Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

Science

Volumn 320, Issue 5882, 2008, Pages 1471-1475

  Lange, Oliver F ^a   Lakomek, Nils Alexander ^a   Farès, Christophe ^a   Schröder, Gunnar F ^a   Walter, Korvin F A ^a   Becker, Stefan ^a   Meiler, Jens ^b   Grubmüller, Helmut ^a   Griesinger, Christian ^a   De Groot, Bert L ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT; UBIQUITIN;

CRYSTAL STRUCTURE; ENTROPY; HETEROGENEITY; PROTEIN; RECOGNITION;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; ENTROPY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; RESIDUAL DIPOLAR COUPLING; TIME; ANIMAL; ANISOTROPY; CHEMICAL STRUCTURE; CHEMISTRY; KINETICS; METABOLISM; NUCLEAR MAGNETIC RESONANCE; PHYSICAL CHEMISTRY; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SOLUTION AND SOLUBILITY; X RAY CRYSTALLOGRAPHY; XENOPUS LAEVIS;

AMINO ACID MOTIFS; ANIMALS; ANISOTROPY; CHEMISTRY, PHYSICAL; CRYSTALLOGRAPHY, X-RAY; ENTROPY; KINETICS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SOLUTIONS; UBIQUITIN; XENOPUS LAEVIS;

EID: 45849131354     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1157092     Document Type: Article

References (47)

1. C. Kolano, J. Helbing, M. Kozinski, W. Sander, P. Hamm, Nature 444, 469 (2006).
2. H. Frauenfelder, P. G. Wolynes, Science 229, 337 (1985).
3. A. Mittermaier, L. E. Kay, Science 312, 224 (2006).
4. L. E. Kay, D. A. Torchia, A. Bax, Biochemistry 28, 8972 (1989).
5. M. Akke, A. Palmer, J. Am. Chem. Soc. 118, 911 (1996).
6. L. Wang et al., Proc. Natl. Acad. Sci. U.S.A. 98, 7684 (2001).
7. G. Lipari, A. Szabo, J. Am. Chem. Soc. 104, 4546 (1982).
8. K. A. Henzler-Wildman et al., Nature 450, 913 (2007).
9. D. D. Boehr, D. McElheny, H. J. Dyson, P. E. Wright, Science 313, 1638 (2006).
10. K. Lindorff-Larsen, R. B. Best, M. A. DePristo, C. M. Dobson, M. Vendruscolo, Nature 433, 128 (2005).
11. B. Richter, J. Gsponer, P. Varnai, X. Salvatella, M. Vendruscolo, J. Biomol. NMR 37, 117 (2007).
12. M. Akke, R. Bruschweiler, A. G. Palmer, J. Am. Chem. Soc. 115, 9832 (1993).
13. D. Yang, Y.-K. Mok, J. D. Forman-Kay, N. A. Farrow, L. E. Kay, J. Mol. Biol. 272, 790 (1997).
14. K. K. Frederick, M. S. Marlow, K. G. Valentine, A. J. Wand, Nature 448, 325 (2007).
15. C. S. Goh, D. Milburn, M. Gerstein, Curr. Opin. Struct. Biol. 14, 104 (2004).
16. R. Grunberg, J. Leckner, M. Nilges, Structure 12, 2125 (2004).
17. J. R. Tolman, J. M. Flanagan, M. A. Kennedy, J. H. Prestegard, Proc. Natl. Acad. Sci. U.S.A. 92, 9279 (1995).
18. J. R. Tolman, J. Am. Chem. Soc. 124, 12020 (2002).
19. N. A. Lakomek et al., Angew. Chem. Int. Ed. 44, 7776 (2005).
20. G. Bouvignies et al., Proc. Natl. Acad. Sci. U.S.A. 102, 13885 (2005).
21. N. A. Lakomek, T. Carlomagno, S. Becker, C. Griesinger, J. Meiler, J. Biomol. NMR 34, 101 (2006).
22. G. Bouvignies, P. Markwick, R. Bruscheweiler, M. Blackledge, J. Am. Chem. Soc. 128, 15100 (2006).
23. P. R. L. Markwick, G. Bouvignies, M. Blackledge, J. Am. Chem. Soc. 129, 4724 (2007).
24. J. Meiler, J. J. Prompers, W. Peti, C. Griesinger, R. Bruschweiler, J. Am. Chem. Soc. 123, 6098 (2001).
25. W. Peti, J. Meiler, R. Bruschweiler, C. Griesinger, J. Am. Chem. Soc. 124, 5822 (2002).
26. L. Hicke, H. L. Schubert, C. P. Hill, Nat. Rev. Mol. Cell Biol. 6, 610 (2005).
27. J. W. Harper, B. A. Schulman, Cell 124, 1133 (2006).
28. P. S. Brzovic, R. E. Klevit, Cell Cycle 5, 2867 (2006).
29. N. Tjandra, A. Bax, Science 278, 1111 (1997).
30. K. B. Briggman, J. R. Tolman, J. Am. Chem. Soc. 125, 10164 (2003).
31. K. Ruan, J. R. Tolman, J. Am. Chem. Soc. 127, 15032 (2005).
32. M. Ottiger, A. Bax, J. Am. Chem. Soc. 120, 12334 (1998).
33. See supporting material on Science Online.
34. F. Massi, M. J. Grey, A. G. Palmer, Protein Sci. 14, 735 (2005).
35. R. B. Best, K. Lindorff-Larsen, M. A. DePristo, M. Vendruscolo, Proc. Natl. Acad. Sci. U.S.A. 103, 10901 (2006).
36. S. L. Chang, N. Tjandra, J. Magn. Reson. 174, 43 (2005).
37. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
38. T. Clackson, J. A. Wells, Science 267, 383 (1995).
39. C. Kiel, L. Serrano, J. Mol. Biol. 355, 821 (2006).
40. L. Penengo et al., Cell 124, 1183 (2006).
41. C. W. Bertoncini et al., Proc. Natl. Acad. Sci. U.S.A. 102, 1430 (2005).
42. E. Z. Eisenmesser et al., Nature 438, 117 (2005).
43. C. Tang, C. D. Schwieters, G. M. Clore, Nature 449, 1078 (2007).
44. L. C. James, P. Roversi, D. S. Tawfik, Science 299, 1362 (2003).
45. K. Sugase, H. J. Dyson, P. E. Wright, Nature 447, 1021 (2007).
46. N. Tjandra, S. E. Feller, R. W. Pastor, A. Bax, J. Am. Chem. Soc. 117, 12562 (1995).
47. We thank A. Munk for suggesting a scaling method for the SCRM order parameters; F. Mulder, A. Bonvin, and N. Tjandra for discussion of the overall scaling of Lipari-Szabo order parameters; K. Giller for the preparation of numerous labeled ubiquitin samples; and A. Mark, K. Riebeseel, E. d'Auvergne, L. Joachimiak, and M. Tyka for carefully reading the manuscript and fruitful discussions. This work was supported by the Max Planck Society (to H.G., C.G., and B.L.dG.), the Fonds der Chemischen Industrie (to C.G.), the German Israel Foundation (to C.G.), the Human Frontier Science Program (to O.F.L.), and the Volkswagen Foundation (to O.F.L.). Coordinates and RDCs have been deposited in the PDB (www.rcsb.org) with the accession number 2k39.