Computing the Minimal Rebinding Effect Included in a Given Kinetics
M. Weber, K. Fackeldey – 2014
In this paper we show that the binding kinetics of a molecular system can be identified by a projection of a continuous process onto a finite number of macro states. We thus interpret binding kinetics as a projection. When projecting onto nonoverlapping macro states the Markovianity is spoiled. As a consequence, the description of, e.g., a receptor-ligand system by a two state kinetics, is not accurate. By assigning a degree of membership to each state, we abandon the nonoverlapping approach. This overlap is crucial for a correct mapping of binding effects by Markov state models with regard to their long time behavior. It enables us to describe the highly discussed rebinding effect, where the spatial arrangement of the system has the be included. By introducing a “degree of fuzziness,” we have an indicator for the strength of the rebinding effect such that the minimal rebinding effect can be derived from an optimization problem. The fuzziness also includes some new paradigms for molecular kinetics. These new model paradigms show good agreement with experimental data.