A mathematical view on the decoupled sites representation (Q1937904)

In this paper, the authors present the mathematical framework in which the decoupled sites representation (DSR) is embedded and which allow to prove its consistence with standard binding theory. To apply the DSR to any molecule, it is necessary to extend the set of binding energies from \(\mathbb{R}\) to a stripe within \(\mathbb{C}\). They find that, contradictorily to a former conjecture, the repulsion of the ligands is not sufficient to guarantee real roots of the binding polynomial. Moreover, the authors show that the DSR is the result of the special structure of a system of polynomial equations with the binding energies of the decoupled system as variables, and generalize their statement. Furthermore, this implies that using a common definition of cooperative binding on the level of interaction energies a meaningful measure of cooperativity between the binding sites cannot be defined solely on the basis of the overall titration. Applying the DSR to those molecules (different types of interacting ligands, such as protons and electrons) might help to understand the biophysical nature of these essential processes, which are the basis of life.