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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Context‐Dependence of the Contribution of Disulfide Bonds to β‐Hairpin Stability
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The SAM domain of the RhoGAP DLC1 binds EF1A1 to regulate cell migration
Zhong, D., Zhang, J., Yang, S., Soh, U. J. K., Buschdorf, J. P., Zhou, Y., Yang, D., & Low, B. C. (2009) · Journal of Cell Science · doi:10.1242/jcs.027482 · Cited by 58
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Mishra, B., Wang, X., Lushnikova, T., Zhang, Y., Golla, R. M., Narayana, J. L., Wang, C., McGuire, T. R., & Wang, G. (2018) · Peptides · doi:10.1016/j.peptides.2018.05.011 · Cited by 58
The C-terminal Domains of Vertebrate CstF-64 and Its Yeast Orthologue Rna15 Form a New Structure Critical for mRNA 3′-End Processing
Qu, X., Pérez‐Cañadillas, J. M., Agrawal, S., Baecke, J. D., Cheng, H.-L. M., Varani, G., & Moore, C. L. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m609981200 · Cited by 58
Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processingPreprint
Szymczyna, B. R., Bowman, J. A. L., McCracken, S. A., Pineda‐Lucena, A., Lü, Y., Cox, B., Lambermon, M. H. L., Graveley, B. R., Arrowsmith, C. H., & Blencowe, B. J. (2003) · Genes & Development · doi:10.1101/gad.1060403 · Cited by 58
NMR Methods for Studying Protein–Protein Interactions Involved in Translation Initiation
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Staphylococcus aureus Uses a Novel Multidomain Receptor to Break Apart Human Hemoglobin and Steal Its Heme
Spirig, T., Malmirchegini, G. R., Zhang, J., Robson, S. A., Sjodt, M., Liu, M., Kumar, K. K., Dickson, C. F., Gell, D. A., Lei, B., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.419119 · Cited by 57
“The structures were improved by iterative rounds of structure calculations in which hydrogen bond restraints, backbone torsion angle restraints obtained from the program TALOS , and side-chain torsion angle restraints were added (45).”
Background
PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination
Lee, W., Stark, J. L., & Markley, J. L. (2014) · Journal of Biomolecular NMR · doi:10.1007/s10858-014-9855-x · Cited by 57
Structural Basis for the Golgi Association by the Pleckstrin Homology Domain of the Ceramide Trafficking Protein (CERT)
Sugiki, T., Takeuchi, K., Yamaji, T., Takano, T., Tokunaga, Y., Kumagai, K., Hanada, K., Takahashi, H. K., & Shimada, I. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.367730 · Cited by 57
“The backbone dihedral angle restraints (58 for and 56 for angles) were obtained from the program TALOS, using the (1)HN, (15)NH, (13)C , (13)C , (13)C , and (1)H chemical shifts (22).”
Method
[Effect of some derivatives of piperidine, piperazine and related compounds on deamination of serotonin, tyramine and benzylamine by pig liver mitochondrial monoamine oxidase].
Prikulis, A. A., Grinberga, B. A., Grinshteĭn, V. I., & Strelka, G. R. (1983) · PubMed · Cited by 57
The NMR structure of the autophagy-related protein Atg8
Kumeta, H., Watanabe, M., Nakatogawa, H., Yamaguchi, M., Ogura, K., Adachi, W., Fujioka, Y., Noda, N. N., Ohsumi, Y., & Inagaki, F. (2010) · Journal of Biomolecular NMR · doi:10.1007/s10858-010-9420-1 · Cited by 57
“As an input for the final calculation of the threedimensional structure of the Atg8 K26P, a total of 2,314 distance and 155 dihedral angle restraints predicted by TALOS program ( Cornilescu et al. 1999 ) was used (Table 1). At each stage, 100 structures were calculated using 30,000 steps of simulated annealing, and a…”
Method
Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
Fonville, J. M., Swart, M., Vokáčová, Z., Sychrovský, V., Šponer, J. E., Šponer, J., Hilbers, C. W., Bickelhaupt, F. M., & Wijmenga, S. S. (2012) · Chemistry - A European Journal · doi:10.1002/chem.201103593 · Cited by 57
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Golovanov, A. P., Hautbergue, G. M., Tintaru, A., Lian, L., & Wilson, S. A. (2006) · RNA · doi:10.1261/rna.212106 · Cited by 57
Intrinsic Instability of BOK Enables Membrane Permeabilization in Apoptosis
Zheng, J. H., Grace, C. R., Guibao, C. D., McNamara, D. E., Llambi, F., Wang, Y., Chen, T., & Moldoveanu, T. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.04.060 · Cited by 57
“9.1.7 (Keller, 2004) http://cara.nmr.ch/doku.php TALOS+ (Cornilescu et al., 1999) https://spin.niddk.nih.gov/bax/software/TALOS/ UNIO’10 v2.”
