Thermodynamical model for insertion and aggregate binding of caffeine to the homopolymer poly(riboadenylate) and model choice by data analysis

This paper describes the model used to estimate the parameters of caffeine-poly(riboadenylate) (poly(A)) interactions from corresponding 1H-NMR measurements. The model of insertion and aggregate binding describes the non-cooperative insertion of a molecule C into an interspace between two monomers of a homopolymer in competition with aggregate binding. It contains two binding constants, K1 for insertion and K2 for the interaction of monomeric A units of the polymer with C molecules in bound aggregates, and two cooperativity parameters, Kcc for stacking of C molecules within aggregates and tau which is thought to be due to conformational adaptation of the polymer to those bound aggregates which cover more than one A unit. In contrast to other models, the size of a binding site (within the aggregates) is less than one monomeric unit, with n denoting the maximum number of C molecules per A unit in bound aggregates. The model is developed for general n by means of the method of sequence-generating functions. For n = 2 and n = 3, the correctness of the model treatment was checked by the matrix method. The model is applicable to the binding of aggregates to homopolymers, which are flexible enough to fit their structure to the aggregates.