Kinetics of CO diffusion in human carbonic anhydrase: a study using molecular dynamics simulations and the Markov-state model.

Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO diffusion in hCA-II is a rate-limiting step in the CO diffusion-binding-reaction process. The equilibrium distribution of CO shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO diffusion into the active site of hCA-II is through a binding pocket where residue Gln contributes to the maximal flux. The simulation results offer a new perspective on the CO hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO sequestration and utilization.