Automated protein backbone assignment using the projection-decomposition approach

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Automated protein backbone assignment using the projection-decomposition approach

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

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Amber

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Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

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HADDOCK

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V-NMR

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Backbone S2

Methyl S2

B-factor

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Shiftx2

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CH3shift- Methyl

ArShift- Aromatic

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Proshift

PPM

CheShift-2- Cα

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Camcoil

Poulsen_rc_CS

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MAXOCC

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CCPN

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NMR sample preparation:

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DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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07-20-2012, 11:13 PM

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Automated protein backbone assignment using the projection-decomposition approach

Automated protein backbone assignment using the projection-decomposition approach

Abstract 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 CHÎ² assignments. For the 128 residue long azurin, missing assignments mostly affect HÎ± and HÎ². Among the remaining backbone (plus CÎ²) 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 CHÎ²resonances 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.

Content Type Journal Article
Category Article
Pages 1-9
DOI 10.1007/s10858-012-9649-y
Authors
- Jonas Fredriksson, Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
- Wolfgang Bermel, Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten, Germany
- Doroteya K. Staykova, Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
- Martin Billeter, Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden

- Journal Journal of Biomolecular NMR
- Online ISSN 1573-5001
- Print ISSN 0925-2738

Source: Journal of Biomolecular NMR

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