STD-NMR: Application to transient interactions between biomolecules-a quantitative approach

European Biophysics Journal

Volumn 40, Issue 12, 2011, Pages 1357-1369

  Angulo, Jesus ^a   Nieto, Pedro M ^a  

^a INSTITUTO DE INVESTIGACIONES QUÍMICAS   (Spain)

Author keywords

Molecular recognition; NMR spectroscopy; Receptor ligand interactions; Saturation transfer difference NMR (STD NMR) spectroscopy

Indexed keywords

LIGAND; PROTEIN;

BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; EPITOPE MAPPING; INSTRUMENTATION; METHODOLOGY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHYSIOLOGY; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; REVIEW; SOLUTION AND SOLUBILITY;

BINDING SITES; EPITOPE MAPPING; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOLUTIONS;

EID: 82455212567     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-011-0749-5     Document Type: Review

References (55)

1. J Angulo B Langpap A Blume T Biet B Meyer NR Krishna H Peters MM Palcic T Peters 2006 Blood group B galactosyltransferase: insights into substrate binding from NMR experiments J Am Chem Soc 128 13529 13538 17031966 10.1021/ja063550r 1:CAS:528:DC%2BD28XpvVCitbc%3D (Pubitemid 44583038)
2. J Angulo I Díaz JJ Reina G Tabarani F Fieschi J Rojo PM Nieto 2008 Saturation transfer difference (STD) NMR spectroscopy characterization of dual binding mode of a mannose disaccharide to DC-SIGN ChemBioChem 9 2225 2227 18720494 10.1002/cbic.200800361 1:CAS:528:DC%2BD1cXht1CltrbP
3. J Angulo PM Enríquez-Navas PM Nieto 2010 Ligand-receptor binding affinities from saturation transfer difference (STD) NMR spectroscopy: the binding isotherm of STD initial growth rates Chem Eur J 16 7803 7812 20496354 10.1002/chem.200903528 1:CAS:528:DC%2BC3cXoslyrsrY%3D
4. FM Assadi-Porter M Tonelli E Maillet K Hallenga O Benard M Max JL Markley 2008 Direct NMR detection of the binding of functional ligands to the human sweet receptor, a heterodimeric family 3 GPCR J Am Chem Soc 130 7212 7213 18481853 10.1021/ja8016939 1:CAS:528:DC%2BD1cXmtVGgs7c%3D (Pubitemid 351813199)
5. A Bernardi D Arosio D Potenza I Sánchez-Medina S Mari FJ Cañada J Jiménez-Barbero 2004 Intramolecular carbohydrate-aromatic interactions and intermolecular van der waals interactions enhance the molecular recognition ability of GM1 glycomimetics for cholera toxin Chem Eur J 10 4395 4406 15378617 10.1002/chem.200400084 1:CAS:528:DC%2BD2cXot1yhtrs%3D
6. J Blobel R Fayos J García O Marimon Y Pérez M Pons 2008 Low-molecular-weight spies of protein-protein interactions Comptes Rendus Chimie 11 499 505 10.1016/j.crci.2007.08.015 1:CAS:528:DC%2BD1cXktl2jurc%3D
7. DA Calarese CN Scanlan MB Zwick S Deechongkit Y Mimura R Kunert P Zhu MR Wormald RL Stanfield KH Roux JW Kelly PM Rudd RA Dwek H Katinger DR Burton IA Wilson 2003 Antibody domain exchange is an immunological solution to carbohydrate cluster recognition Science 300 2065 2071 12829775 10.1126/science.1083182 1:CAS:528:DC%2BD3sXkvVOrsLk%3D (Pubitemid 36760127)
8. DA Calarese HK Lee CY Huang MD Best RD Astronomo RL Stanfield H Katinger DR Burton CH Wong IA Wilson 2005 Dissection of the carbohydrate specificity of the broadly neutralizing-anti-HIV-1 antibody 2G12 Proc Natl Acad Sci USA 102 13372 13377 16174734 10.1073/pnas.0505763102 1:CAS:528:DC%2BD2MXhtVygsbnP (Pubitemid 41420854)
9. LP Calle FJ Canada J Jimenez-Barbero 2011 Application of NMR methods to the study of the interaction of natural products with biomolecular receptors Nat Prod Rep 28 1118 1125 21487589 10.1039/c0np00071j 1:CAS:528: DC%2BC3MXmsFGgsro%3D
10. A Canales R Matesanz NM Gardner JM Andreu I Paterson JF Díaz J Jiménez-Barbero 2008 The bound conformation of microtubule-stabilizing agents: NMR insights into the bioactive 3D structure of discodermolide and dictyostatin Chem Eur J 14 7557 7569 18449868 10.1002/chem.200800039 1:CAS:528:DC%2BD1cXhtFaksrnI
