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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Martino, L., He, Y., Hands‐Taylor, K. L. D., Valentine, E. R., Kelly, G. P., Giancola, C., & Conte, M. R. (2009) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07159.x · Cited by 52
The Modular Structure of SIP Facilitates Its Role in Stabilizing Multiprotein Assemblies,
Bhattacharya, S., Lee, Y., Michowski, W., Jastrzębska, B., Filipek, A., Kuźnicki, J., & Chazin, W. (2005) · Biochemistry · doi:10.1021/bi0502689 · Cited by 52
Regulation of RhoGEF Activity by Intramolecular and Intermolecular SH3 Domain Interactions
Schiller, M. R., Chakrabarti, K., King, G. F., Schiller, N. I., Eipper, B. A., & Maciejewski, M. W. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512482200 · Cited by 52
The Solution Structure of the Regulatory Domain of Tyrosine Hydroxylase
Zhang, S., Huang, T., Ilangovan, U., Hinck, A. P., & Fitzpatrick, P. F. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.12.015 · Cited by 52
“BackboneΦ andψ restraints were obtained by analysis of the backbone chemical shifts using TALOS [36].”
Method
Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA
Liu, L., Su, Q., Zhang, J., Ji, P., Shi, Y., & Wu, J. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.06.014 · Cited by 52
“The restrains for backbone dihedral angles (U and w) in secondary structures were obtained by TALOS+ program (Cornilescu et al., 1999; Shen et al., 2009) calculation on the basis of chemical shift information.”
Method
The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region
Apellániz, B., Rujas, E., Serrano, S., Morante, K., Tsumoto, K., Caaveiro, J. M. M., Jiménez, M. A., & Nieva, J. L. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.644351 · Cited by 53
“Distance constraints were obtained from the cross-peaks present in 150-ms two-dimensional (1)H-(1)H NOESY spectra, which were integrated using the standard SPARKY integration subroutine (SPARKY3), and the dihedral angle restraints for and angles were derived from (1)H and (13)C chemical shifts using the program TALOS…”
Method
Mutations in the Hydrophobic Core of Ubiquitin Differentially Affect Its Recognition by Receptor Proteins
Haririnia, A., Verma, R., Purohit, N., Twarog, M. Z., Deshaies, R. J., Bolon, D. N. A., & Fushman, D. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.11.016 · Cited by 52
Structure and Dynamics of Helix-0 of the N-BAR Domain in Lipid Micelles and Bilayers
Löw, C., Weininger, U., Lee, H., Schweimer, K., Neundorf, I., Beck‐Sickinger, A. G., Pastor, R. W., & Balbach, J. (2008) · Biophysical Journal · doi:10.1529/biophysj.108.134155 · Cited by 51
Solution Structure and Calcium-Binding Properties of M-Crystallin, A Primordial βγ-Crystallin from Archaea
Barnwal, R. P., Jobby, M. K., Devi, K. M., Sharma, Y., & Chary, K. V. R. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.058 · Cited by 52
Three-dimensional structure of the actinoporin sticholysin I. Influence of long-distance effects on protein function
García‐Linares, S., Castrillo, I., Bruix, M., Menéndez, M., Alegre‐Cebollada, J., Martínez‐del‐Pozo, Á., & Gavilanes, J. G. (2013) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2013.01.005 · Cited by 52
NMR Structure of the S-Linked Glycopeptide Sublancin 168
Gonzalo, C. V. G. D., Zhu, L., Oman, T. J., & van der Donk, W. A. (2014) · ACS Chemical Biology · doi:10.1021/cb4008106 · Cited by 52
Solution Structure of the MAPK Phosphatase PAC-1 Catalytic Domain
Farooq, A., Plotnikova, O. V., Chaturvedi, G., Yan, S. X., Zeng, L., Zhang, Q., & Zhou, M. (2003) · Structure · doi:10.1016/s0969-2126(02)00943-7 · Cited by 52
Three-Dimensional Structure in Lipid Micelles of the Pediocin-like Antimicrobial Peptide Curvacin A,
Haugen, H. S., Fimland, G., Nissen-Meyer, J., & Kristiansen, P. E. (2005) · Biochemistry · doi:10.1021/bi051215u · Cited by 52
The Six Zinc Fingers of Metal-responsive Element Binding Transcription Factor-1 Form Stable and Quasi-ordered Structures with Relatively Small Differences in Zinc Affinities
