Catalytic Strategies of Nucleolytic Ribozymes
The ability of RNA molecules to selectively and efficiently catalyze complex chemical transformation has vast implications. Our understanding of the mechanisms of RNA catalysis have been greatly advanced by the study of small nucleolytic RNA enzymes, or ribozymes, that have evolved naturally in viruses and living organisms, or artificially through high-throughput in vitro selection techniques . Experimental structural and mechanistic work, along with computational simulations have provided deep insight into the mechanism of these model ribozyme systems. Very recently, there has been a surge in progress in the determination of crystallographic structures of ribozymes [2–6] that have provided a departure point for theoretical investigations that aim to bridge the gap between structural and mechanistic measurements, and provide a detailed dynamical picture of mechanism at atomic-level resolution. In this way, molecular simulations have the potential to unify the interpretations of a broad range of experimental data and establish a consensus view of mechanism . Ultimately, multiscale simulations, together with experiments, afford the tools needed to gain predictive insight into catalysis, including control factors that regulate selectivity and reactivity, that may guide rational design efforts.
In the present work, results from multiscale molecular simulations are presented for a series of ribozymes for which crystallographic data has recently become available, including the twister , Varkud satallite virus (VS)  and pistol  ribozymes. These results uncover recurring themes, as well as new twists, in the catalytic strategies taken by ribozymes that are apparent only when broadly analyzing their structure, biochemical characterization and detailed mechanisms predicted by molecular simulations. The interpretations of experimental data afforded by new multiscale molecular simulation results uncover general principles and provide predictive insight into the catalytic mechanisms of nucleolytic ribozymes that may guide rational design efforts.