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

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Abstract

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 that this facilitates solvent and buffer exchange around His-64, thereby facilitating the intermolecular proton-transfer step. We also find that the motion of His-64 is limited in all three cases to occupying the “in” orientation (∼7 Å from the zinc ion, while the so-called “out” conformer is further away), which suggests that fluctuations of this residue between the in and out conformers have a limited influence on the intramolecular proton transfer. However, due to the limited time scales of our simulations, this needs to be examined in more detail. Importantly, though, we find that His-64 acts as a “gate-keeper” between the inner active site region (characterized by localized water molecules) and the outer (bulk) region, which is characterized by relatively freely diffusing water molecules. This function of His-64 has not been realized previously. In the inner active site we have identified relatively long-lived water bridges between the zinc-bound water or hydroxide and the imidazole or imidazolium side chain of His-64. The lengths of these bridges vary between two and six water molecules, and the preferred bridge depends on the protonation of the active site. We estimate that the probability of water bridge formation is low (at most ∼1.5 kcal/mol) and that water bridge formation is not the rate-limiting step in the proton-transfer process (transfer from zinc-bound water to an active site water is rate-limiting).

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