Solution nuclear magnetic resonance spectroscopy techniques for probing intermolecular interactions

Chemistry and Biology

Volumn 12, Issue 9, 2005, Pages 961-971

  Pellecchia, Maurizio ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

KINETICS; METABOLISM; METHODOLOGY; MOLECULAR PROBE; NUCLEAR MAGNETIC RESONANCE; REVIEW;

ENZYMES; KINETICS; MOLECULAR PROBES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR;

EID: 25144456011     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2005.08.013     Document Type: Review

References (95)

1. R.A. Carr, M. Congreve, C.W. Murray, and D.C. Rees Fragment-based lead discovery: leads by design Drug Discov. Today 10 2005 987 992
2. M. Congreve, R. Carr, C. Murray, and H. Jhoti A 'rule of three' for fragment-based lead discovery? Drug Discov. Today 8 2003 876 877
3. D.A. Erlanson, and S.K. Hansen Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly Curr. Opin. Chem. Biol. 8 2004 399 406
4. D.A. Erlanson, R.S. McDowell, and T. O'Brien Fragment-based drug discovery J. Med. Chem. 47 2004 3463 3482
5. D.A. Erlanson, J.A. Wells, and A.C. Braisted Tethering: fragment-based drug discovery Annu. Rev. Biophys. Biomol. Struct. 33 2004 199 223
6. A. Gill, A. Cleasby, and H. Jhoti The discovery of novel protein kinase inhibitors by using fragment-based high-throughput X-ray crystallography ChemBioChem 6 2005 506 512
7. M.J. Hartshorn, C.W. Murray, A. Cleasby, M. Frederickson, I.J. Tickle, and H. Jhoti Fragment-based lead discovery using X-ray crystallography J. Med. Chem. 48 2005 403 413
8. W.R. Moore Jr. Maximizing discovery efficiency with a computationally driven fragment approach Curr. Opin. Drug Discov. Devel. 8 2005 355 364
9. D.C. Rees, M. Congreve, C.W. Murray, and R. Carr Fragment-based lead discovery Nat. Rev. Drug Discov. 3 2004 660 672
10. M. Schade, and H. Oschkinat NMR fragment screening: tackling protein-protein interaction targets Curr. Opin. Drug Discov. Devel. 8 2005 365 373
11. H.O. Villar, J. Yan, and M.R. Hansen Using NMR for ligand discovery and optimization Curr. Opin. Chem. Biol. 8 2004 387 391
12. E.R. Zartler, and M.J. Shapiro Fragonomics: fragment-based drug discovery Curr. Opin. Chem. Biol. 9 2005 366 370
13. A. Kumar, R.R. Ernst, and K. Wüthrich A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation network in biological macromolecules Biochem. Biophys. Res. Commun. 95 1980 1 6
14. M.G. Bo Nobel Lectures in Chemistry 1991-1995 1997 World Scientific Publishing Company Singapore
15. R.R. Ernst, G. Bodenhausen, and A. Wokaun Principles of Nuclear Magnetic Resonance in One and Two Dimensions 1987 Oxford University Press New York
16. K. Wüthrich NMR studies of structure and function of biological macromolecules Biosci. Rep. 23 2003 119 168
17. K. Wüthrich NMR of Proteins and Nucleic Acids 1986 Wiley & Son New York
18. 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin Biochemistry 29 1990 4659 4667
19. L.E. Kay, M. Ikura, R. Tschudin, and A. Bax 3-dimensional triple-resonance NMR-spectroscopy of isotopically enriched proteins J. Magn. Res. 89 1990 496 514
20. 13C enriched proteins J. Biomol. NMR 1 1991 99 104
21. 15N NMR backbone assignments and secondary structure of human interferon-γ Biochemistry 31 1992 8180 8190
22. K.H. Gardner, and L.E. Kay The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins Annu. Rev. Biophys. Biomol. Struct. 27 1998 357 406
23. L.E. Kay NMR methods for the study of protein structure and dynamics Biochem. Cell Biol. 75 1997 1 15
24. J.G. Pelton, and D.E. Wemmer Heteronuclear NMR pulse sequences applied to biomolecules Annu. Rev. Phys. Chem. 46 1995 139 167
25. B. Whitehead, C.J. Craven, and J.P. Waltho Double and triple resonance NMR methods for protein assignment Methods Mol. Biol. 60 1997 29 52
