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Automated protein backbone assignment using the projection-decomposition approach

Artikel i vetenskaplig tidskrift
Författare Jonas Fredriksson
Wolfgang Bermel
Doroteya Staykova
Martin Billeter
Publicerad i Journal of Biomolecular NMR
Volym 54
Nummer/häfte 1
Sidor 43-51
ISSN 0925-2738
Publiceringsår 2012
Publicerad vid Institutionen för kemi och molekylärbiologi
Sidor 43-51
Språk en
Länkar dx.doi.org/10.1007/s10858-012-9649-...
Ämnesord NMR; Protein structure; Projection spectroscopy; Multi-way decomposition
Ämneskategorier Numerisk analys, Strukturbiologi, Molekylär biofysik

Sammanfattning

Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CHb assignments. For the 128 residue long azurin, missing assignments mostly affect Ha and Hb. Among the remaining backbone (plus Cb) nuclei 97.5 % could be assigned with 1.0 % differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5 % of the backbone and CHbresonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach.

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