Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes

Journal of the American Chemical Society

Volumn 128, Issue 11, 2006, Pages 3696-3702

  Pintacuda, Guido ^a,b   Park, Ah Young ^a   Keniry, Max A ^a   Dixon, Nicholas E ^a   Otting, Gottfried ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b Laboratoire de Chimie Organique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; ESCHERICHIA COLI; IONS; MAGNETIC SUSCEPTIBILITY; MATHEMATICAL MODELS; NUCLEAR MAGNETIC RESONANCE; PROTEINS; RARE EARTH ELEMENTS;

MOLECULAR FRAMES; PROTEIN-PROTEIN COMPLEXES; QUANTUM COHERENCE; THREE-DIMENSIONAL (3D) STRUCTURES;

COMPLEXATION;

ERBIUM; ESCHERICHIA COLI PROTEIN; EXONUCLEASE; LANTHANIDE;

ARTICLE; CHEMICAL LABELING; COMPLEX FORMATION; ESCHERICHIA COLI; MAGNETISM; NUCLEAR MAGNETIC RESONANCE; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUANTUM MECHANICS; THREE DIMENSIONAL IMAGING;

DNA POLYMERASE III; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI PROTEINS; LANTHANOID SERIES ELEMENTS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS;

EID: 33645390370     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja057008z     Document Type: Article

References (53)

