Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement

J Biomol NMR. 2010 Jul;47(3):205-19. doi: 10.1007/s10858-010-9424-x. Epub 2010 Jun 15.

Abstract

Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by (1)H- (1)H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic (1)H- (13)C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures.

Publication types

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

MeSH terms

  • Anisotropy
  • Carbon Isotopes / chemistry*
  • Crystallography, X-Ray
  • Databases, Nucleic Acid
  • Molecular Dynamics Simulation
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation*
  • RNA / chemistry*

Substances

  • Carbon Isotopes
  • RNA