(304f) How CO2 Diffuses into the Active Site of Carbonic Anhydrase: A Study By Molecular Dynamics Simulation and Multi-Scale Markov-State Modeling

While a significantly enhanced capture of CO₂ has been accomplished with the aid of carbonic anhydrase (CA), which catalyzes the conversion of CO₂ to bicarbonate at an extremely fast rate, the molecular mechanism for the diffusion of CO₂ from the bulk aqueous phase into the active site of CA is not yet established. Here, we present theoretical results from molecular dynamics (MD) simulation and multi-scale Markov-state modeling (MSM) of the CO₂ diffusion process using carbonic anhydrase (α-human CA II, EC 4.2.1.1) as a model enzyme. CO₂ diffusion along the natural gateway of CA was illustrated with a two-dimensional free energy landscape along two reaction coordinates, i.e., the CO₂ distance (center of mass) from a water molecule attached to the zinc complex, and the orientation angle formed by O_H2O-C_CO2-O_CO2 atoms. Two distinct diffusion modes were identified using the Perron cluster cluster analysis (PCCA) in combination withthe flux analysis for the transition rate matrix of the coarse-grained Markov state model (CG-MSM). The simulation results for K_m, one key parameter of the Michaelis-Menten equation, agreed well with that from the experimental data. Moreover, the multi-scale MSM indicated a preferential accumulation of CO₂ at the hydrophobic pockets inside CA. A good understanding of the molecular events underpinning enzyme kinetics will be helpful for both molecular re-engineering of CA by either chemical or genetic methods as well as for process intensification or renovation for CA-assisted CO₂ capture and utilization.