Journal of Biomolecular NMR

, Volume 63, Issue 1, pp 39–52 | Cite as

Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

  • Joshua D. Brown
  • Michael F. Summers
  • Bruce A. Johnson
Article

Abstract

The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and 1H and 13C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA 1H and 13C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

Keywords

RNA Chemical shift Secondary structure NMR signal assignment and validation 

Notes

Acknowledgments

This research was supported by Grants from the National Institute of General Medical Sciences of the National Institutes of Health (NIGMS, R01 GM42561 to MFS and P50 GM 103297 to BAJ), and JDB was supported by a NIGMS Grant for maximizing student diversity, NIGMS R25 GM 055036. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Supplementary material

10858_2015_9961_MOESM1_ESM.pdf (790 kb)
Supplementary material 1 (PDF 789 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Howard Hughes Medical InstituteUniversity of Maryland Baltimore CountyBaltimoreUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of Maryland Baltimore CountyBaltimoreUSA
  3. 3.One Moon Scientific, Inc.WestfieldUSA
  4. 4.CUNY Advanced Science Research CenterNew YorkUSA

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