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Structure. 2015 Oct 6;23(10):1958-1966. doi: 10.1016/j.str.2015.07.019. Epub 2015 Sep 10.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Author information

1
Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
2
Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
3
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
4
Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: rienstra@illinois.edu.

Abstract

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure.

PMID:
26365800
PMCID:
PMC4786943
DOI:
10.1016/j.str.2015.07.019
[Indexed for MEDLINE]
Free PMC Article

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