RNA pseudoknots compose a three‐dimensional structural motif that is present in the catalytic cores of some ribozymes, and are also capable of stimulating ribosomal frameshifts. Furthermore, their complex topology and non‐canonical hairpin‐loop composition make pseudoknots an essential structural motif with which to study the RNA folding process. Here we report our analysis of nearly 20,000 independent all‐atom molecular dynamics simulations of the ribosomal frame‐shifting pseudoknot of Luteovirus and the tmRNA pseudoknot from Aquifex aeolicus, which share global topology but have only ~50% sequence similarity. Using the Folding@Home distributed computing network and our new Pathway Enumeration sampling method, a cumulative sampling time of over 100 μs was achieved for each of these pseudoknots. K‐means clustering was used to identify 27 conformational microstates for each pseudoknot and similar folding pathways were identified for these two sequences. In agreement with our earlier work, this study suggests that native state topology is a predominate factor in the RNA folding mechanism.This work was made possible by the worldwide Folding@Home volunteers who contributed invaluable processor time, Women & Philanthropy, and a Research Corporation Cottrell College Science Award.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.