Abstract
Determination of the protonation state of enzymes is a challenging problem in computational biophysics largely due to the vast number of possible protonic configurations. The protonation state dynamics of respiratory complex I was investigated via Monte Carlo and asynchronous dynamics simulations and a novel eigenvector analysis. Many low lying states were identified and examined. The analysis revealed that the protonic states form a quasi-continuous band of energies, which are highly correlated and inhomogeneous. Many states have similar energies, but differ significantly in their protonic composition. In order to transfer from one such state to another, a large number of protons should be exchanged simultaneously raising the question of the ergodicity of protonation dynamics of such systems.