Potter, B. M., Feng, L., Parasuram, P., Matskevich, V. A., Wilson, J. A., Andrews, G. K., & Laity, J. H. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m505217200 · Cited by 52
Structural Basis for the Interaction between the Cytoplasmic Domain of the Hyaluronate Receptor Layilin and the Talin F3 Subdomain
Wegener, K. L., Basran, J., Bagshaw, C. R., Campbell, I. D., Roberts, G. C. K., Critchley, D. R., & Barsukov, I. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.06.087 · Cited by 54
Automated structure determination of proteins with the SAIL-FLYA NMR method
Takeda, M., Ikeya, T., Güntert, P., & Kainosho, M. (2007) · Nature Protocols · doi:10.1038/nprot.2007.423 · Cited by 52
The solution structure of PapGII from uropathogenic Escherichia coli and its recognition of glycolipid receptors
Sung, M., Fleming, K., Chen, H. A., & Matthews, S. (2001) · EMBO Reports · doi:10.1093/embo-reports/kve133 · Cited by 52
Applications of solid state NMR to the structural characterization of amyloid fibrils: methods and results
Tycko, R. (2003) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/s0079-6565(03)00003-7 · Cited by 52
High-throughput three-dimensional protein structure determination
Heinemann, U., Illing, G., & Oschkinat, H. (2001) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(00)00226-3 · Cited by 52
Structure of Mth11/ Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P
Boomershine, W. P., McElroy, C. A., Tsai, H., Wilson, R. C., Gopalan, V., & Foster, M. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2535887100 · Cited by 52
Structure of the Neural (N-) Cadherin Prodomain Reveals a Cadherin Extracellular Domain-like Fold without Adhesive Characteristics
Koch, A., Farooq, A., Shan, W., Zeng, L., Colman, D., & Zhou, M. (2004) · Structure · doi:10.1016/j.str.2004.02.034 · Cited by 53
Ras Homolog Enriched in Brain (Rheb) Enhances Apoptotic Signaling*
Karassek, S., Berghaus, C., Schwarten, M., Goemans, C. G., Ohse, N., Kock, G., Jockers, K. F. G., Neumann, S., Gottfried, S., Herrmann, C., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.095968 · Cited by 54
Structure of a Ca2+-Myristoyl Switch Protein That Controls Activation of a Phosphatidylinositol 4-Kinase in Fission Yeast
Lim, S., Strahl, T., Thorner, J. W., & Ames, J. B. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.208868 · Cited by 51
The Structural and Dynamic Response of MAGI-1 PDZ1 with Noncanonical Domain Boundaries to the Binding of Human Papillomavirus E6
Charbonnier, S., Nominé, Y., Ramírez, J., Luck, K., Chappelle, A., Stote, R. H., Travé, G., Kieffer, B., & Atkinson, R. A. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.01.015 · Cited by 49
“Predictions of backbone Φ and Ψ angles were obtained from resonance assignments using the program TALOS.69 Composite 760 Response of MAGI-1 PDZ1 to Binding of HPV E6 chemical shift changes were calculated on a per-residue basis using all nuclei of each residue that were assigned in the spectra of both liganded and unl…”
MethodInfluential
A comparison of BRCT domains involved in nonhomologous end-joining: Introducing the solution structure of the BRCT domain of polymerase lambda
Mueller, G. A., Moon, A. F., DeRose, E. F., Havener, J. M., Ramsden, D. A., Pedersen, L. C., & London, R. E. (2008) · DNA repair · doi:10.1016/j.dnarep.2008.04.018 · Cited by 51
Determination of solution structure and lipid micelle location of an engineered membrane peptide by using one NMR experiment and one sample
Wang, G. (2007) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2007.08.005 · Cited by 51
Protein Structure Refinement Using 13Cα Chemical Shift Tensors
Wylie, B. J., Schwieters, C. D., Oldfield, E., & Rienstra, C. M. (2009) · Journal of the American Chemical Society · doi:10.1021/ja804041p · Cited by 51
Structural and functional characterization of an atypical activation domain in erythroid Krüppel-like factor (EKLF)
Mas, C., Lussier-Price, M., Soni, S., Morse, T., Arseneault, G., Lello, P. D., Lafrance‐Vanasse, J., Bieker, J. J., & Omichinski, J. G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017029108 · Cited by 51
“Backbone dihedral angles were derived with the program TALOS (46).”