11. R Caraballo H Dong JP Ribeiro J Jimenez-Barbero O Ramstrom 2010 Direct STD NMR identification of beta-galactosidase inhibitors from a virtual dynamic hemithioacetal system Angewandte Chemie-Int Ed 49 589 593 1:CAS:528: DC%2BC3cXktlaksw%3D%3D
12. B Claasen M Axmann R Meinecke B Meyer 2005 Direct observation of ligand binding to membrane proteins in living cells by a saturation transfer double difference (STDD) NMR spectroscopy method shows a significantly higher affinity of integrin alpha(IIb)beta(3) in native platelets than in liposomes J Am Chem Soc 127 916 919 15656629 10.1021/ja044434w 1:CAS:528:DC%2BD2cXhtFGgsLvP (Pubitemid 40144290)
13. S Di Micco C Bassarello G Bifulco R Riccio L Gomez-Paloma 2006 Differential-frequency saturation transfer difference NMR spectroscopy allows the detection of different ligand-DNA binding modes Angew Chem Int Ed 45 224 228 10.1002/anie.200501344 1:CAS:528:DC%2BD28XlslymsA%3D%3D (Pubitemid 43017512)
14. T Diercks JP Ribeiro FJ Cañada S André J Jiménez-Barbero H-J Gabius 2009 Fluorinated carbohydrates as lectin ligands: versatile sensors in 19F-detected saturation transfer difference NMR spectroscopy Chem Eur J 15 5666 5668 19388026 10.1002/chem.200900168 1:CAS:528:DC%2BD1MXms1ektLw%3D
15. PM Enríquez-Navas M Marradi D Padro J Angulo S Penadés 2011 A solution NMR study of the interactions of oligomannosides and the anti-HIV-1 2G12 antibody reveals distinct binding modes for branched ligands Chem Eur J 17 1547 1560 21268157 10.1002/chem.201002519
16. K Feher P Groves G Batta J Jimenez-Barbero C Muhle-Goll KE Kover 2008 Competition saturation transfer difference experiments improved with isotope editing and filtering schemes in NMR-based screening J Am Chem Soc 130 17148 17153 19053472 10.1021/ja804468k 1:CAS:528:DC%2BD1cXhsVWksrfO
17. Forsen S, Hoffman RA (1963) Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance. J. Chem. Phys. 39:2892 -2901
18. T Haselhorst AK Munster-Kuhnel M Oschlies J Tiralongo R Gerardy-Schahn M von Itzstein 2007 Direct detection of ligand binding to sepharose-immobilised protein using saturation transfer double difference (STDD) NMR spectroscopy Biochem Biophys Res Commun 359 866 870 17574211 10.1016/j.bbrc.2007.05.204 1:CAS:528:DC%2BD2sXmvV2isr4%3D (Pubitemid 46946899)
19. T Haselhorst JM Garcia T Islam CC Jimmy J Lai Faith M Rose John JS Nicholls P Malik M von Itzstein 2008 Avian influenza H5-containing virus-like particles (VLPs): host-cell receptor specificity by STD NMR spectroscopy Angew Chem Int Ed 47 1910 1912 10.1002/anie.200704872 1:CAS:528:DC%2BD1cXjtFGisrk%3D
20. H Huang J Milojevic G Melacini 2008 Analysis and optimization of saturation transfer difference NMR experiments designed to map early self-association events in amyloidogenic peptides J Phys Chem B 112 5795 5802 18410162 10.1021/jp7118718 1:CAS:528:DC%2BD1cXksFyku70%3D (Pubitemid 351704596)
21. Hyde EI, Birdsall B, Roberts GCK, Feeney J, Burgen ASV (1980) Proton nuclear magnetic resonance saturation transfer studies of coenzyme binding to lactobacilus-casei dihydrofolate-reductase Biochemistry 19:3738-3746 (Pubitemid 10023288)
22. V Jayalakshmi NR Krishna 2002 Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes J Magn Reson 155 106 118 11945039 10.1006/jmre.2001.2499 1:CAS:528:DC%2BD38Xis1yhtbw%3D
23. V Jayalakshmi NR Krishna 2004 CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities J Magn Reson 168 36 45 15082247 10.1016/j.jmr.2004.01.017 1:CAS:528:DC%2BD2cXjtVWitr8%3D
24. V Jayalakshmi NR Krishna 2005 Determination of the conformation of trimethoprim in the binding pocket of bovine dihydrofolate reductase from a STD-NMR intensity-restrained CORCEMA-ST optimization J Am Chem Soc 127 14080 14084 16201830 10.1021/ja054192f 1:CAS:528:DC%2BD2MXhtVWhsLjJ (Pubitemid 41437056)
