Computer modelling of polymer decomposition by active interactions with enzyme molecules. A simulation of RNA digestion by ribonuclease.

Abstract

A model of 200 polymer molecules each 70 units of length with randomly located susceptible and resistant links was elaborated. The production of mono-, di-, tri-unit and other fragments in repeating random interactions of polymer (P) with the polymer--cleaving enzyme (E) was calculated. Analysis of the calculations performed that the polymer molecules with an initial count of 70-units disappeared, imitating the first order kinetics with a half-life of about 0.37 x 10(3) P/E interactions. The production of fragments 30-69 units long was small and the life of those molecules was limited to a range from 0.5 x 10(3) to 5 x 10(3) P/E interactions. The mean polymer length decreases to one third at 10(3) P/E interactions. The production of single-unit fragments followed a sigmoidal relationship. The first reaction period, with increasing number of single-unit fragments per 10(3) P/E interactions, corresponded to a decrease in the mean polymer length to about 10 units. Then the production of one-unit fragments decreased and stopped at about 10(5) P/E interactions. This model could be used for analysis of RNA fragmentation processes by any number of RNA-ribonuclease interactions. Further development of this model would be of help in understanding the effect of various nucleotide sequences on the RNA digestion process.