On the simulation of enzymatic digest patterns: the fragmentation of oligomeric and polymeric galacturonides by endo-polygalacturonase II

摘要

A simulation methodology for predicting the time-course of enzymaticdigestions is described. The model is based solely on the enzyme's subsitearchitecture and concomitant binding energies. This allows subsite bindingenergies to be used to predict the evolution of the relative amounts ofdifferent products during the digestion of arbitrary mixtures of oligomeric orpolymeric substrates. The methodology has been specifically demonstrated bystudying the fragmentation of a population of oligogalacturonides of varyingdegrees of polymerization, when digested by endo-polygalacturonase II (endo-PGII) from Aspergillus niger.