Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology

The catalytic properties of RNA have been a subject of fascination and intense research since their discovery over 30 years ago. Very recently, several classes of nucleolytic ribozymes have emerged and been characterized structurally. Among these, the twister ribozyme has been center-stage and a topic of debate about its architecture and mechanism owing to conflicting interpretations of different crystal structures and in some cases conflicting interpretations of the same functional data. In the present work, we attempt to clean up the mechanistic debris generated by twister ribozymes using a comprehensive computational RNA enzymology approach aimed to provide a unified interpretation of existing structural and functional data. Simulations in the crystalline environment and in solution provide insight into the origins of observed differences in crystal structures and coalesce on a common active site architecture and dynamical ensemble in solution. We use GPU-accelerated free energy methods with enhanced sampling to ascertain microscopic nucleobase pKa values of the implicated general acid and base, from which predicted activity-pH profiles can be compared directly with experiments. Next, ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with full dynamic solvation under periodic boundary conditions are used to determine mechanistic pathways through multidimensional free energy landscapes for the reaction. We then characterize the rate-controlling transition state and make predictions about kinetic isotope effects and linear free energy relations. Computational mutagenesis is performed to explain the origin of rate effects caused by chemical modifications and to make experimentally testable predictions. Finally, we provide evidence that helps to resolve conflicting issues related to the role of metal ions in catalysis. Throughout each stage, we highlight how a conserved L-platform structural motif, together with a key L-anchor residue, forms the characteristic active site scaffold enabling each of the catalytic strategies to come together for not only the twister ribozyme but also the majority of the known small nucleolytic ribozyme classes.