BackgroundMethodInfluential
Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin plantaricin EF
Fimland, N., Rogne, P., Fimland, G., Nissen-Meyer, J., & Kristiansen, P. E. (2008) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2008.05.003 · Cited by 57
NMR Solution Structure of Lipocalin-type Prostaglandin D Synthase
Shimamoto, S., Yoshida, T., Inui, T., Gohda, K., Kobayashi, Y., Fujimori, K., Tsurumura, T., Aritake, K., Urade, Y., & Ohkubo, T. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700123200 · Cited by 57
Structure, Dynamics and Heparin Binding of the C-terminal Domain of Insulin-like Growth Factor-binding Protein-2 (IGFBP-2)
Kuang, Z., Yao, S., Keizer, D. W., Wang, C. C., Bach, L. A., Forbes, B. E., Wallace, J. C., & Norton, R. S. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.09.006 · Cited by 57
Measurement of Multiple ψ Torsion Angles in Uniformly 13C,15N-Labeled α-Spectrin SH3 Domain Using 3D 15N−13C−13C−15N MAS Dipolar-Chemical Shift Correlation Spectroscopy
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Gozansky, E. K., Louis, J. M., Caffrey, M. S., & Clore, G. M. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.11.003 · Cited by 57
13Cα and 13Cβ chemical shifts as a tool to delineate β-hairpin structures in peptides
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Conserved Themes in Target Recognition by the PAH1 and PAH2 Domains of the Sin3 Transcriptional Corepressor
Sahu, S. C., Swanson, K. A., Kang, R. S.-O., Huang, K., Brubaker, K., Ratcliff, K., & Radhakrishnan, I. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.11.079 · Cited by 56
Structural Basis of E2–25K/UBB+1 Interaction Leading to Proteasome Inhibition and Neurotoxicity
Ko, S., Kang, G. B., Song, S. M., Lee, J., Shin, D. Y., Yun, J.-H., Sheng, Y., Cheong, C., Jeon, Y. H., Jung, Y., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.145219 · Cited by 56
Human Mismatch Repair Protein MSH6 Contains a PWWP Domain That Targets Double Stranded DNA
Laguri, C., Duband‐Goulet, I., Friedrich, N., Axt, M., Belin, P., Callebaut, I., Gilquin, B., Zinn‐Justin, S., & Couprie, J. (2008) · Biochemistry · doi:10.1021/bi7024639 · Cited by 56
Rac regulates its effector phospholipase Cγ2 through interaction with a split pleckstrin homology domain
Walliser, C., Retlich, M., Harris, R., Everett, K. L., Josephs, M. B., Vatter, P., Esposito, D., Driscoll, P. C., Katan, M., Gierschik, P., et al. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m803316200 · Cited by 56
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Solution structure and backbone dynamics of the DNA‐binding domain of FOXP1: Insight into its domain swapping and DNA binding
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“The / and y backbone dihedral angles were also calculated by TALOS program.(59) Data were processed and analyzed using the Bruker TOPSPIN 1.”
Method
Structure of the Minimal Interface Between ApoE and LRP
Guttman, M., Prieto, J. H., Handel, T. M., Domaille, P. J., & Komives, E. A. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.03.022 · Cited by 56
Structure and function of a bacterial Fasciclin I Domain Protein elucidates function of related cell adhesion proteins such as TGFBIp and periostin
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“1 [36] using a final set of 1788 distance restraints obtained from NOESY spectra (approximately 13 restraints per residue), and 148 angle restraints from TALOS [37].”
MethodInfluential
Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State
Cornilescu, G., Ulijasz, A. T., Cornilescu, C. C., Markley, J. L., & Vierstra, R. D. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.08.034 · Cited by 56
Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update
Du, P., Andrec, M., & Levy, R. M. (2003) · Protein Engineering Design and Selection · doi:10.1093/protein/gzg052 · Cited by 56
Probing the Interactions of Early Polyketide Intermediates with the Actinorhodin ACP from S. coelicolor A3(2)
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A New Quinoline BRD4 Inhibitor Targets a Distinct Latent HIV-1 Reservoir for Reactivation from Other “Shock” Drugs
Abner, E., Stoszko, M., Zeng, L., Chen, H., Izquierdo‐Bouldstridge, A., Konuma, T., Zorita, E. V., Fanunza, E., Zhang, Q., Mahmoudi, T., et al. (2018) · Journal of Virology · doi:10.1128/jvi.02056-17 · Cited by 54
“Structure quality was assessed by CNS, ARIA, and PROCHECK analysis (61, 62).”
Method
Structure of a Mannan-specific Family 35 Carbohydrate-Binding Module: Evidence for Significant Conformational Changes upon Ligand Binding
Tunnicliffe, R. B., Bolam, D. N., Pell, G., Gilbert, H. J., & Williamson, M. P. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.01.038 · Cited by 56
Solution Structure of ZipA, a Crucial Component ofEscherichia coliCell Division
Moy, F. J., Glasfeld, E., Mosyak, L., & Powers, R. (2000) · Biochemistry · doi:10.1021/bi0009690 · Cited by 56
Solid-State NMR Spectroscopy of Human Immunodeficiency Virus Fusion Peptides Associated with Host-Cell-Like Membranes: 2D Correlation Spectra and Distance Measurements Support a Fully Extended Conformation and Models for Specific Antiparallel Strand Registries
Qiang, W., Bodner, M. L., & Weliky, D. P. (2008) · Journal of the American Chemical Society · doi:10.1021/ja077302m · Cited by 56
Structure of human PRL‐3, the phosphatase associated with cancer metastasis
Kim, K., Song, J.-S., Jee, J.-G., Sheen, M. R., Lee, C., Lee, T. G., Ro, S., Cho, J. M., Lee, W., Yamazaki, T., et al. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.03.062 · Cited by 56

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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