A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.

ABSTRACT: RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path. Building upon recent crystallographic data, our results provide a

SUBMITTER: Lee TS 

PROVIDER: S-EPMC5072530 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature