Mechanism of Protein digestion

A number of enzyme digestion assays show apparent first-order kinetics of reactant disappearance. There are four explanations of this phenomenon: (i) the reaction is dominated by a first-order limiting step, (ii) the digestion follows a pseudo-first order kinetics under the excess of a reactant species, (iii) the first-order kinetics is only applicable to the slow transient of the reaction, and (iv) the aggregate behavior of the reaction pathway produces behavior indistinguishable from the first-order kinetics. In this paper we theoretically investigate the kinetics for protein digestion by mathematically formulating rate equations for two proposed mechanisms namely the one by one mechanism and zipper mechanism. Our analysis shows that the kinetics of protein digestion would follow apparent first-order kinetics irrespective of the mechanism for low initial substrate concentration with respect to the initial enzyme concentration. Also our results provide an explanation for the experimental observations and suggest new experimental protocol that could reveal information on the mechanism of digestion. Futher, we are exploring possibilities to distinguish between one-by-one and zipper mechanisms. Our examination has revealed interesting facts which could me implemented experimentally.