Pritišanac I, Würz JM, Alderson TR, Güntert P. Automatic structure-based NMR methyl resonance assignment in large proteins.
Nat Commun 2019;
10:4922. [PMID:
31664028 PMCID:
PMC6820720 DOI:
10.1038/s41467-019-12837-8]
[Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/02/2019] [Indexed: 11/10/2022] Open
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.
The structures and dynamics of large proteins can be studied with methyl-based NMR but peak assignment is still challenging. Here the authors present MethylFLYA that allows automated assignment of methyl groups and apply it to five proteins with molecular weights in the range from 28 to 358 kDa.
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