Student or educator? Sign up with your school email and get 6 months of Pro free.
Cited by 1,460

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Using chemical shift perturbation to characterise ligand binding

Williamson, Mike P.·2013·Progress in Nuclear Magnetic Resonance Spectroscopy

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.pnmrs.2013.02.001

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 1 references

Research works printed but not linked: 100

  1. Zuiderweg, 2002, Mapping protein-protein interactions in solution by NMR spectroscopy, Biochemistry, 41, 1, 10.1021/bi011870b · DOI · Paper page
  2. Pervushin, 1997, Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution, Proc. Natl. Acad. Sci. USA, 94, 12366, 10.1073/pnas.94.23.12366 · DOI · Paper page
  3. Golovanov, 2007, Isotopically discriminated NMR spectroscopy: a tool for investigating complex protein interactions in vitro, J. Am. Chem. Soc., 129, 6528, 10.1021/ja070505q · DOI
  4. McCoy, 2002, Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations, J. Am. Chem. Soc., 124, 11758, 10.1021/ja026166c · doi:10.1021/ja026166c
  5. Shuker, 1996, Discovering high-affinity ligands for proteins: SAR by NMR, Science, 274, 1531, 10.1126/science.274.5292.1531 · DOI · Paper page
  6. Williamson, 2009, Automated protein structure calculation from NMR data, J. Biomol. NMR, 43, 131, 10.1007/s10858-008-9295-6 · DOI
  7. Zech, 2004, Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy, J. Am. Chem. Soc., 126, 13948, 10.1021/ja040086m · DOI
  8. Kohlhoff, 2009, Fast and accurate predictions of protein NMR chemical shifts from interatomic distances, J. Am. Chem. Soc., 131, 13894, 10.1021/ja903772t · DOI · Paper page
  9. Robustelli, 2012, Interpreting protein structural dynamics from NMR chemical shifts, J. Am. Chem. Soc., 134, 6365, 10.1021/ja300265w · DOI
  10. Xu, 2002, Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C’ chemical shifts in peptides using density functional theory, Biopolymers, 65, 408, 10.1002/bip.10276 · DOI
  11. de Dios, 1993, Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach, Science, 260, 1491, 10.1126/science.8502992 · DOI · Paper page
  12. Sitkoff, 1997, Density functional calculations of proton chemical shifts in model peptides, J. Am. Chem. Soc., 119, 12262, 10.1021/ja9721430 · doi:10.1021/ja9721430
  13. Williamson, 1993, Empirical comparisons of models for chemical shift calculation in proteins, J. Magn. Reson. Ser. B, 101, 63, 10.1006/jmrb.1993.1008 · DOI
  14. Iwadate, 1999, Cα and Cβ carbon-13 chemical shifts in proteins from an empirical database, J. Biomol. NMR, 13, 199, 10.1023/A:1008376710086 · DOI · Paper page
  15. Bundi, 1979, 1H NMR parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH, Biopolymers, 18, 285, 10.1002/bip.1979.360180206 · DOI · Paper page
  16. Merutka, 1995, Random coil 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG, J. Biomol. NMR, 5, 14, 10.1007/BF00227466 · DOI · Paper page
  17. Wishart, 1995, 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. 1. Investigations of nearest-neighbor effects, J. Biomol. NMR, 5, 67, 10.1007/BF00227471 · DOI · Paper page
  18. Schwarzinger, 2001, Sequence-dependent correction of random coil NMR chemical shifts, J. Am. Chem. Soc., 123, 2970, 10.1021/ja003760i · DOI · Paper page
  19. De Simone, 2009, Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins, J. Am. Chem. Soc., 131, 16332, 10.1021/ja904937a · DOI
  20. Tamiola, 2010, Sequence-specific random coil chemical shifts of intrinsically disordered proteins, J. Am. Chem. Soc., 132, 18000, 10.1021/ja105656t · DOI · Paper page
