Theoretical examination of two opposite mechanisms proposed for hepatitis delta virus ribozyme

Two mechanisms were previously proposed for the hepatitis delta virus (HDV) ribozyme where an active-site cytosine residue (C75) either functioned as a general base to deprotonate the 2'-OH at the rupture site or as a general acid to protonate the O5' leaving group. Here, we reported the first theoretical examination of the two mechanisms using a combination of the quantum mechanics (QM)/molecular mechanics (MM), molecular dynamics (MD), and near-attack-conformation (NAC) techniques. Our theoretical results supported the C75-acid mechanism, which was demonstrated to have an unfavorable starting geometry (in agreement with the crystallographic data) but a significantly lower energy barrier as compared to the C75-base mechanism. Therefore, the chemical details of the transition state in the HDV ribozyme may dramatically differ from those inferred from the structural studies.