Abstract The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [1H,1H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6â??10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated.
Content Type Journal Article
Category Article
Pages 1-14
DOI 10.1007/s10858-012-9645-2
Authors
Pedro Serrano, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Bill Pedrini, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Biswaranjan Mohanty, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Michael Geralt, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
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A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information....
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Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of...
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The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has...
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The introduction of nuclear magnetic resonance (NMR) spectroscopy as a second method for protein structure determination at atomic resolution, in addition to x-ray diffraction in single crystals, has already led to a significant increase in the number of known protein structures. The NMR method provides data that are in many ways...
The J-UNIO protocol for automated protein structure determination by NMR in solution
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