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Nucleic Acids Res. 2015 Sep 3;43(15):7260-9. doi: 10.1093/nar/gkv708. Epub 2015 Jul 17.

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.

Author information

1
Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy.
2
Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 265, Via Bonomea I-34136 Trieste, Italy bussi@sissa.it.

Abstract

Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whether ENM approaches can be successfully extended to this class of biomolecules. This issue is tackled here by considering various families of elastic networks of increasing complexity applied to a representative set of RNAs. The fluctuations predicted by the alternative ENMs are stringently validated by comparison against extensive molecular dynamics simulations and SHAPE experiments. We find that simulations and experimental data are systematically best reproduced by either an all-atom or a three-beads-per-nucleotide representation (sugar-base-phosphate), with the latter arguably providing the best balance of accuracy and computational complexity.

PMID:
26187990
PMCID:
PMC4551938
DOI:
10.1093/nar/gkv708
[Indexed for MEDLINE]
Free PMC Article

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