25. V Jayalakshmi T Biet T Peters NR Krishna 2004 Refinement of the conformation of UDP-galactose bound to galactosyltransferase using the STD NMR intensity-restrained CORCEMA optimization J Am Chem Soc 126 8610 8611 15250687 10.1021/ja048703u 1:CAS:528:DC%2BD2cXltVCnsLg%3D (Pubitemid 38955699)
26. Jimenez-Barbero J, Peters T (2002) NMR spectroscopy of glycoconjugates. VCH, Weinheim
27. KE Kover P Groves J Jimenez-Barbero G Batta 2007 Molecular recognition and screening using a N-15 group selective STD NMR method J Am Chem Soc 129 11579 11582 17722925 10.1021/ja073291l (Pubitemid 47555576)
28. KE Kover E Weber TA Martinek E Monostori G Batta 2010 N-15 and C-13 group-selective techniques extend the scope of STD NMR detection of weak host-guest interactions and ligand screening ChemBioChem 11 2182 2187 20878964 10.1002/cbic.201000317 1:CAS:528:DC%2BC3cXhsVKktr7K
29. CA Lepre JM Moore JW Peng 2004 Theory and applications of NMR-based screening in pharmaceutical research Chem Rev 104 3641 3675 15303832 10.1021/cr030409h 1:CAS:528:DC%2BD2cXlvFGiurY%3D
30. H Maaheimo P Kosma L Brade H Brade T Peters 2000 Mapping the binding of synthetic disaccharides representing epitopes of chlamydial lipopolysaccharide to antibodies with NMR Biochemistry 39 12778 12788 11041842 10.1021/bi000780o 1:CAS:528:DC%2BD3cXmslyqurY%3D
31. S Mari D Serrano-Gomez FJ Canada AL Corbi J Jimenez-Barbero 2005 1D saturation transfer difference NMR experiments on living cells: the DC-SIGN/oligomannose interaction Angew Chem Int Ed 44 296 298 10.1002/anie.200461574 1:CAS:528:DC%2BD2MXjsFWhtw%3D%3D (Pubitemid 40094991)
32. JN Martin EM Munoz C Schwergold F Souard JL Asensio J Jimenez-Barbero J Canada C Vicent 2005 Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions J Am Chem Soc 127 9518 9533 15984879 10.1021/ja050794n 1:CAS:528:DC%2BD2MXkvVejurc%3D (Pubitemid 40934764)
33. M Mayer TL James 2002 Detecting ligand binding to a small RNA target via saturation transfer difference NMR experiments in D2O and H2O J Am Chem Soc 124 13376 13377 12418877 10.1021/ja027526z 1:CAS:528:DC%2BD38XnvV2ltLs%3D (Pubitemid 35285902)
34. M Mayer TL James 2004 NMR-based characterization of phenothiazines as a RNA binding scaffold J Am Chem Soc 126 4453 4460 15053636 10.1021/ja0398870 1:CAS:528:DC%2BD2cXhvFCqu7o%3D (Pubitemid 38453903)
35. M Mayer B Meyer 1999 Characterization of ligand binding by saturation transfer difference NMR spectroscopy Angewandte Chemie-Int Ed 38 1784 1788 10.1002/(SICI)1521-3773(19990614)38:12<1784::AID-ANIE1784>3.0.CO;2-Q 1:CAS:528:DyaK1MXktVCntb0%3D (Pubitemid 29290947)
36. M Mayer B Meyer 2001 Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor J Am Chem Soc 123 6108 6117 11414845 10.1021/ja0100120 1:CAS:528:DC%2BD3MXktFamsbg%3D (Pubitemid 32888480)
37. S Megy G Bertho J Gharbi-Benarous N Evrard-Todeschi G Coadou E Segeral C Iehle E Quemeneur R Benarous JP Girault 2005 STD and TRNOESY NMR studies on the conformation of the oncogenic protein beta-catenin containing the phosphorylated motif DpSGXXpS bound to the beta-TrCP protein J Biol Chem 280 29107 29116 15927956 10.1074/jbc.M501628200 1:CAS:528:DC%2BD2MXntVegsL4%3D (Pubitemid 41161361)
38. B Meyer T Peters 2003 NMR Spectroscopy techniques for screening and identifying ligand binding to protein receptors Angewandte Chemie-Int Ed 42 864 890 10.1002/anie.200390233 1:CAS:528:DC%2BD3sXitFWltL4%3D (Pubitemid 36314024)
39. Moseley HNB, Curto EV, Krishna NR (1995) Complete relaxation and conformational exchange matrix (CORCEMA) analysis of NOESY spectra of interacting systems; two-dimensional transferred NOESY. J Magn Reson Ser B, 108:243-261
