A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate.

Heteronuclear multidimensional NMR structural studies have been performed on a hammerhead ribozyme complexed with a cleaved and an uncleaved substrate. The NMR data demonstrate that the three helices surrounding the conserved catalytic core hammerhead are stably formed in both complexes. Evidence is also presented that indicates that the sheared G-A base pairs in the conserved core are formed in the absence of Mg2+. The NMR structural data demonstrate that there is a significant structural change of the conserved core of the hammerhead ribozyme-substrate complex upon cleavage of the substrate. Molecular dynamics calculations were performed to generate models of the ribozyme-cleaved substrate complex, and these results are used to help understand the mechanism of the hammerhead cleavage reaction.