Natural-like function in artificial WW domains

Nature

Volumn 437, Issue 7058, 2005, Pages 579-583

  Russ, William P ^a   Lowery, Drew M ^b   Mishra, Prashant ^a   Yaffe, Michael B ^b   Ranganathan, Rama ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; MOLECULAR STRUCTURE; MUTAGENESIS; POLYPEPTIDES;

PEPTIDES; PROTEIN SEQUENCES; TERTIARY STRUCTURES;

PROTEINS;

AMINO ACID; PEPTIDE; PROLINE; PROTEIN; PEPTIDE FRAGMENT; PEPTIDE LIBRARY; RECOMBINANT PROTEIN;

BIOLOGY;

AMINO ACID SEQUENCE; ARTICLE; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN TARGETING; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; THERMODYNAMICS;

AMINO ACID SEQUENCE; BINDING SITES; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PEPTIDE LIBRARY; PROLINE; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 25644442464     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature03990     Document Type: Article

References (30)

1. Voigt, C. A., Kauffman, S. & Wang, Z. G. Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem. 55, 79-160 (2000).
2. Socolich, M. et al. Evolutionary information for specifying a protein fold. Nature doi:10.1038/nature03991 (this issue).
3. Lockless, S. W. & Ranganathan, R. Evolutionary conserved pathways of energetic connectivity in protein families. Science 286, 295-299 (1999).
4. Suel, G. M., Lockless, S. W., Wall, M. A. & Ranganathan, R. Evolutionary conserved networks of residues mediate allosteric communication in proteins. Nature Struct. Biol. 10, 59-69 (2003).
5. Bedford, M. T., Sarbassova, D., Xu, J., Leder, P. & Yaffe, M. B. A novel pro-Arg motif recognized by WW domains. J. Biol. Chem. 275, 10359-10369 (2000).
6. Chen, H. I. & Sudol, M. The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules. Proc. Natl Acad. Sci. USA 92, 7819-7823 (1995).
7. Ermekova, K. S. et al. The WW domain of neural protein FE65 interacts with proline-rich motifs in Mena, the mammalian homolog of Drosophila enabled. J. Biol. Chem. 272, 32869-32877 (1997).
8. Lu, P. J., Zhou, X. Z., Shen, M. & Lu, K. P. Function of WW domains as phosphoserine- or phosphothreonine-binding modules. Science 283, 1325-1328 (1999).
9. Zarrinpar, A. & Lim, W. A. Converging on proline: the mechanism of WW domain peptide recognition. Nature Struct. Biol. 7, 611-613 (2000).
10. Kanelis, V., Rotin, D. & Forman-Kay, J. D. Solution structure of a Nedd4 WW domain-ENaC peptide complex. Nature Struct. Biol. 8, 407-412 (2001).
11. Verdecia, M. A., Bowman, M. E., Lu, K. P., Hunter, T. & Noel, J. P. Structural basis for phosphoserine-proline recognition by group IV WW domains. Nature Struct. Biol. 7, 639-643 (2000).
12. Kato, Y. et al. Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification. J. Biol. Chem. 279, 31833-31841 (2004).
13. Hu, H. et al. A map of WW domain family interactions. Proteomics 4, 643-655 (2004).
14. Otte, L. et al. WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains. Protein Sci. 12, 491-500 (2003).
15. Chen, H. I. et al. Characterization of the WW domain of human yes-associated protein and its polyproline-containing ligands. J. Biol. Chem. 272, 17070-17077 (1997).
16. Espanel, X. & Sudol, M. A single point mutation in a group I WW domain shifts its specificity to that of group II WW domains. J. Biol. Chem. 274, 17284-17289 (1999).
17. Kasanov, J., Pirozzi, G., Uveges, A. J. & Kay, B. K. Characterizing Class I WW domains defines key specificity determinants and generates mutant domains with novel specificities. Chem. Biol. 8, 231-241 (2001).
18. Toepert, F., Pires, J. R., Landgraf, C., Oschkinat, H. & Schneider-Mergener, J. Synthesis of an array comprising 837 variants of the hYAP WW protein domain. Angew. Chem. Int. Edn Engl. 40, 897-900 (2001).
19. Huang, X. et al. Structure of a WW domain containing fragment of dystrophin in complex with β-dystroglycan. Nature Struct. Biol. 7, 634-638 (2000).
20. Carter, P. J., Winter, G., Wilkinson, A. J. & Fersht, A. R. The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell 38, 835-840 (1984).
21. + channel pore through mutant cycles with a peptide inhibitor. Science 268, 307-310 (1995).
22. Dahiyat, B. I. & Mayo, S. L. De novo protein design: fully automated sequence selection. Science 278, 82-87 (1997).
23. Dwyer, M. A., Looger, L. L. & Hellinga, H. W. Computational design of a biologically active enzyme. Science 304, 1967-1971 (2004).
24. Kortemme, T. et al. Computational redesign of protein-protein interaction specificity. Nature Struct. Mol. Biol. 11, 371-379 (2004).
25. Kraemer-Pecore, C. M., Lecomte, J. T. & Desjarlais, J. R. A de novo redesign of the WW domain. Protein Sci. 12, 2194-2205 (2003).
26. Harbury, P. B., Plecs, J. J., Tidor, B., Alber, T. & Kim, P. S. High-resolution protein design with backbone freedom. Science 282, 1462-1467 (1998).
27. Kuhlman, B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364-1368 (2003).
28. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
29. Ferguson, N., Johnson, C. M., Macias, M., Oschkinat, H. & Fersht, A. Ultrafast folding of WW domains without structured aromatic clusters in the denatured state. Proc. Natl Acad. Sci. USA 98, 13002-13007 (2001).
30. Delano, W. L. The PyMOL Molecular Graphics System 〈http://www.pymol. org〉 (2002).