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J Biomol NMR. 2015 Dec;63(4):389-402. doi: 10.1007/s10858-015-9998-4. Epub 2015 Nov 13.

CH3-specific NMR assignment of alanine, isoleucine, leucine and valine methyl groups in high molecular weight proteins using a single sample.

Author information

1
Université Grenoble Alpes, IBS, 38044, Grenoble, France.
2
CNRS, IBS, 38044, Grenoble, France.
3
CEA, IBS, 38044, Grenoble, France.
4
Chemistry and Biology of Metals Laboratory, University Grenoble Alpes, 38027, Grenoble, France.
5
Université Grenoble Alpes, IBS, 38044, Grenoble, France. Dominique.Marion@ibs.fr.
6
CNRS, IBS, 38044, Grenoble, France. Dominique.Marion@ibs.fr.
7
CEA, IBS, 38044, Grenoble, France. Dominique.Marion@ibs.fr.
8
Biomolecular NMR Spectroscopy Group, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044, Grenoble Cedex 9, France. Dominique.Marion@ibs.fr.

Abstract

A new strategy for the NMR assignment of aliphatic side-chains in large perdeuterated proteins is proposed. It involves an alternative isotopic labeling protocol, the use of an out-and-back (13)C-(13)C TOCSY experiment ((H)C-TOCSY-C-TOCSY-(C)H) and an optimized non-uniform sampling protocol. It has long been known that the non-linearity of an aliphatic spin-system (for example Ile, Val, or Leu) substantially compromises the efficiency of the TOCSY transfers. To permit the use of this efficient pulse scheme, a series of optimized precursors were designed to yield linear (13)C perdeuterated side-chains with a single protonated CH3 group in these three residues. These precursors were added to the culture medium for incorporation into expressed proteins. For Val and Leu residues, the topologically different spin-systems introduced for the pro-R and pro-S methyl groups enable stereospecific assignment. All CH3 can be simultaneously assigned on a single sample using a TOCSY experiment. It only requires the tuning of a mixing delay and is thus more versatile than the relayed COSY experiment. Enhanced resolution and sensi-tivity can be achieved by non-uniform sampling combined with the removal of the large JCC coupling by deconvolution prior to the processing by iterative soft thresholding. This strategy has been used on malate synthase G where a large percentage of the CH3 groups could be correlated directly up to the backbone Ca. It is anticipated that this robust combined strategy can be routinely applied to large proteins.

KEYWORDS:

Aliphatic side-chains; Isotopic labeling; NMR spectroscopy; Proteins; Stereospecific assignment

PMID:
26566791
DOI:
10.1007/s10858-015-9998-4
[Indexed for MEDLINE]

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