Automatic 13C chemical shift reference correction for unassigned protein NMR spectra

Xi Chen, Andrey Smelter, Hunter N.B. Moseley

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Poor chemical shift referencing, especially for 13C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional protein structure. Our algorithm named Bayesian Model Optimized Reference Correction (BaMORC) can detect and correct 13C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure. By combining the BaMORC methodology with a new intra-peaklist grouping algorithm, we created a combined method called Unassigned BaMORC that utilizes only unassigned experimental peak lists and the amino acid sequence. Unassigned BaMORC kept all experimental three-dimensional HN(CO)CACB-type peak lists tested within ± 0.4 ppm of the correct 13C reference value. On a much larger unassigned chemical shift test set, the base method kept 13C chemical shift referencing errors to within ± 0.45 ppm at a 90% confidence interval. With chemical shift assignments, Assigned BaMORC can detect and correct 13C chemical shift referencing errors to within ± 0.22 at a 90% confidence interval. Therefore, Unassigned BaMORC can correct 13C chemical shift referencing errors when it will have the most impact, right before protein resonance assignment and other downstream analyses are started. After assignment, chemical shift reference correction can be further refined with Assigned BaMORC. These new methods will allow non-NMR experts to detect and correct 13C referencing error at critical early data analysis steps, lowering the bar of NMR expertise required for effective protein NMR analysis.

Original languageEnglish
Pages (from-to)11-28
Number of pages18
JournalJournal of Biomolecular NMR
Volume72
Issue number1-2
DOIs
StatePublished - Oct 1 2018

Bibliographical note

Funding Information:
Acknowledgements This work was supported in part by National Science Foundation grant NSF 1252893 (Hunter N.B. Moseley) and National Institutes of Health grant NIH UL1TR001998-01 (Philip Kern).

Publisher Copyright:
© 2018, The Author(s).

Keywords

  • Carbon chemical shift
  • Protein NMR
  • Reference correction
  • Statistical modeling

ASJC Scopus subject areas

  • Biochemistry
  • Spectroscopy

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