Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism

Abstract

The hammerhead ribozyme is a small, intensively studied catalytic RNA, and has been used as a prototype for understanding how RNA catalysis works. In 2003, the importance of a set of tertiary contacts that appear in natural sequences of the hammerhead RNA was finally understood. The presence of these contact regions in stems I and II in 'full-length hammerhead ribozymes' is accompanied by an up to 1000-fold catalytic rate enhancement, indicating a profound structural effect upon the active site. Although the new structure resolved most of what appeared to be irreconcilable differences with mechanistic studies in solution, it did so in a way that is simultaneously reconcilable with earlier crystallographic mechanistic studies, within the limits imposed by the truncated sequence of the minimal hammerhead. Here we present an analysis of the correspondence between the full-length and minimal hammerhead crystal structures, using adiabatic morphing calculations that for the first time test the hypothesis that the minimal hammerhead structure occasionally visits the active conformation, both in solution and in the crystalline state in a sterically allowed manner, and argue that this is the simplest hypothesis that consistently explains all of the experimental observations.