Cited by 2,957Advanced NMR Techniques and ApplicationsProtein Structure and DynamicsMolecular spectroscopy and chirality

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Protein backbone angle restraints from searching a database for chemical shift and sequence homology

Cornilescu, Gabriel, Delaglio, Frank, Bax, Ad·1999·Journal of Biomolecular NMR

DOI 10.1023/a:1008392405740

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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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Authors: Cornilescu, G., Delaglio, F., & Bax, A.
Affiliations: National Institutes of Health (US)
ORCID: Cornilescu, Gabriel
Delaglio, Frank
Bax, Ad
Venue: Journal of Biomolecular NMR
Publisher: Springer Science and Business Media LLC
Published: 1999-03
Volume: 13
Issue: 3
Pages: 289-302
ISSN: 0925-2738 (ISSN-L)
1573-5001
DOI: 10.1023/a:1008392405740
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: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
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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Protein backbone angle restraints from searching a database for chemical shift and sequence homology

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