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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Solution Structure of the BHRF1 Protein From Epstein-Barr Virus, a Homolog of Human Bcl-2
Huang, Q., Petros, A. M., Virgin, H. W., Fesik, S. W., & Olejniczak, E. T. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.08.007 · Cited by 87
Solution Structure of Human Saposin C: pH-Dependent Interaction with Phospholipid Vesicles
de Alba, E., Weiler, S., & Tjandra, N. (2003) · Biochemistry · doi:10.1021/bi0301338 · Cited by 87
Contribution of E3-Ubiquitin Ligase Activity to HIV-1 Restriction by TRIM5α rh : Structure of the RING Domain of TRIM5α
Lienlaf, M., Hayashi, F., Nunzio, F. D., Tochio, N., Kigawa, T., Yokoyama, S., & Diaz‐Griffero, F. (2011) · Journal of Virology · doi:10.1128/jvi.00497-11 · Cited by 91
The C-Terminal BAG Domain of BAG5 Induces Conformational Changes of the Hsp70 Nucleotide- Binding Domain for ADP-ATP Exchange
Arakawa, A., Handa, N., Ohsawa, N., Shida, M., Kigawa, T., Hayashi, F., Shirouzu, M., & Yokoyama, S. (2010) · Structure · doi:10.1016/j.str.2010.01.004 · Cited by 86
“Dihedral angle restraints were derived using the program TALOS (Cornilescu et al., 1999).”
Method
Structural and Energetic Determinants of Apo Calmodulin Binding to the IQ Motif of the NaV1.2 Voltage-Dependent Sodium Channel
Feldkamp, M. D., Yu, L. P., & Shea, M. A. (2011) · Structure · doi:10.1016/j.str.2011.02.009 · Cited by 86
“In addition, 109 Φ and angular restraints derived from an analysis of C, N, Cα, Hα, and Cβ chemical shifts using the TALOS program (Cornilescu et al., 1999) were included in the structural calculations.”
Method
Mammalian SCAN Domain Dimer Is a Domain-Swapped Homolog of the HIV Capsid C-Terminal Domain
Ivanov, D., Stone, J. R., Maki, J. L., Collins, T., & Wagner, G. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.12.015 · Cited by 86
Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D28K
Kojetin, D. J., Venters, R. A., Kordys, D. R., Thompson, R. J., Kumar, R., & Cavanagh, J. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1112 · Cited by 88
A ‘three‐pronged’ binding mechanism for the SAP/SH2D1A SH2 domain: structural basis and relevance to the XLP syndrome
Hwang, P. M., Li, C., Morra, M., Lillywhite, J., Muhandiram, D. R., Gertler, F. B., Terhorst, C., Kay, L. E., Pawson, T. J., Forman-Kay, J. D., et al. (2002) · The EMBO Journal · doi:10.1093/emboj/21.3.314 · Cited by 87
Solution Structure of Selenoprotein W and NMR Analysis of Its Interaction with 14-3-3 Proteins
Aachmann, F. L., Fomenko, D. E., Soragni, A., Gladyshev, V. N., & Dikiy, A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m705410200 · Cited by 86
Solution Structure of the SEA Domain from the Murine Homologue of Ovarian Cancer Antigen CA125 (MUC16)
Maeda, T., Inoue, M., Koshiba, S., Yabuki, T., Aoki, M., Nunokawa, E., Seki, E., Matsuda, T., Motoda, Y., Kobayashi, A., et al. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309417200 · Cited by 86
Structure of the Ubiquitin-interacting Motif of S5a Bound to the Ubiquitin-like Domain of HR23B
Fujiwara, K., Tenno, T., Sugasawa, K., Jee, J., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, F., & Shirakawa, M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309448200 · Cited by 86
A Protein Contortionist: Core Mutations of GB1 that Induce Dimerization and Domain Swapping
Byeon, I. L., Louis, J. M., & Gronenborn, A. M. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00928-8 · Cited by 85
Structure of hnRNP D Complexed with Single-stranded Telomere DNA and Unfolding of the Quadruplex by Heterogeneous Nuclear Ribonucleoprotein D
Enokizono, Y., Konishi, Y., Nagata, K., Ouhashi, K., Uesugi, S., Ishikawa, F., & Katahira, M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m411822200 · Cited by 86
Solution Structure of a Hydrocarbon Stapled Peptide Inhibitor in Complex with Monomeric C-terminal Domain of HIV-1 Capsid
Bhattacharya, S., Zhang, H., Debnath, A. K., & Cowburn, D. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.c800048200 · Cited by 86
Structure of the Na,K-ATPase Regulatory Protein FXYD1 in Micelles
Teriete, P., Franzin, C. M., Choi, J., & Marassi, F. M. (2007) · Biochemistry · doi:10.1021/bi700391b · Cited by 85
Solution structure and interaction surface of the C-terminal domain from p47: A major p97-cofactor involved in SNARE disassembly
Yuan, X., Shaw, A., Zhang, X., Kondo, H., Lally, J., Freemont, P. S., & Matthews, S. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4864 · Cited by 85
Structural Basis for the Recognition of Methylated Histone H3K36 by the Eaf3 Subunit of Histone Deacetylase Complex Rpd3S
Xu, C., Cui, G., Botuyan, M. V., & Mer, G. (2008) · Structure · doi:10.1016/j.str.2008.08.008 · Cited by 85
Solution Structure and Ligand Recognition of the WW Domain Pair of the Yeast Splicing Factor Prp40
Wiesner, S., Stier, G., Sattler, M., & Macías, M. J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01145-2 · Cited by 83
Weaponization of a Hormone: Convergent Recruitment of Hyperglycemic Hormone into the Venom of Arthropod Predators
Undheim, E. A. B., Grimm, L. L., Low, C.-F., Morgenstern, D., Herzig, V., Zobel-Thropp, P. A., Pineda, S. S., Habib, R., Dziemborowicz, S., Fry, B. G., et al. (2015) · Structure · doi:10.1016/j.str.2015.05.003 · Cited by 83
“Backbone dihedral-angle restraints were derived from TALOS chemical shift analysis (Cornilescu et al., 1999); the restraint range was set to twice the estimated SD.”
