BINDING OF SUBSTRATE CO2 TO THE ACTIVE-SITE OF HUMAN CARBONIC ANHYDRASE-II - A MOLECULAR-DYNAMICS STUDY

Molecular dynamics has been used to study binding of substrate CO2 to the active site of human carbonic anhydrase II. Three potential CO2 binding sites have been located. The first is at the active-site hydrophobic pocket (the analytically productive site), where CO2 is ≈ 3.5 Å from the zinc ion and interacts with His-94, His-119, Val-121, Val-143, Leu-198, Thr-199, the zinc ion, and the zinc-bound hydroxide ion. The second CO2 binding site is ≈6 Å from the zinc ion, where CO2 interactswith His-64, His-94, Leu-198, Thr-200, Pro-201, Pro-202, and some active-site water molecules. The third CO2 binding site is ≈10 Å from the zinc ion, is largely solvated by water molecules, and interacts with His-64, Asn-67, and Gin-92. At these three CO2 binding sites, the CO2 molecule is highly localized (the average Zn - CO2 distance fluctuation is ≈1 Å) and favors the linear binding orientation toward the zinc ion. This linear binding orientation of CO2 and its electrostatic interaction with the zinc ion direct diffusion of CO2 toward the zinc ion and facilitate the nucleophilic attack from O of the zinc-bound OH- to C of CO2 in the productive hydrophobic binding site. Finally, the two CO2 binding sites outside the hydrophobic binding pocket, which may represent two intermediate states along the CO2 binding pathway, could play important roles as a CO2 relay.