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Kinetics of CO2 Diffusion in Human Carbonic Anhydrase: A Study by Molecular Dynamics Simulation and the Markov-State Model

Abstract

Molecular dynamics (MD) simulation, in combination with the Markov-state model (MSM), was applied to probing CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 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 CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 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 CO2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln136 contributes to the maximal flux. The simulation results offer a new perspective on the CO2 hydration kinetics and useful insights toward development of novel biochemical processes for more efficient CO2 sequestration and utilization.

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Publication details

The article was received on 10 Feb 2017, accepted on 07 Apr 2017 and first published on 07 Apr 2017


Article type: Paper
DOI: 10.1039/C7CP00887B
Citation: Phys. Chem. Chem. Phys., 2017, Accepted Manuscript
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    Kinetics of CO2 Diffusion in Human Carbonic Anhydrase: A Study by Molecular Dynamics Simulation and the Markov-State Model

    G. Chen, X. Kong, D. Lu, J. Wu and Z. Liu, Phys. Chem. Chem. Phys., 2017, Accepted Manuscript , DOI: 10.1039/C7CP00887B

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