Method
Variability of the15N Chemical Shielding Tensors in the B3 Domain of Protein G from15N Relaxation Measurements at Several Fields. Implications for Backbone Order Parameters
Hall, J. B., & Fushman, D. (2006) · Journal of the American Chemical Society · doi:10.1021/ja060406x · Cited by 83
AbrB-like Transcription Factors Assume a Swapped Hairpin Fold that Is Evolutionarily Related to Double-Psi β Barrels
Coles, M. P., Djuranović, S., Söding, J., Frickey, T., Koretke, K. K., Truffault, V., Martin, J., & Lupas, A. N. (2005) · Structure · doi:10.1016/j.str.2005.03.017 · Cited by 83
Improving the Accuracy of NMR Structures of Large Proteins Using Pseudocontact Shifts as Long-Range Restraints
Gaponenko, V., Sarma, S. P., Altieri, A. S., Horita, D. A., Li, J., & Byrd, R. A. (2004) · Journal of Biomolecular NMR · doi:10.1023/b:jnmr.0000013706.09264.36 · Cited by 84
The N–Terminal Tail of hERG Contains an Amphipathic α–Helix That Regulates Channel Deactivation
Ng, C., Hunter, M. J., Perry, M., Mobli, M., Ke, Y., Kuchel, P. W., King, G. F., Stock, D., & Vandenberg, J. I. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016191 · Cited by 82
“A total of 2634 distance constraints were derived from 3D 1H–15N and 1H–13C NOESY data, 24 hydrogen bond constraints were derived from the 1H–13C NOESY data (based on amide protons that were still observable afte exchange of the sample into D2O buffer), and 178 dihedral angle constraints (w,y) were derived from TALOS…”
Method
Structural insights into the role of the Smoothened cysteine-rich domain in Hedgehog signalling
Rana, R., Carroll, C. E., Lee, H., Bao, J., Marada, S., Grace, C. R., Guibao, C. D., Ogden, S. K., & Zheng, J. (2013) · Nature Communications · doi:10.1038/ncomms3965 · Cited by 84
Structure of Tightly Membrane-Bound Mastoparan-X, a G-Protein-Activating Peptide, Determined by Solid-State NMR
Todokoro, Y., Yumen, I., Fukushima, K., Kang, S., Park, J.-S., Kohno, T., Wakamatsu, K., Akutsu, H., & Fujiwara, T. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.082735 · Cited by 82
Structural Basis for the Interaction of Lipopolysaccharide with Outer Membrane Protein H (OprH) from Pseudomonas aeruginosa
Edrington, T. C., Kintz, E. N., Goldberg, J. B., & Tamm, L. K. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.280933 · Cited by 85
Prion Fibrillization Is Mediated by a Native Structural Element That Comprises Helices H2 and H3
Adrover, M., Pauwels, K., Prigent, S., de Chiara, C., Xu, Z., Chapuis, C., Pastore, A., & Rezaei, H. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.111815 · Cited by 82
Structure and Mode of Action of the Membrane-permeabilizing Antimicrobial Peptide Pheromone Plantaricin A
Kristiansen, P. E., Fimland, G., Mantzilas, D., & Nissen-Meyer, J. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m501620200 · Cited by 82
Structure and Activity of (2,8)-Dicarba-(3,12)-cystino α-ImI, an α-Conotoxin Containing a Nonreducible Cystine Analogue
MacRaild, C. A., Illesinghe, J., van Lierop, B. J., Townsend, A. L., Chebib, M., Livett, B. G., Robinson, A. J., & Norton, R. S. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm8011504 · Cited by 82
Structure of Bombyx mori chemosensory protein 1 in solution
Jansen, S., Chmelík, J., Žı́dek, L., Padrta, P., Novák, P., Zdráhal, Z., Picimbon, J., Löfstedt, C., & Sklenář, V. (2007) · Archives of Insect Biochemistry and Physiology · doi:10.1002/arch.20205 · Cited by 82
Induced Fit and “Lock and Key” Recognition of 5S RNA by Zinc Fingers of Transcription Factor IIIA
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Angular dependence of 1J(Ni,Cα i) and 2J(Ni,Cα (i − 1)) coupling constants measured in J-modulated HSQCs
Wirmer, J., & Schwalbe, H. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1015384805098 · Cited by 82
The Ig fold of the core binding factor α Runt domain is a member of a family of structurally and functionally related Ig-fold DNA-binding domains
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The Tertiary Structure and Backbone Dynamics of Human Prolactin
Keeler, C., Dannies, P. S., & Hodsdon, M. E. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00367-x · Cited by 82
The SPRY domain of SSB-2 adopts a novel fold that presents conserved Par-4–binding residues
Masters, S. L., Yao, S., Willson, T. A., Zhang, J., Palmer, K. R., Smith, B. J., Babon, J. J., Nicola, N. A., Norton, R. S., & Nicholson, S. E. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1034 · Cited by 82
TFIIH contains a PH domain involved in DNA nucleotide excision repair
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Solution Structure of B. subtilis Acyl Carrier Protein
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The Human Type I Interferon Receptor
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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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