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J Biomol NMR. 2017 Dec;69(4):215-227. doi: 10.1007/s10858-017-0149-y. Epub 2017 Nov 2.

Automatic methyl assignment in large proteins by the MAGIC algorithm.

Author information

1
Université Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.
2
Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. paolo.rossi@stjude.org.
3
Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
4
Deparment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. babis.kalodimos@stjude.org.

Abstract

Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25-50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.

KEYWORDS:

Automatic methyl assignment; Exhaustive search; Large proteins; Methyl labeling; Model-based methyl assignment; NMR

PMID:
29098507
PMCID:
PMC5764113
[Available on 2018-12-01]
DOI:
10.1007/s10858-017-0149-y
[Indexed for MEDLINE]

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