Solvent Dynamics and Mechanism of Proton Transfer in Human Carbonic Anhydrase II

In this paper we describe the first all-atom aqueous-phase MD simulations of human carbonic anhydrase II in three protonation states relevant to the rate-limiting intramolecular proton-transfer step. In particular, we have examined the zinc−water form of the enzyme (CHOH), the zinc−hydroxide form of the enzyme with a doubly protonated His-64 (COHH, the putative intramolecular proton-transfer proton-accepting residue), and the native zinc−hydroxide form (COH) of the enzyme (i.e., with an unprotonated His-64). From these MD simulations (up to ∼1 ns in length) we have studied in detail the dynamics of these three systems. Overall the dynamics of the three systems do not vary significantly (e.g., the active site region is rigid, the number of long-lived hydrogen bonds is constant, etc.) with the exception of COHH. In this case the residues that line the entrance to the active site cavity (near the location of His-64) undergo significantly higher fluctuations than in the CHOH and COH cases. It is postulated th...