopolygalacturonase II--octagalacturonate complex

The endopolygalacturonase II enzyme from A. niger was studied with an octameric fragment of -1,4-D-polygalacturonic acid. We present an approach to modeling the complex using MD simulations and offer a structural in terpretation for the expe rimental data given by amide exchange mass spectrometry and site-directed mutagenesis studies. The detailed model predicts a conformational change in the linear fo rm of the bound substrate to an activated bent form, which is supported by the experimental data given. The bent conformation of the substrate partially transverses the primary binding cleft and occupies a newly proposed secondary binding region, thus giving insight into the cleavage pathway for the endopolygalacturonase II enzyme.