  21. Kjaergaard, 2011, Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution, J. Biomol. NMR, 50, 157, 10.1007/s10858-011-9508-2 · DOI · Paper page
  22. Han, 2011, SHIFTX2: significantly improved protein chemical shift prediction, J. Biomol. NMR, 50, 43, 10.1007/s10858-011-9478-4 · DOI · Paper page
  23. Arai, 2012, Quantitative analysis of multisite protein-ligand interactions by NMR: binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP, J. Am. Chem. Soc., 134, 3792, 10.1021/ja209936u · DOI
  24. Granot, 1983, Determination of dissociation constants of 1:1 complexes from NMR data: optimization of the experimental setup by statistical analysis of simulated experiments, J. Magn. Reson., 55, 216
  25. Fielding, 2007, NMR methods for the determination of protein-ligand dissociation constants, Prog. Nucl. Magn. Reson. Spectrosc., 51, 219, 10.1016/j.pnmrs.2007.04.001 · DOI · Paper page
  26. Markin, 2012, Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations, J. Biomol. NMR, 53, 125, 10.1007/s10858-012-9630-9 · DOI
  27. Vaynberg, 2006, Weak protein-protein interactions as probed by NMR spectroscopy, Trends Biotechnol., 24, 22, 10.1016/j.tibtech.2005.09.006 · DOI
  28. Baxter, 1997, Multiple interactions between polyphenols and a salivary proline-rich protein repeat result in complexation and precipitation, Biochemistry, 36, 5566, 10.1021/bi9700328 · DOI · Paper page
  29. Tomlinson, 2010, Structural origins of pH-dependent chemical shifts in the B1 domain of protein G, Proteins, Proteins: Struct. Funct. Bioinf., 78, 3000, 10.1002/prot.22825 · doi:10.1002/prot.22825
  30. McCoy, 2000, Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations, J. Biomol. NMR, 18, 189, 10.1023/A:1026508025631 · doi:10.1023/a:1026508025631
  31. Carbajo, 2005, Structure of the F1-binding domain of the stator of bovine F1Fo-ATPase and how it binds an α-subunit, J. Mol. Biol., 351, 824, 10.1016/j.jmb.2005.06.012 · DOI
  32. Schumann, 2007, Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions, J. Biomol. NMR, 39, 275, 10.1007/s10858-007-9197-z · DOI · Paper page
  33. Stratmann, 2011, Quantitative use of chemical shifts for the modeling of protein complexes, Proteins: Struct. Funct. Bioinf., 79, 2662, 10.1002/prot.23090 · DOI
  34. Hajduk, 2000, NMR-based screening of proteins containing 13C-labeled methyl groups, J. Am. Chem. Soc., 122, 7898, 10.1021/ja000350l · DOI
  35. Goto, 1999, A robust and cost-effective method for the production of Val, Leu, Ileδ1 methyl-protonated 15N-, 13C-, 2H-labeled proteins, J. Biomol. NMR, 13, 369, 10.1023/A:1008393201236 · DOI · Paper page
  36. Gelis, 2007, Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR, Cell, 131, 756, 10.1016/j.cell.2007.09.039 · DOI · Paper page
  37. Hamel, 2005, The contact interface of a 120 kD CheA-CheW complex by methyl TROSY interaction spectroscopy, J. Am. Chem. Soc., 127, 9676, 10.1021/ja052517m · DOI
  38. Wiesner, 2007, Autoinhibition of the HECT-Type ubiquitin ligase smurf2 through its C2 domain, Cell, 130, 651, 10.1016/j.cell.2007.06.050 · DOI · Paper page
  39. Huth, 2007, Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies, Chem. Biol. Drug Des., 70, 1, 10.1111/j.1747-0285.2007.00535.x · DOI
  40. Yuan, 2001, Calmodulin binding properties of peptide analogues and fragments of the calmodulin-binding domain of simian immunodeficiency virus transmembrane glycoprotein 41, Biopolymers, 58, 50, 10.1002/1097-0282(200101)58:1<50::AID-BIP60>3.0.CO;2-S · doi:10.1002/1097-0282(200101)58:1<50::aid-bip60>3.0.co;2-s
  41. Szczepankiewicz, 2003, Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy, J. Am. Chem. Soc., 125, 4087, 10.1021/ja0296733 · DOI
  42. Stoffregen, 2012, Methionine scanning as an NMR tool for detecting and analyzing biomolecular interaction surfaces, Structure, 20, 573, 10.1016/j.str.2012.02.012 · DOI
  43. Quinternet, 2012, Unraveling complex small-molecule binding mechanisms by using simple NMR spectroscopy, Chem. Eur. J., 18, 3969, 10.1002/chem.201101983 · doi:10.1002/chem.201101983
  44. Stevens, 2001, Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity, Nature Struct. Biol., 8, 947, 10.1038/nsb1101-947 · DOI
  45. Hardman, 1995, Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy, Biochemistry, 34, 16596, 10.1021/bi00051a007 · DOI · Paper page
  46. Allain, 1999, Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding, EMBO J., 18, 2563, 10.1093/emboj/18.9.2563 · DOI · Paper page
  47. Coggins, 2003, Structure of the LpxC deacetylase with a bound substrate-analog inhibitor, Nature Struct. Biol., 10, 645, 10.1038/nsb948 · DOI
  48. Williamson, 1997, Mapping the binding site for matrix metalloproteinase on the N-terminal domain of the tissue inhibitor of metalloproteinases-2 by NMR chemical shift perturbation, Biochemistry, 36, 13882, 10.1021/bi9712091 · DOI
  49. Terada, 1999, Nuclear magnetic resonance and molecular dynamics studies on the interactions of the Ras-binding domain of Raf-1 with wild-type and mutant Ras proteins, J. Mol. Biol., 286, 219, 10.1006/jmbi.1998.2472 · DOI
  50. Wishart, 1991, Relationship between nuclear magnetic resonance chemical shift and protein secondary structure, J. Mol. Biol., 222, 311, 10.1016/0022-2836(91)90214-Q · DOI · Paper page
  51. Urbaniak, 2002, Solution structure of a novel chromoprotein derived from apo-Neocarzinostatin and a synthetic chromophore, Biochemistry, 41, 11731, 10.1021/bi0262146 · doi:10.1021/bi0262146
  52. Simpson, 1999, A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity, Struct. Fold. Des., 7, 853, 10.1016/S0969-2126(99)80108-7 · DOI
  53. Pellecchia, 2000, Structural insights into substrate binding by the molecular chaperone DnaK, Nature Struct. Biol., 7, 298, 10.1038/74062 · DOI
  54. Farmer, 1996, Localizing the NADP+ binding site on the MurB enzyme by NMR, Nature Struct. Biol., 3, 995, 10.1038/nsb1296-995 · DOI · Paper page
  55. DeRose, 2003, Elucidation of the ε-θ subunit interface of Escherichia coli DNA polymerase III by NMR spectroscopy, Biochemistry, 42, 3635, 10.1021/bi0205451 · doi:10.1021/bi0205451
  56. Morrison, 2003, Solution NMR study of the interaction between NTF2 and nucleoporin FxFG repeats, J. Mol. Biol., 333, 587, 10.1016/j.jmb.2003.08.050 · doi:10.1016/j.jmb.2003.08.050
  57. Lüttgen, 2002, Transcriptional regulation by antitermination. Interaction of RNA with NusB protein and NusB/NusE protein complex of Escherichia coli, J. Mol. Biol., 316, 875, 10.1006/jmbi.2001.5388 · DOI
  58. London, 1993, Chemical shift and linewidth characteristics of reversibly bound ligands, J. Magn. Reson. Ser. A, 104, 190, 10.1006/jmra.1993.1208 · doi:10.1006/jmra.1993.1208
  59. Sudmeier, 1980, Dependence of NMR lineshape analysis upon chemical rates and mechanisms: implications for enzyme histidine titrations, J. Magn. Reson., 40, 377
  60. Kovrigin, 2012, NMR line shapes and multi-state binding equilibria, J. Biomol. MR, 53, 257, 10.1007/s10858-012-9636-3 · DOI
  61. Feeney, 1979, Effects of intermediate exchange processes on the estimation of equilibrium constants by NMR, J. Magn. Reson., 33, 519
  62. Koharudin, 2011, Structure-function analysis of a CVNH-LysM lectin expressed during plant infection by the rice blast fungus Magnaporthe oryzae, Structure, 19, 662, 10.1016/j.str.2011.03.004 · DOI
  63. McInnes, 2000, NMR study of the differential contributions of residues of transforming growth factor alpha to association with its receptor, Prot. Eng., 13, 143, 10.1093/protein/13.3.143 · DOI
  64. Rao, 1989, Nuclear magnetic resonance line-shape analysis and determination of exchange rates, Meth. Enzymol., 176, 279, 10.1016/0076-6879(89)76016-X · doi:10.1016/0076-6879(89)76016-x
  65. Krajewski, 2005, NMR indicates that the small molecule RITA does not block p53-MDM2 binding in vitro, Nature Med., 11, 1135, 10.1038/nm1105-1135 · DOI
  66. Mittag, 2004, Tracing kinetic intermediates during ligand binding, J. Am. Chem. Soc., 126, 9017, 10.1021/ja0392519 · doi:10.1021/ja0392519
  67. Hammond, 1986, Dihydrofolate reductase 1H resonance assignments and coenzyme-induced conformational changes, J. Mol. Biol., 188, 81, 10.1016/0022-2836(86)90483-3 · doi:10.1016/0022-2836(86)90483-3
  68. Foster, 1998, Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA, J. Biomol. NMR, 12, 51, 10.1023/A:1008290631575 · DOI
  69. Craven, 1996, Complexes formed between calmodulin and the antagonists J-8 and TFP in solution, Biochemistry, 35, 10287, 10.1021/bi9605043 · doi:10.1021/bi9605043
  70. Rajagopal, 1997, Demonstration of protein-protein interaction specificity by NMR chemical shift mapping, Protein Sci., 6, 2624, 10.1002/pro.5560061214 · doi:10.1002/pro.5560061214
  71. Worrall, 2003, Transient protein interactions studied by NMR spectroscopy: the case of cytochrome c and adrenodoxin, Biochemistry, 42, 7068, 10.1021/bi0342968 · DOI
  72. Krishnamoorthy, 2010, Auto-FACE: an NMR based binding site mapping program for fast chemical exchange protein-ligand systems, PLoS ONE, 5, e8943, 10.1371/journal.pone.0008943 · doi:10.1371/journal.pone.0008943
  73. Lowe, 2012, Determining binding constants from 1H NMR titration data using global and local methods: a case study using [n]polynorbornane-based anion hosts, Supramol. Chem., 24, 585, 10.1080/10610278.2012.688972 · doi:10.1080/10610278.2012.688972
  74. Konuma, 2013, Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism, Proteins: Struct. Funct. Bioinf., 81, 107, 10.1002/prot.24166 · DOI
  75. Selvaratnam, 2011, Mapping allostery through the covariance analysis of NMR chemical shifts, Proc. Natl Acad. Sci. USA, 108, 6133, 10.1073/pnas.1017311108 · DOI · Paper page
  76. Barelier, 2010, Discovery of fragment molecules that bind the human peroxiredoxin 5 active site, PLoS ONE, 5, e9744, 10.1371/journal.pone.0009744 · DOI
  77. Shih, 2012, On the use of distance constraints in protein-protein docking computations, Proteins: Struct. Funct. Bioinf., 80, 194, 10.1002/prot.23179 · DOI
  78. Schieborr, 2005, How much NMR data is required to determine a protein-ligand complex structure?, Chembiochem, 6, 1891, 10.1002/cbic.200500092 · DOI
  79. Palma, 2000, BiGGER: A new (soft) docking algorithm for predicting protein interactions, Proteins: Struct. Funct. Genet., 39, 372, 10.1002/(SICI)1097-0134(20000601)39:4<372::AID-PROT100>3.0.CO;2-Q · DOI · Paper page
  80. Morelli, 2000, Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex, Biochemistry, 39, 2530, 10.1021/bi992306s · DOI
  81. Morelli, 2001, A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data, Protein Sci., 10, 2131, 10.1110/ps.07501 · DOI
  82. Stark, 2008, Rapid protein-ligand costructures using chemical shift perturbations, J. Am. Chem. Soc., 130, 535, 10.1021/ja0737974 · DOI
  83. Clore, 2003, Docking of protein-protein complexes on the basis of highly ambiguous intermolecular distance restraints derived from 1HN/15N chemical shift mapping and backbone 15N–1H residual dipolar couplings using conjoined rigid body/torsion angle dynamics, J. Am. Chem. Soc., 125, 2902, 10.1021/ja028893d · DOI
  84. Krzeminski, 2010, SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes, BMC Bioinf., 11, 51, 10.1186/1471-2105-11-51 · doi:10.1186/1471-2105-11-51
  85. Medek, 2000, The use of differential chemical shifts for determining the binding site location and orientation of protein-bound ligands, J. Am. Chem. Soc., 122, 1241, 10.1021/ja993921m · DOI
  86. Lugovskoy, 2002, A novel approach for characterizing protein ligand complexes: molecular basis for specificity of small-molecule Bcl-2 inhibitors, J. Am. Chem. Soc., 124, 1234, 10.1021/ja011239y · DOI
  87. Riedinger, 2008, Analysis of chemical shift changes reveals the binding modes of isoindolinone inhibitors of the MDM2-p53 interaction, J. Am. Chem. Soc., 130, 16038, 10.1021/ja8062088 · DOI
  88. Shen, 2008, Consistent blind protein structure generation from NMR chemical shift data, Proc. Natl Acad. Sci. USA, 105, 4685, 10.1073/pnas.0800256105 · DOI · Paper page
  89. Cavalli, 2007, Protein structure determination from NMR chemical shifts, Proc. Natl Acad. Sci. USA, 104, 9615, 10.1073/pnas.0610313104 · DOI · Paper page
  90. McCoy, 2002, Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations, J. Am. Chem. Soc., 124, 2104, 10.1021/ja017242z · DOI
  91. Cioffi, 2008, Determination of protein-ligand binding modes using complexation-induced changes in 1H NMR chemical shift, J. Med. Chem., 51, 2512, 10.1021/jm701194r · DOI
  92. Cioffi, 2008, Influence of conformational flexibility on complexation-induced changes in chemical shift in a neocarzinostatin protein – ligand complex, J. Med. Chem., 51, 4488, 10.1021/jm800075r · DOI
  93. Cioffi, 2009, Use of quantitative 1H NMR chemical shift changes for ligand docking into barnase, J. Biomol. NMR, 43, 11, 10.1007/s10858-008-9286-7 · DOI
  94. Wang, 2004, Pose scoring by NMR, J. Am. Chem. Soc., 126, 11430, 10.1021/ja047695e · DOI
  95. Wang, 2005, Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations, J. Am. Chem. Soc., 127, 5310, 10.1021/ja042616k · DOI
  96. González-Ruiz, 2009, Steering protein-ligand docking with quantitative NMR chemical shift perturbations, J. Chem. Inf. Model., 49, 2260, 10.1021/ci900188r · DOI
  97. Neal, 2003, Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts, J. Biomol. NMR, 26, 215, 10.1023/A:1023812930288 · DOI · Paper page
  98. Montalvao, 2008, Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex, J. Am. Chem. Soc., 130, 15990, 10.1021/ja805258z · DOI
  99. Cavalli, 2011, Using chemical shifts to determine structural changes in proteins upon complex formation, J. Phys. Chem. B, 115, 9491, 10.1021/jp202647q · DOI
  100. Hass, 2008, Probing electric fields in proteins in solution by NMR spectroscopy, Proteins: Struct. Funct. Bioinf., 72, 333, 10.1002/prot.21929 · DOI

Cited by

See all 1,460

Metadata

Authors
Williamson, M. P.
Venue
Progress in Nuclear Magnetic Resonance Spectroscopy
Publisher
Elsevier BV
Published
2013-08
Volume
73
Pages
1-16
ISSN
0079-6565 (ISSN-L)
OpenAlex
W2132180320
Cited by
1,460
References
1
FWCI
26.98
Type
journal article
Language
en
Update notices
erratum (2014-07-01)
Open access
closed
Licence
  • www.elsevier.com/tdm/userlicense/1.0/ (tdm)
  • www.elsevier.com/legal/tdmrep-license (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Using chemical shift perturbation to characterise ligand binding. https://app.cochat.ai/papers/10.1016/j.pnmrs.2013.02.001
The paper
Williamson, M. P. (2013). Using chemical shift perturbation to characterise ligand binding. Progress in Nuclear Magnetic Resonance Spectroscopy. https://doi.org/10.1016/j.pnmrs.2013.02.001

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.