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Title: ON THE SIMULATION OF ENZYMATIC DIGEST PATTERNS

Author
item HUNT, JONATHAN - MASSEY UNIV, NEW ZEALAND
item Cameron, Randall - Randy
item WILLIAMS, MARTIN A - MASSEY UNIV, NEW ZEALAND

Submitted to: Biochimica et Biophysica Acta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2006
Publication Date: 12/1/2006
Citation: Hunt, J.J., Cameron, R., Williams, M.A.K. 2006. On the simulation of enzymatic digest patterns: The fragmentation of oligomeric and polymeric galacturonides by endo-polygalacturonase II. Biochimica et Biophysica Acta. 1760:1669-1703.

Interpretive Summary: A model to predict the degradation of pectin by a fungal enzyme has been tested and found to accurately describe the degradation of large pectin fragments. The model is based solely on the interaction energy between the enzyme and substrate. The model has potential applications for predicting functional properties of enzyme treated biopolymers such as pectin or other polysaccharides. It will also be useful for structural mapping of complex biopolymers and describing the relationship between polymer structures and resulting functionalities.

Technical Abstract: A simulation methodology for predicting the time-course of enzymatic digestions is described. The model is based solely on the enzyme’s sub-site architecture and concomitant binding energies. This allows sub-site binding energies to be used to predict the evolution of the relative amounts of different products during the digestion of arbitrary mixtures of oligomeric or polymeric substrates. The methodology has been specifically demonstrated by studying the fragmentation of a population of oligogalacturonides of varying degrees of polymerization, when digested by endo-polygalacturonase II (endo-PG II) from Aspergillus niger.