26. K. Ozawa, M.J. Headlam, P.M. Schaeffer, B.R. Henderson, N.E. Dixon, and G. Otting Optimization of an Escherichia coli system for cell-free synthesis of selectively N-labelled proteins for rapid analysis by NMR spectroscopy Eur. J. Biochem. 271 2004 4084 4093
27. M.P. Williamson, T.F. Havel, and K. Wuthrich Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry J. Mol. Biol. 182 1985 295 315
28. G. Wagner, W. Braun, T.F. Havel, T. Schaumann, N. Go, and K. Wüthrich Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN J. Mol. Biol. 196 1987 611 639
29. P. Guntert Automated NMR structure calculation with CYANA Methods Mol. Biol. 278 2004 353 378
30. D. Zheng, Y.J. Huang, H.N. Moseley, R. Xiao, J. Aramini, G.V. Swapna, and G.T. Montelione Automated protein fold determination using a minimal NMR constraint strategy Protein Sci. 12 2003 1232 1246
31. T. Herrmann, P. Guntert, and K. Wüthrich Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS J. Biomol. NMR 24 2002 171 189
32. H. Schwalbe, T. Carlomagno, M. Hennig, J. Junker, B. Reif, C. Richter, and C. Griesinger Cross-correlated relaxation for measurement of angles between tensorial interactions Methods Enzymol. 338 2001 35 81
33. K. Wüthrich Nuclear magnetic resonance studies of internal mobility in globular proteins Biochem. Soc. Symp. 46 1981 17 37
34. D. Kern, and E.R. Zuiderweg The role of dynamics in allosteric regulation Curr. Opin. Struct. Biol. 13 2003 748 757
35. K. Pervushin, R. Riek, G. Wider, and K. Wüthrich 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 1997 12366 12371
36. K. Pervushin Impact of transverse relaxation optimized spectroscopy (TROSY) on NMR as a technique in structural biology Q. Rev. Biophys. 33 2000 161 197
37. A. Bax Weak alignment offers new NMR opportunities to study protein structure and dynamics Protein Sci. 12 2003 1 16
38. J.H. Prestegard, C.M. Bougault, and A.I. Kishore Residual dipolar couplings in structure determination of biomolecules Chem. Rev. 104 2004 3519 3540
39. N.K. Goto, K.H. Gardner, G.A. Mueller, R.C. Willis, and L.E. Kay A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15N-, 13C-, 2H-labeled proteins J. Biomol. NMR 13 1999 369 374
40. L.E. Kay, and K.H. Gardner Solution NMR spectroscopy beyond 25 kDa Curr. Opin. Struct. Biol. 7 1997 722 731
41. T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, and G.T. Montelione Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment Proc. Natl. Acad. Sci. USA 99 2002 8009 8014
42. D. Cowburn, and T.W. Muir Segmental isotopic labeling using expressed protein ligation Methods Enzymol. 339 2001 41 54
43. D. Cowburn, A. Shekhtman, R. Xu, J.J. Ottesen, and T.W. Muir Segmental isotopic labeling for structural biological applications of NMR Methods Mol. Biol. 278 2004 47 56
44. A. Romanelli, A. Shekhtman, D. Cowburn, and T.W. Muir Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction Proc. Natl. Acad. Sci. USA 101 2004 6397 6402
45. S. Zuger, and H. Iwai Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies Nat. Biotechnol. 23 2005 736 740
46. W.G. Hol Structural genomics for science and society Nat. Struct. Biol. 7 Suppl 2000 964 966
47. E. Kupce, and R. Freeman Projection-reconstruction of three-dimensional NMR spectra J. Am. Chem. Soc. 125 2003 13958 13959
48. E. Kupce, and R. Freeman Reconstruction of the three-dimensional NMR spectrum of a protein from a set of plane projections J. Biomol. NMR 27 2003 383 387
49. E. Kupce, and R. Freeman Fast multi-dimensional Hadamard spectroscopy J. Magn. Reson. 163 2003 56 63
50. E. Kupce, and R. Freeman Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy J. Am. Chem. Soc. 126 2004 6429 6440
51. E. Kupce, and R. Freeman Fast reconstruction of four-dimensional NMR spectra from plane projections J. Biomol. NMR 28 2004 391 395
52. S. Hiller, F. Fiorito, K. Wüthrich, and G. Wider Automated projection spectroscopy (APSY) Proc. Natl. Acad. Sci. USA 102 2005 10876 10881
