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J Mol Biol. 2012 Aug 3;421(1):6-26. doi: 10.1016/j.jmb.2012.03.002. Epub 2012 Mar 13.

Discrete RNA libraries from pseudo-torsional space.

Author information

1
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.

Abstract

The discovery that RNA molecules can fold into complex structures and carry out diverse cellular roles has led to interest in developing tools for modeling RNA tertiary structure. While significant progress has been made in establishing that the RNA backbone is rotameric, few libraries of discrete conformations specifically for use in RNA modeling have been validated. Here, we present six libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone, comparable to phi and psi in the protein backbone. We evaluate the ability of each library to represent single nucleotide backbone conformations, and we show how individual library fragments can be assembled into dinucleotides that are consistent with established RNA backbone descriptors spanning from sugar to sugar. We then use each library to build all-atom models of 20 test folds, and we show how the composition of a fragment library can limit model quality. Despite the limitations inherent in using discretized libraries, we find that several hundred discrete fragments can rebuild RNA folds up to 174 nucleotides in length with atomic-level accuracy (<1.5 Å RMSD). We anticipate that the libraries presented here could easily be incorporated into RNA structural modeling, analysis, or refinement tools.

PMID:
22425640
PMCID:
PMC3422622
DOI:
10.1016/j.jmb.2012.03.002
[Indexed for MEDLINE]
Free PMC Article

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