RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution) (original) (raw)

  1. Jane S. Richardson1,
  2. Bohdan Schneider2,
  3. Laura W. Murray1,
  4. Gary J. Kapral1,
  5. Robert M. Immormino1,
  6. Jeffrey J. Headd1,
  7. David C. Richardson1,
  8. Daniela Ham2,
  9. Eli Hershkovits3,
  10. Loren Dean Williams4,
  11. Kevin S. Keating5,
  12. Anna Marie Pyle6,
  13. David Micallef7,
  14. John Westbrook7, and
  15. Helen M. Berman7
  16. 1Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710-3711, USA
  17. 2Institute of Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, CZ-16610 Prague, Czech Republic
  18. 3School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
  19. 4School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
  20. 5Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
  21. 6Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
  22. 7Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA

Abstract

A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle δεζαβγδ combinations empirically found favorable for the sugar-to-sugar “suite” unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for δεζ and a lowercase letter for αβγδ, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

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