Microscopic modeling of ligand diffusion through the protein leghemoglobin: computer simulations and experiments

The diffusion of carbon monoxide through lupine leghemoglobin was investigated. The potential of mean force, the transition-state theory rate constant, the friction kernel, the transmission coefficient, and the diffusion constant were calculated. The computations are based on our previous exploration of the diffusion dynamics using the mean field method (LES) 12 and our calculation of the reaction coordinate. 13 The back of the heme pocket (close to phenylalanine 44 and phenylalanine 29) is a shallow free energy minimum for the dissociated ligand