Major groove width variations in RNA structures determined by NMR and impact of 13C r
 

Abstract Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1Hâ?? 1H 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 1Hâ?? 13C 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.

• Content Type Journal Article
• DOI 10.1007/s10858-010-9424-x
• Authors
  • Blanton S. Tolbert, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
  • Yasuyuki Miyazaki, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
  • Shawn Barton, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
  • Benyam Kinde, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
  • Patrice Starck, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
  • Rashmi Singh, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
  • Ad Bax, NIDDK, National Institutes of Health Laboratory of Chemical Physics Bethesda MD 208992 USA
  • David A. Case, Rutgers University Department of Chemistry & Chemical Biology and BioMaPS Institute 610 Taylor Road Piscataway NJ 08854-8087 USA
  • Michael F. Summers, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738
  • Journal Volume Volume 47
  • Journal Issue Volume 47, Number 3

Source: Journal of Biomolecular NMR