40. AT Neffe M Bilang B Meyer 2006 Synthesis and optimization of peptidomimetics as HIV entry inhibitors against the receptor protein CD4 using STD NMR and ligand docking Org Biomol Chem 4 3259 3267 17036114 10.1039/b605380g 1:CAS:528:DC%2BD28Xotl2nsbg%3D (Pubitemid 44289453)
41. AT Neffe M Bilang I Gruneberg B Meyer 2007 Rational optimization of the binding affinity of CD4 targeting peptidomimetics with potential anti HIV activity J Med Chem 50 3482 3488 17602545 10.1021/jm070206b 1:CAS:528: DC%2BD2sXmvFKqsLo%3D (Pubitemid 47195457)
42. Neuhaus D, Williamson MP (2000) The nuclear overhauser effect in structural and conformational analysis. Wiley-VCH, New York
43. M Pellecchia DS Sem K Wuthrich 2002 NMR in drug discovery Nat Rev Drug Discov 1 211 219 12120505 10.1038/nrd748 1:CAS:528:DC%2BD38XitFClt74%3D (Pubitemid 37361424)
44. M Pellecchia I Bertini D Cowburn C Dalvit E Giralt W Jahnke TL James SW Homans H Kessler C Luchinat B Meyer H Oschkinat J Peng H Schwalbe G Siegal 2008 Perspectives on NMR in drug discovery: a technique comes of age Nat Rev Drug Discov 7 738 745 19172689 10.1038/nrd2606 1:CAS:528:DC%2BD1cXhtVGgtL%2FK
45. P Peñalver F Marcelo J Jiménez-Barbero C Vicent 2011 Carbohydrate recognition at the minor-groove of the self-complementary duplex d(CGCGAATTCGCG)2 by a synthetic glyco-oligoamide Chem Eur J 17 4561 4570 21259350 10.1002/chem.201003027
46. A Pereira TA Pfeifer TA Grigliatti RJ Andersen 2009 Functional cell-based screening and saturation transfer double-difference NMR have identified haplosamate a as a cannabinoid receptor agonist ACS Chem Biol 4 139 144 19175306 10.1021/cb800264k 1:CAS:528:DC%2BD1MXhtV2lur8%3D
47. Rademacher C, Peters T (2008) Molecular recognition of ligands by native viruses and virus-like particles as studied by NMR experiments. In: Peters T (ed) Bioactive conformation II, vol 273. Springer, Berlin/Heidelberg, pp 183-202
48. C Rademacher NR Krishna M Palcic F Parra T Peters 2008 NMR experiments reveal the molecular basis of receptor recognition by a calicivirus J Am Chem Soc 130 3669 3675 18302385 10.1021/ja710854r 1:CAS:528:DC%2BD1cXitl2ksL4%3D (Pubitemid 351456072)
49. C Rademacher J Guiard PI Kitov B Fiege KP Dalton F Parra DR Bundle T Peters 2011 Targeting norovirus infection-multivalent entry inhibitor design based on NMR experiments Chem Eur J 17 7442 7453 21567493 10.1002/chem.201003432 1:CAS:528:DC%2BC3MXnslSlt7k%3D
50. C Räuber S Berger 2010 13C-NMR detection of STD spectra Magn Reson Chem 48 91 93 20024889
51. JP Ribeiro S André FJ Cañada H-J Gabius AP Butera RJ Alves J Jiménez-Barbero 2010 Lectin-based drug design: combined strategy to identify lead compounds using STD NMR spectroscopy, solid-phase assays and cell binding for a plant toxin model Chem Med Chem 5 415 419 20094999 1:CAS:528:DC%2BC3cXjslensL4%3D
52. V Roldós FJ Cañada J Jiménez-Barbero 2011 Carbohydrate-protein interactions: a 3D view by NMR ChemBioChem 12 990 1005 21500331 10.1002/cbic.201000705
53. F Souard E Muñoz P Peñalver C Badía R del Villar-Guerra JL Asensio J Jiménez-Barbero C Vicent 2008 Sugar-oligoamides: bound-state conformation and DNA minor-groove-binding description by TR-NOESY and differential-frequency saturation-transfer- difference experiments Chem Eur J 14 2435 2442 18203226 10.1002/chem.200701103 1:CAS:528:DC%2BD1cXltVOktb0%3D
54. M Vogtherr T Peters 2000 Application of NMR based binding assays to identify key hydroxy groups for intermolecular recognition J Am Chem Soc 122 6093 6099 10.1021/ja0001916 1:CAS:528:DC%2BD3cXjslGlur8%3D (Pubitemid 30451114)
55. JL Wagstaff S Vallath JF Marshall RA Williamson MJ Howard 2010 Two-dimensional heteronuclear saturation transfer difference NMR reveals detailed integrin alpha v beta 6 protein-peptide interactions Chem Commun 46 7533 7535 10.1039/c0cc01846e 1:CAS:528:DC%2BC3cXht1ClsLzL