Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.

ABSTRACT: A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions fo

SUBMITTER: Mustoe AM 

PROVIDER: S-EPMC4705646 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature