Evaluation of intramolecular interaction between complementary domains, connected with a flexible chain

A method for the evaluation of the effective binding parameters for the interaction between two complementary domains connected with a flexible chain is suggested. The calculations are based on the assumption that the chain is absolutely flexible and does not hinder free relative diffusion of the domains in the solution but does not allow the domains to move away from each other further than the length of the chain. Then, if the distance between the connected domains and the affinity of the interaction between disconnected domains are known, the suggested method allows calculation so-called "local concentration" of the domains relative to each other. On this basis, it is possible to estimate the upper limit to the fractional content of domains in complex, which, when constrained by the linking polypeptide chain, may be much higher than implied by the absolute concentrations of the domains.