53. M. Pellecchia, B. Becattini, K.J. Crowell, R. Fattorusso, M. Forino, M. Fragai, D. Jung, T. Mustelin, and L. Tautz NMR-based techniques in the hit identification and optimisation processes Expert Opin. Ther. Targets 8 2004 597 611
54. C.A. Lepre, J.M. Moore, and J.W. Peng Theory and applications of NMR-based screening in pharmaceutical research Chem. Rev. 104 2004 3641 3676
55. J. Moore, N. Abdul-Manan, J. Fejzo, M. Jacobs, C. Lepre, J. Peng, and X. Xie Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design J. Synchrotron Radiat. 11 2004 97 100
56. M.A. Johnson, and B.M. Pinto NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions Carbohydr. Res. 339 2004 907 928
57. J. Clarkson, and I.D. Campbell Studies of protein-ligand interactions by NMR Biochem. Soc. Trans. 31 2003 1006 1009
58. R.A. Rodriguez-Mias, and M. Pellecchia Use of selective Trp side chain labeling to characterize protein-protein and protein-ligand interactions by NMR spectroscopy J. Am. Chem. Soc. 125 2003 2892 2893
59. M. Pellecchia, D. Meininger, Q. Dong, E. Chang, R. Jack, and D.S. Sem NMR-based structural characterization of large protein-ligand interactions J. Biomol. NMR 22 2002 165 173
60. M. Pellecchia, D.S. Sem, and K. Wüthrich NMR in drug discovery Nat. Rev. Drug Discov. 1 2002 211 219
61. D.S. Sem, B. Bertolaet, B. Baker, E. Chang, A.D. Costache, S. Coutts, Q. Dong, M. Hansen, V. Hong, and X. Huang Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox Chem. Biol. 11 2004 185 194
62. M. Pellecchia, D. Meininger, A.L. Shen, R. Jack, C.B. Kasper, and D.S. Sem SEA-TROSY (solvent exposed amides with TROSY): a method to resolve the problem of spectral overlap in very large proteins J. Am. Chem. Soc. 123 2001 4633 4634
63. S.B. Shuker, P.J. Hajduk, R.P. Meadows, and S.W. Fesik Discovering high-affinity ligands for proteins: SAR by NMR Science 274 1996 1531 1534
64. P.J. Hajduk, D.J. Augeri, J. Mack, R. Mendoza, J. Yang, S.F. Betz, and S.W. Fesik NMR-based screening of proteins containing 13C-labeled methyl groups J. Am. Chem. Soc. 122 2000 7898 7904
65. P.J. Hajduk, G. Sheppard, D.G. Nettesheim, E.T. Olejniczak, S.B. Shuker, R.P. Meadows, D.H. Steinman, G.M. Carrera, P.A. Marcotte, and J. Severin Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR J. Am. Chem. Soc. 119 1997 5818 5827
66. A. Medek, P.J. Hajduk, J. Mack, and S.W. Fesik The use of differential chemical shifts for determining the binding site location and orientation of protein-bound ligands J. Am. Chem. Soc. 122 2000 1241 1242
67. M.A. McCoy, and D.F. Wyss Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations J. Am. Chem. Soc. 124 2002 2104 2105
68. M. Pellecchia, P. Sebbel, U. Hermanns, K. Wüthrich, and R. Glockshuber Pilus chaperone FimC-adhesin FimH interactions mapped by TROSY-NMR Nat. Struct. Biol. 6 1999 336 339
69. D. Choudhury, A. Thompson, V. Stojanoff, S. Langermann, J. Pinkner, S.J. Hultgren, and S.D. Knight X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli Science 285 1999 1061 1066
70. T. Oltersdorf, S.W. Elmore, A.R. Shoemaker, R.C. Armstrong, D.J. Augeri, B.A. Belli, M. Bruncko, T.L. Deckwerth, J. Dinges, and P.J. Hajduk An inhibitor of Bcl-2 family proteins induces regression of solid tumours Nature 435 2005 677 681
71. I. Solomon Relaxation processes in a system of two spins Phys. Rev. 99 1955 559 565
72. M. Mayer, and B. Meyer Characterization of ligand binding by saturation transfer difference NMR spectroscopy Ang. Chem. Int. Ed. 38 1999 1784 1788
73. J. Klein, R. Meinecke, M. Mayer, and B. Meyer Detecting binding affinity to immobilized receptor proteins in compound libraries by HR-MAS STD NMR J. Am. Chem. Soc. 121 1999 5336 5337
74. H. Moller, N. Serttas, H. Paulsen, J.M. Burchell, J. Taylor- Papadimitriou, and B. Meyer NMR-based determination of the binding epitope and conformational analysis of MUC-1 glycopeptides and peptides bound to the breast cancer-selective monoclonal antibody SM3 Eur. J. Biochem. 269 2002 1444 1455