Method
Solution Structures of Rat Amylin Peptide: Simulation, Theory, and Experiment
Reddy, A. S., Wang, L., Lin, Y., Ling, Y. L., Chopra, M., Zanni, M. T., Skinner, J. L., & Pablo, J. J. D. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.10.029 · Cited by 51
The PN2-3 Domain of Centrosomal P4.1-associated Protein Implements a Novel Mechanism for Tubulin Sequestration
Cormier, A., Clément, M., Knossow, M., Lachkar, S., Savarin, P., Toma, F., Sobel, A., Gigant, B., & Curmi, P. A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m808249200 · Cited by 51
Solution structure of a BolA‐like protein fromMus musculus
Kasai, T., Inoue, M., Koshiba, S., Yabuki, T., Aoki, M., Nunokawa, E., Seki, E., Matsuda, T., Matsuda, N., Tomo, Y., et al. (2004) · Protein Science · doi:10.1110/ps.03401004 · Cited by 51
NMR solution structures of actin depolymerizing factor homology domains
Goroncy, A. K., Koshiba, S., Tochio, N., Tomizawa, T., Sato, M., Inoue, M., Watanabe, S., Hayashizaki, Y., Tanaka, A., Kigawa, T., et al. (2009) · Protein Science · doi:10.1002/pro.248 · Cited by 51
Solution and Crystal Structures of mRNA Exporter Dbp5p and Its Interaction with Nucleotides
Fan, J., Cheng, Z., Zhang, J., Noble, C. G., Zhou, Z., Song, H., & Yang, D. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.03.004 · Cited by 51
Recognition and Cleavage of Related to Ubiquitin 1 (Rub1) and Rub1-Ubiquitin Chains by Components of the Ubiquitin-Proteasome System
Singh, R. K., Zerath, S., Kleifeld, O., Scheffner, M., Glickman, M. H., & Fushman, D. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.022467 · Cited by 51
“Using these resonances along with predictions of protein backbone dihedral angles made by TALOS (44), we computed a model structure of Rub1 using the CS-Rosetta approach (45, 46), which resulted in an ensemble of nine closely related low-energy structures (Fig.”
Method
A Single Mutation Promotes Amyloidogenicity through a Highly Promiscuous Dimer Interface
Peterson, F. C., Baden, E. M., Owen, B. A. L., Volkman, B. F., & Ramı́rez-Alvarado, M. (2010) · Structure · doi:10.1016/j.str.2010.02.012 · Cited by 51
Solution Structure of the Flexible Class II Ubiquitin-conjugating Enzyme Ubc1 Provides Insights for Polyubiquitin Chain Assembly
Merkley, N., & Shaw, G. S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409576200 · Cited by 52
NMR Solution Structure and Dynamics of an Exchangeable Apolipoprotein, Locusta migratoria Apolipophorin III
Fan, D., Zheng, Y., Yang, D., & Wang, J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m208486200 · Cited by 51
An ACP Structural Switch: Conformational Differences between the Apo and Holo Forms of the Actinorhodin Polyketide Synthase Acyl Carrier Protein
Evans, S. E., Williams, C., Arthur, C. J., Burston, S. G., Simpson, T. J., Crosby, J. C., & Crump, M. P. (2008) · ChemBioChem · doi:10.1002/cbic.200800180 · Cited by 51

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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