1. Abbreviations that were used follow: ε186, the N-terminal domain (residues 2-186) of the ε subunit of E. coli DNA polymerase III; 3D, three-dimensional; HSQC, heteronuclear single quantum coherence; NMR, nuclear magnetic resonance; NOE, nuclear Overhauser effect; PAS, principal axes system; PCS, pseudocontact shifts; rmsd, root-mean-square deviation.
2. Bertini, L.; Luchinat, C.; Parigi, G. Prog. Nucl. Magn. Reson. Spectrosc. 2002, 40, 249-273.
3. Allegrozzi, M.; Bertini, I.; Janik, M. B. L.; Lee, Y. M.; Lin, G. H.; Luchinat, C. J. Am. Chem. Soc. 2000, 122, 4154-4161.
4. Banci, L.; Bertini, I.; Gori-Savellini, G.; Romagnoli, A.; Turano, P.; Cremonini, M. A.; Luchinat, C.; Gray, H. B. Proteins 1997, 29, 68-76.
5. Banci, L.; Bertini, I.; Cremonini, M. A.; Gori-Savellini, G.; Luchinat, C.; Wüthrich, K.; Güntert, P. J. Biomol. NMR 1998, 12, 553-557.
6. Hus, J. C.; Marion, D.; Blackledge, M. J. Mol. Biol. 2000, 298, 927-936.
7. Banci, L.; Bertini, I.; Cavallaro, G.; Giachetti, A.; Luchinat, C.; Parigi, G. J. Biomol. NMR 2004, 28, 249-261.
8. Ubbink, M.; Ejdebäck, M.; Karlsson, B. G.; Bendall, D. S. Structure 1998. 6, 323-335.
9. Nocek, J. M.; Huang, K.; Hoffman, B. M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2538-2543.
10. Diaz-Moreno, I.; Diaz-Quintana, A.; De la Rosa, M. A.; Ubbink, M. J. Biol. Chem. 2005, 280, 18908-18915.
11. Gochin, M. J. Biomol. NMR 1998, 12, 243-257.
12. Tu, K.; Gochin, M. J. Am. Chem. Soc. 1999, 121, 9276-9285.
13. Gochin, M. Structure 2000, 8, 441-452.
14. Pintacuda, G.; Keniry, M. A.; Huber, T.; Park, A. Y.; Dixon, N. E.; Otting, G. J. Am. Chem. Soc. 2004, 126, 2963-2970.
15. Hamdan, S.; Carr, P. D.; Brown, S. E.; Ollis, D. L.; Dixon, N. E. Structure 2002, 10, 535-546.
16. Keniry, M. A.; Park, A. Y.; Owen, E. A.; Hamdan, S.; Pintacuda, G.; Otting, G.; Dixon, N. E. J. Bacteriol. 2006, submitted for publication.
17. Brautigam, C. A.; Aschheim, K.; Steitz, T. A. Chem. Biol. 1999, 6, 901-908.
18. Frey, M. W.; Frey, S. T.; Horrocks, W. D., Jr.; Kaboord, B. F.; Benkovic, S. J. Chem. Biol. 1996, 3, 393-403.
19. Keniry, M. A.; Berthon, H. A.; Yang, J. Y.; Miles, C. S.; Dixon, N. E. Protein Sci. 2000, 9, 721-733.
20. Otting, G.; Wüthrich, K. Q. Rev. Biophys. 1990, 23, 39-96.
21. Schwieters, C. D.; Kuszewski, J. J.; Tjandra, N.; Clore, G. M. J. Magn. Reson. 2003, 160, 65-73.
22. Sass, J.; Cordier, F.; Hoffmann, A.; Rogowski, M.; Cousin, A.; Omichinsky, J. G.; Löwen, H.; Grzesiek, S. J. Am. Chem. Soc. 1999, 121, 2047-2055.
23. Al-Hashimi, H. M.; Valafar, H.; Terrell, M.; Zartler, E. R.; Eidsness, M. K.; Prestegard, J. H. J. Magn. Reson. 2000, 143, 402-406.
24. Fischer, M. W.; Losonczi, J. A.; Weaver, J. L.; Prestegard, J. H. Biochemistry 1999, 38, 9013-9022.
25. DeRose, E. F.; Darden, T.; Harvey, S.; Gabel, S.; Perrino, F. W.; Schaaper, R. M.; London, R. E. Biochemistry 2003, 42, 3635-3644.
26. Barbieri, R.; Bertini, I.; Cavallaro, G.; Lee, Y. M.; Luchinat, C.; Rosato, A. J. Am. Chem. Soc. 2002, 124, 5581-5587.
27. Bertini, I.; Luchinat, C.; Parigi, G. Solution NMR of Paramagnetic Molecules: Applications to Metallobiomolecules and Models; Elsevier: Amsterdam, 2001.
28. Ghose, R.; Prestegard, J. H. J. Magn. Reson. 1997, 128, 138-143.
29. Boisbouvier, J.; Gans, P.; Blackledge, M.; Brutscher, B.; Marion, D. J. Am. Chem. Soc. 1999, 121, 7700-7701.
30. Pintacuda, G.; Moshref, A.; Leonchiks, A.; Sharipo, A.; Otting, G. J. Biomol. NMR 2004, 29, 351-361.
31. Donaldson, L. W.; Skrynnikov, N. R.; Choy, W. Y.; Muhandiram, D. R.; Sarkar, B.; Forman-Kay, J. D.; Kay, L. E. J. Am. Chem. Soc. 2001, 123, 9843-9847.
32. Mal, T. K.; Ikura, M.; Kay, L. E. J. Am. Chem. Soc. 2002, 124, 14002-14003.
33. Iwahara, J.; Anderson, D. E.; Murphy, E. C.; Clore, G. M. J. Am. Chem. Soc. 2003, 125, 6634-6635.
34. Iwahara, J.; Schwieters, C. D.; Clore, G. M. J. Am. Chem. Soc. 2004, 126, 5879-5896.
35. Schmitz, C.; John, M.; Park, A. Y.; Dixon, N. E.; Pintacuda, G.; Otting, G.; Huber, T. J. Biomol. NMR 2006. in press.
36. Clore, G. M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9021-9025.
37. Dosset, P.; Hus, J. C.; Marion, D.; Blackledge, M. J. Biomol. NMR 2001, 20, 223-231.
38. Clore, G. M.; Schwieters, C. D. J. Am. Chem. Soc. 2003, 125, 2902-2912.
39. Dvoretsky, A.; Gaponenko, V.; Rosevear, P. R. FEBS Lett. 2002, 528, 189-192.
40. Gaponenko, V.; Altieri, A. S.; Li, J.; Byrd, R. A. J. Biomol. NMR 2002, 24, 143-148.
41. Gaponenko, V.; Sarma, S. P.; Altieri, A. S.; Horita, D. A.; Li, J.; Byrd, R. A. J. Biomol. NMR 2004, 2004, 28, 205-212.
42. Ikegami, T.; Verdier, L.; Sakhaii, P.; Grimme, S.; Pescatore, B.; Saxena, K.; Fiebig, K. M.; Griesinger, C. J. Biomol. NMR 2004, 29, 339-349.
43. Prudêncio, M.; Rohovec, J.; Peters, J. A.; Tocheva, E.; Boulanger, M. J.; Murphy, M. E.; Hupkes, H. J.; Kosters, W.; Impagliazzo, A.; Ubbink, M. Chem.-Eur. J. 2004, 10, 3252-3260.
44. Leonov, A.; Voigt, B.; Rodriguez-Castaneda, F.; Sakhaii, P.; Griesinger, C. Chem.-Eur. J. 2005, 11, 3342-3348.
45. Ma, C.; Opella, S. J. J. Magn. Reson. 2000, 146, 381-384.
46. Wöhnert, J.; Franz, K. J.; Nitz, M.; Imperiali, B.; Schwalbe, H. J. Am. Chem. Soc. 2003, 125, 13338-13339.
47. Bertini, I.; Janik, M. B. L.; Lee, Y. M.; Luchinat, C.; Rosato, A. J. Am. Chem. Soc. 2001, 123, 4181-4188.
48. Ramirez, B. E.; Bax, A. J. Am. Chem. Soc. 1998, 120, 9106-9107.
49. Studwell-Vaughan, P. S.; O'Donnell, M. J. Biol. Chem. 1993, 268, 11785-11791.
50. Taft-Benz, S. A.; Schaaper, R. M. J. Bacteriol. 2004, 186, 2774-2780.
51. Breyer, W. A.; Matthews, B. W. Nat. Struct. Biol. 2000, 7, 1125-1128.
52. Koradi, R.; Billeter, M.; Wüthrich, K. J. Mol. Graphics 1996, 14, 51-55.
53. Mueller, G. A.; Kirby, T. W.; DeRose, E. F.; Li, D.; Schaaper, R. M.; London, R. E. J. Bacteriol. 2005, 187, 7081-7089.