Covariance NMR processing and analysis for protein assignment

Bradley J. Harden, Dominique P. Frueh

Research output: ResearchChapter

Abstract

During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

LanguageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages353-373
Number of pages21
Volume1688
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1688
ISSN (Print)1064-3745

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Keywords

  • 4D spectra
  • Covariance
  • NMR
  • Peak lists
  • Resonance assignment
  • Spectral derivative

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Harden, B. J., & Frueh, D. P. (2018). Covariance NMR processing and analysis for protein assignment. In Methods in Molecular Biology (Vol. 1688, pp. 353-373). (Methods in Molecular Biology; Vol. 1688). Humana Press Inc.. DOI: 10.1007/978-1-4939-7386-6_16

Covariance NMR processing and analysis for protein assignment. / Harden, Bradley J.; Frueh, Dominique P.

Methods in Molecular Biology. Vol. 1688 Humana Press Inc., 2018. p. 353-373 (Methods in Molecular Biology; Vol. 1688).

Research output: ResearchChapter

Harden, BJ & Frueh, DP 2018, Covariance NMR processing and analysis for protein assignment. in Methods in Molecular Biology. vol. 1688, Methods in Molecular Biology, vol. 1688, Humana Press Inc., pp. 353-373. DOI: 10.1007/978-1-4939-7386-6_16
Harden BJ, Frueh DP. Covariance NMR processing and analysis for protein assignment. In Methods in Molecular Biology. Vol. 1688. Humana Press Inc.2018. p. 353-373. (Methods in Molecular Biology). Available from, DOI: 10.1007/978-1-4939-7386-6_16
Harden, Bradley J. ; Frueh, Dominique P./ Covariance NMR processing and analysis for protein assignment. Methods in Molecular Biology. Vol. 1688 Humana Press Inc., 2018. pp. 353-373 (Methods in Molecular Biology).
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