75. M. Mayer, and B. Meyer 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 2001 6108 6117
76. C. Dalvit, P. Pevarello, M. Tato, M. Veronesi, A. Vulpetti, and M. Sundstrom Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water J. Biomol. NMR 18 2000 65 68
77. H. Takahashi, T. Nakanishi, K. Kami, Y. Arata, and I. Shimada A novel NMR method for determining the interfaces of large protein-protein complexes Nat. Struct. Biol. 7 2000 220 223
78. N. Nishida, H. Sumikawa, M. Sakakura, N. Shimba, H. Takahashi, H. Terasawa, E.I. Suzuki, and I. Shimada Collagen-binding mode of vWF-A3 domain determined by a transferred cross-saturation experiment Nat. Struct. Biol. 10 2003 53 58
79. G.M. Clore, and A.M. Gronenborn Theory of the time-dependent transferred nuclear Overhauser effect - applications to structural analysis of ligand-protein complexes in solution J. Magn. Reson. 53 1983 423 442
80. A. Kline SAR by NOE? The NMR Newsletter 13 1997 472
81. D. Li, E.F. DeRose, and R.E. London The inter-ligand Overhauser effect: a powerful new NMR approach for mapping structural relationships of macromolecular ligands J. Biomol. NMR 15 1999 71 76
82. J. Fejzo, C.A. Lepre, J.W. Peng, G.W. Bemis, M.A. Murcko, and J.M. Moore The SHAPES strategy: an NMR-based approach for lead generation in drug discovery Chem. Biol. 6 1999 755 769
83. B. Becattini, S. Sareth, D. Zhai, K.J. Crowell, M. Leone, J.C. Reed, and M. Pellecchia Targeting apoptosis via chemical design: inhibition of bid-induced cell death by small organic molecules Chem. Biol. 11 2004 1107 1117
84. E.M. Driggers, C.W. Liu, D.E. Wemmer, and P.G. Schultz Structure of the Michaelis complex of an efficient antibody acyl transferase determined by transferred nuclear Overhauser enhancement spectroscopy J. Am. Chem. Soc. 120 1998 1945 1958
85. Becattini, B., and Pellacchia, M. (2005). SAR by ILOEs: an NMR-based approach to reverse chemical genetics. Chem. Eur. J. 11, in press. 10.1002/chem.2005.00.636
86. P.J. Hajduk, E.T. Olejniczak, and S.W. Fesik One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules J. Am. Chem. Soc. 119 1997 12257 12261
87. W. Jahnke, S. Rudisser, and M. Zurini Spin label enhanced NMR screening J. Am. Chem. Soc. 123 2001 3149 3150
88. W. Jahnke, B. Lawrence, L. Perez, G. Paris, A. Strauss, G. Fendrich, and C.M. Nalin Second-site NMR screening with a spin-labeled first ligand J. Am. Chem. Soc. 122 2000 7394 7395
89. S. Vanwetswinkel, R.J. Heetebrij, J. van Duynhoven, J.G. Hollander, D.V. Filippov, P.J. Hajduk, and G. Siegal TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery Chem. Biol. 12 2005 207 216
90. R. Fattorusso, D. Jung, K.J. Crowell, M. Forino, and M. Pellecchia Discovery of a novel class of reversible non-peptide caspase inhibitors via a structure-based approach J. Med. Chem. 48 2005 1649 1656
91. C. Dalvit, P.E. Fagerness, D.T. Hadden, R.W. Sarver, and B.J. Stockman Fluorine-NMR experiments for high-throughput screening: theoretical aspects, practical considerations, and range of applicability J. Am. Chem. Soc. 125 2003 7696 7703
92. C. Dalvit, E. Ardini, M. Flocco, G.P. Fogliatto, N. Mongelli, and M. Veronesi A general NMR method for rapid, efficient, and reliable biochemical screening J. Am. Chem. Soc. 125 2003 14620 14625
93. M. Forino, S. Johnson, T.Y. Wong, D.V. Rozanov, A.Y. Savinov, W. Li, R. Fattorusso, B. Becattini, A.J. Orry, and D. Jung Efficient synthetic inhibitors of anthrax lethal factor Proc. Natl. Acad. Sci. USA 102 2005 9499 9504
94. C. Dalvit, E. Ardini, G.P. Fogliatto, N. Mongelli, and M. Veronesi Reliable high-throughput functional screening with 3-FABS Drug Discov. Today 9 2004 595 602
95. P.J. Hajduk, J. Dinges, G.F. Miknis, M. Merlock, T. Middleton, D.J. Kempf, D.A. Egan, K.A. Walter, T.S. Robins, and S.B. Shuker NMR-based discovery of lead inhibitors that block DNA binding of the human papillomavirus E2 protein J. Med. Chem. 40 1997 3144 3150