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Journal of Biomolecular NMR

, Volume 47, Issue 3, pp 205–219 | Cite as

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

  • Blanton S. Tolbert
  • Yasuyuki Miyazaki
  • Shawn Barton
  • Benyam Kinde
  • Patrice Starck
  • Rashmi Singh
  • Ad Bax
  • David A. Case
  • Michael F. Summers
Article

Abstract

Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1H 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 1H 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.

Keywords

NMR RNA structure determination Isotope labeling Residual dipolar coupling Residual chemical shift anisotropy 

Notes

Acknowledgments

Support from the NIH (GM42561 to M.F.S., GM45811 to D.A.C.) and the Intramural Research Program of the NIDDK, NIH (DK029051-03 to A.B.) is gratefully acknowledged. B.K., P.S., S.B. and R.S. are UMBC Meyerhoff Scholars and were supported by an HHMI undergraduate education grant.

Supplementary material

10858_2010_9424_MOESM1_ESM.pdf (312 kb)
A suite of scripts for generating restraints to maintain aromatic base planarity and ideal bond angles, generating Amber compatible RCSA and RDC restraints, performing MPI-based Amber structure calculations, facilitating semi-automated structure analysis with Pymol and X3DNA, and Bruker-compatible IMC pulse sequence, parameter, and sample data files, are available for download at: www.hhmi.umbc.edu/downloads. Coordinates for the final, refined [DIS]2 structures, and associated experimental RDC and RCSA values, have been deposited (PDB 2kyd (rscb 101717) and BMRB 16980, respectively). Details on the implementation of RCSAs in Amber, and raw NMR frequencies and calculated RDC, RCSA and PRCSA values for [DIS]2. (PDF 311 kb)

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Blanton S. Tolbert
    • 1
    • 2
  • Yasuyuki Miyazaki
    • 1
  • Shawn Barton
    • 1
  • Benyam Kinde
    • 1
  • Patrice Starck
    • 1
  • Rashmi Singh
    • 1
  • Ad Bax
    • 3
  • David A. Case
    • 4
  • Michael F. Summers
    • 1
  1. 1.Howard Hughes Medical Institute and Department of Chemistry and BiochemistryUniversity of Maryland Baltimore CountyBaltimoreUSA
  2. 2.Department of Chemistry and BiochemistryMiami University of OhioOxfordUSA
  3. 3.Laboratory of Chemical PhysicsNIDDK, National Institutes of HealthBethesdaUSA
  4. 4.Department of Chemistry & Chemical Biology and BioMaPS InstituteRutgers UniversityPiscatawayUSA

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