Automatic structure-based NMR methyl resonance assignment in large proteins

Iva Pritišanac, Julia M. Würz, T. Reid Alderson and Peter Güntert ()
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Iva Pritišanac: Goethe University Frankfurt am Main
Julia M. Würz: Goethe University Frankfurt am Main
T. Reid Alderson: NIDDK, National Institutes of Health
Peter Güntert: Goethe University Frankfurt am Main

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-12837-8

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