The DOI matches its Crossref record; 75 of the 75 references it cites were found in a registry or an index.
Protein backbone angle restraints from searching a database for chemical shift and sequence homology
Abstract
Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C alpha, 13C beta, 13C', 1H alpha and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar phi and psi backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 degrees. Approximately 3% of the predictions made by TALOS are found to be in error.
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“As the changes in 15N chemical shifts that underlie the resonance line-broadening process are primarily dependent on the backbone torsion angles [60]”
From Differential conformational dynamics in the closely homologous FK506-binding domains of FKBP51 and FKBP52 (2014) · cites this paper as [60]
Citations
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Dikeakos, J. D., Di Lello, P., Lacombe, M.-J., Ghirlando, R., Legault, P., Reudelhuber, T. L., & Omichinski, J. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809576106 · Cited by 40
Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5
Lemak, A., Yee, A., Wu, H., Yap, D., Zeng, H., Dombrovski, L., Houliston, S., Aparicio, S., & Arrowsmith, C. H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077020 · Cited by 36
“The restraints for backbone w and y torsion angles were derived from chemical shifts of backbone atoms using TALOS [42].”
MethodKang, H.-S., Nelson, M. L., Mackereth, C. D., Schärpf, M., Graves, B. J., & McIntosh, L. P. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.01.054 · Cited by 25
Mustafi, S. M., LeMaster, D. M., & Hernández, G. (2014) · Biochemical Journal · doi:10.1042/bj20140232 · Cited by 25
“As the changes in 15 N chemical shifts that underlie the resonance line-broadening process are primarily dependent on the backbone torsion angles [60], the substantially elevated R 2 values from Glu 110 to Leu 128 across the entire β 4 – β 5 loop as well as into the β 3a strand suggest an…”
Metadata
- Authors
- Cornilescu, G., Delaglio, F., & Bax, A.
- Affiliations
- National Institutes of Health (US)
- Venue
- Journal of Biomolecular NMR
- Published
- 1999-03
- Volume
- 13
- Issue
- 3
- Pages
- 289-302
- ISSN
- 0925-2738 (ISSN-L)
- 1573-5001
- OpenAlex
- W1589295940
- Cited by
- 2,957
- References
- 75
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 15 · 2023: 9 · 2022: 19 · 2021: 21 · 2020: 37 · 2019: 27 · 2018: 35 · 2017: 42 · 2016: 53 · 2015: 67 · 2014: 87 · 2013: 112 · 2012: 141
- FWCI
- 52.55
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Biomolecular NMR (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Molecular spectroscopy and chirality
- Keywords
- Talos, sequence homology, 13C NMR chemical shifts, 15N chemical shifts, protein structure prediction, X-ray structure comparison, database searching
- MeSH terms
- Amino Acid Sequence, Animals, Computer Graphics, Enzymes, Humans, Molecular Sequence Data, Protein Conformation, Proteins, Software, HIV Protease, Sequence Homology, Amino Acid, Nuclear Magnetic Resonance, Biomolecular, Databases as Topic
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