A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

Nucleic Acids Res. 2018 Feb 28;46(4):1674-1683. doi: 10.1093/nar/gkx1269.

Abstract

We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Molecular*
  • Nucleotide Motifs
  • Nucleotides / chemistry
  • RNA / chemistry*
  • RNA, Double-Stranded / chemistry

Substances

  • Nucleotides
  • RNA, Double-Stranded
  • RNA