Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding-unbinding reaction in Myoglobin

The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase may be well modelled theoretically by means of molecular dynamics simulations, the perturbed matrix method (PMM) and statistical mechanics, as we provided in previous articles. In this paper, we describe the theoretical framework, discussing thoroughly its crucial points, and apply the model to an important biochemical reaction: the Haem carbon monoxide binding-unbinding reaction in Myoglobin, specifically investigating the reaction step involving the carbon-iron chemical bond formation (disruption) which is of particular biochemical interest.