Comparative Study of Stability and Activity of Wild-Type and Mutant Human Carbonic Anhydrase II Enzymes Using Molecular Dynamics and Docking Simulations

Abstract

The human carbonic anhydrase II (HCA II) enzyme is a cytosolic protein located in the membrane of red blood cells. A zinc ion (Zn2+) in this enzyme makes it an excellent example of a metalloenzyme that reversible hydration of carbon dioxide (CO2). Considering the critical role of the HCA II, computational methods such as molecular docking, molecular dynamics (MD) simulation, and molecular mechanic/Poisen-Boltzman surface area (MMPBSA) analysis are used to study the structure and dynamics of the wild-type enzyme and the mutant enzyme with two ligands, CO2, and 4-nitrophenyl acetate. Our results of MD simulation of a wild-type enzyme with 4-nitrophenyl acetate ligand show that it created essential effects on the fluctuation of this enzyme and made it more unstable and less compact than the same enzyme without ligand. In the MD simulation of the mutant enzyme with 4-nitrophenyl acetate ligand, no significant difference is observed between this enzyme with and without ligand, but the solvent accessible surface area (SASA) measure of the mutant enzyme without ligand is higher. The affinity of the wild-type enzyme to the 4-nitrophenyl acetate ligand is notably higher than the mutant enzyme with the same ligand. The reason for this difference in stability is the mutation of Ala 65 to Leu (A65L). Furthermore, results showed that wild-type enzyme and mutant enzyme with CO2 ligand are more favorable in stability and flexibility than the same enzymes without ligand. These results can help in the engineering and design of new variants of carbonic anhydrase enzyme.