期刊
JOURNAL OF BIOMOLECULAR NMR
卷 57, 期 2, 页码 193-204出版社
SPRINGER
DOI: 10.1007/s10858-013-9779-x
关键词
Automated resonance assignment; Automated NOESY assignment; Protein structure determination; CASD-NMR; FLYA; CYANA
资金
- Lichtenberg program of the Volkswagen Foundation
- Deutsche Forschungsgemeinschaft (DFG)
- Grants-in-Aid for Scientific Research [25440032] Funding Source: KAKEN
Protein structure determination by NMR can in principle be speeded up both by reducing the measurement time on the NMR spectrometer and by a more efficient analysis of the spectra. Here we study the reliability of protein structure determination based on a single type of spectra, namely nuclear Overhauser effect spectroscopy (NOESY), using a fully automated procedure for the sequence-specific resonance assignment with the recently introduced FLYA algorithm, followed by combined automated NOE distance restraint assignment and structure calculation with CYANA. This NOESY-FLYA method was applied to eight proteins with 63-160 residues for which resonance assignments and solution structures had previously been determined by the Northeast Structural Genomics Consortium (NESG), and unrefined and refined NOESY data sets have been made available for the Critical Assessment of Automated Structure Determination of Proteins by NMR project. Using only peak lists from three-dimensional C-13- or N-15-resolved NOESY spectra as input, the FLYA algorithm yielded for the eight proteins 91-98 % correct backbone and side-chain assignments if manually refined peak lists are used, and 64-96 % correct assignments based on raw peak lists. Subsequent structure calculations with CYANA then produced structures with root-mean-square deviation (RMSD) values to the manually determined reference structures of 0.8-2.0 if refined peak lists are used. With raw peak lists, calculations for 4 proteins converged resulting in RMSDs to the reference structure of 0.8-2.8 , whereas no convergence was obtained for the four other proteins (two of which did already not converge with the correct manual resonance assignments given as input). These results show that, given high-quality experimental NOESY peak lists, the chemical shift assignments can be uncovered, without any recourse to traditional through-bond type assignment experiments, to an extent that is sufficient for calculating accurate three-dimensional structures.
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