Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction.

We have performed molecular dynamics (MD) calculations by using one of the recently solved crystal structures of a hammerhead ribozyme. By rotating the alpha, beta, gamma, delta, epsilon, and zeta torsion angles of the phosphate linkage of residue 17, the nucleobase at the cleavage site was slightly rotated out of the active site toward the solution. Unconstrained MD simulations exceeding 1 ns were performed on this starting structure solvated in water with explicit counter ions and two Mg2+ ions at the active site. Our results reveal that near attack conformations consistently were formed in the simulation. These near attack conformations are characterized by assumption of the 2'-hydroxyl to a near in-line position for attack on the -O-(PO2-)-O- phosphorous. Also during the time course of the MD study, one Mg2+ moved immediately to associate with a pro-R phosphate oxygen in the conserved core region, and the second Mg2+ remained associated with the pro-R oxygen on the phosphate linkage undergoing hydrolysis. These results are in accord with a one-metal ion mechanism of catalysis and give insight into the possible roles of many of the conserved residues in the ribozyme.