Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

Biophys J. 2005 May;88(5):3466-85. doi: 10.1529/biophysj.104.054916. Epub 2005 Feb 18.

Abstract

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent molecular dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in domain III, and for the K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenine / chemistry
  • Amino Acid Motifs
  • Base Pairing*
  • Base Sequence
  • Biophysics / methods*
  • Catalysis
  • Computer Simulation
  • Crystallography, X-Ray
  • Cytosine / chemistry
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Oscillometry
  • Peptide Elongation Factor G / chemistry
  • Protein Conformation
  • Protein Structure, Secondary
  • RNA / chemistry*
  • RNA, Ribosomal, 23S / chemistry
  • RNA, Small Nuclear / chemistry
  • RNA, Transfer / chemistry
  • Ribosomes / chemistry
  • Software
  • Time Factors
  • X-Rays

Substances

  • Macromolecular Substances
  • Peptide Elongation Factor G
  • RNA, Ribosomal, 23S
  • RNA, Small Nuclear
  • U4 small nuclear RNA
  • RNA
  • Cytosine
  • RNA, Transfer
  • Adenine