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

• Published in: Structure (London) Vol. 23; no. 10; pp. 1958 - 1966
• Main Authors: Courtney, Joseph M., Ye, Qing, Nesbitt, Anna E., Tang, Ming, Tuttle, Marcus D., Watt, Eric D., Nuzzio, Kristin M., Sperling, Lindsay J., Comellas, Gemma, Peterson, Joseph R., Morrissey, James H., Rienstra, Chad M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 06-10-2015
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Carbon Isotopes; Crystallography, X-Ray; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene Expression; Humans; Nuclear Magnetic Resonance, Biomolecular; Protein Disulfide-Isomerases - chemistry; Protein Disulfide-Isomerases - genetics; Protein Disulfide-Isomerases - metabolism; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Research Design; Software; Streptococcus - chemistry; Structural Homology, Protein; Thromboplastin - chemistry; Thromboplastin - genetics; Thromboplastin - metabolism; Ubiquitin - chemistry; Ubiquitin - genetics; Ubiquitin - metabolism
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2015.07.019

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 13C-13C 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.
[Display omitted]
•An algorithm to numerically compare NMR spectra and protein structures is developed•An unassigned 13C-13C NMR spectrum can be used to identify the correct protein fold•Resonance assignments are not needed to use NMR data in structure development
Courtney et al. have developed an algorithm that scores protein structural models against a previously unanalyzed NMR spectrum. This method, named COMPASS, does not require chemical shift assignments and identifies the correct structure in most cases within 1.5 Å RMSD of the reference structure.