Automatic structure-based NMR methyl resonance assignment in large proteins

Nat Commun. 2019 Oct 29;10(1):4922. doi: 10.1038/s41467-019-12837-8.

Abstract

Isotopically labeled methyl groups provide NMR probes in large, otherwise deuterated proteins. However, the resonance assignment constitutes a bottleneck for broader applicability of methyl-based NMR. Here, we present the automated MethylFLYA method for the assignment of methyl groups that is based on methyl-methyl nuclear Overhauser effect spectroscopy (NOESY) peak lists. MethylFLYA is applied to five proteins (28-358 kDa) comprising a total of 708 isotope-labeled methyl groups, of which 612 contribute NOESY cross peaks. MethylFLYA confidently assigns 488 methyl groups, i.e. 80% of those with NOESY data. Of these, 459 agree with the reference, 6 were different, and 23 were without reference assignment. MethylFLYA assigns significantly more methyl groups than alternative algorithms, has an average error rate of 1%, modest runtimes of 0.4-1.2 h, and can handle arbitrary isotope labeling patterns and data from other types of NMR spectra.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Automation / methods*
  • Methylation
  • Models, Molecular
  • Molecular Weight
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Proteins / chemistry*
  • Software

Substances

  • Proteins