ArticleProceedings of the National Academy of Sciences of the United States of America2008
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
- Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.Biophysical journal · 2019Article
- AutomaticJournal of biomolecular NMR · 2018Article
- Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin.The journal of physical chemistry. B · 2017Article
- Perspective: Quantum mechanical methods in biochemistry and biophysics.The Journal of chemical physics · 2016Article
- Article
- Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.Nucleic acids research · 2014Article
- Physics-based method to validate and repair flaws in protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
- Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.Journal of biomolecular NMR · 2013Article
- Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).PloS one · 2013Article
- The protein amide ¹H(N) chemical shift temperature coefficient reflects thermal expansion of the N-H···O=C hydrogen bond.Journal of biomolecular NMR · 2013Article
- Improved chemical shift prediction by Rosetta conformational sampling.Journal of biomolecular NMR · 2012Article
- Identification of helix capping and b-turn motifs from NMR chemical shifts.Journal of biomolecular NMR · 2012Article
- VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy.Journal of biomolecular NMR · 2012Article
- Chemical shift tensors: theory and application to molecular structural problems.Progress in nuclear magnetic resonance spectroscopy · 2011Review
- SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network.Journal of biomolecular NMR · 2010Article
- Advances in protein NMR provided by the NIGMS Protein Structure Initiative: impact on drug discovery.Current opinion in drug discovery & development · 2010Review
- Site-specific backbone amide (15)N chemical shift anisotropy tensors in a small protein from liquid crystal and cross-correlated relaxation measurements.Journal of the American Chemical Society · 2010Article
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10 authors.
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Abstract
A recently determined set of 20 NMR-derived conformations of a 48-residue all-alpha-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed (13)C(alpha) chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed (13)C(alpha) chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed (13)C(alpha) chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed (13)C(alpha) chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-A resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed (13)C(alpha) chemical shifts in solution than the 3BHP crystal structure. In addition, the (13)C(alpha)-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.
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