Domain-swapped dimeric structure of a stable and functional de Novo Four-Helix bundle protein, WA20

Journal of Physical Chemistry B

Volumn 116, Issue 23, 2012, Pages 6789-6797

  Arai, Ryoichi ^a,b   Kobayashi, Naoya ^a   Kimura, Akiho ^a,d   Sato, Takaaki ^a   Matsuo, Kyoko ^a   Wang, Anna F ^b,f   Platt, Jesse M ^b,e   Bradley, Luke H ^b,c   Hecht, Michael H ^b  

^a SHINSHU UNIVERSITY   (Japan)

^b PRINCETON UNIVERSITY   (United States)

^c UNIVERSITY OF KENTUCKY   (United States)

^d Kaigen Pharma Co Ltd   (Japan)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

^f HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GENES; MONOMERS; PROTEINS;

AMINO ACID SEQUENCE; COMBINATORIAL LIBRARY; DIMERIC STRUCTURE; HELICAL BUNDLE; HYDROPHOBIC POCKETS; MONOMERIC PROTEINS; MULTIMERIC; MULTIWAVELENGTH ANOMALOUS DISPERSIONS; NON-POLAR; NOVO PROTEINS; SMALL ANGLE X-RAY SCATTERING; SUBSTRATE-BINDING SITES; SYNTHETIC GENES; THIRD GENERATION;

DIMERS;

EID: 84862297294     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp212438h     Document Type: Article

References (49)

1. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82-87
2. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Science 2003, 302, 1364-1368
3. Keefe, A. D.; Szostak, J. W. Nature 2001, 410, 715-718
4. Kamtekar, S.; Schiffer, J. M.; Xiong, H.; Babik, J. M.; Hecht, M. H. Science 1993, 262, 1680-1685
5. Hecht, M. H.; Das, A.; Go, A.; Bradley, L. H.; Wei, Y. Protein Sci. 2004, 13, 1711-1723
6. Bradley, L. H.; Kleiner, R. E.; Wang, A. F.; Hecht, M. H.; Wood, D. W. Protein Eng., Des. Sel. 2005, 18, 201-207
7. Wei, Y.; Liu, T.; Sazinsky, S. L.; Moffet, D. A.; Pelczer, I.; Hecht, M. H. Protein Sci. 2003, 12, 92-102
8. West, M. W.; Wang, W.; Patterson, J.; Mancias, J. D.; Beasley, J. R.; Hecht, M. H. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11211-11216
9. Roy, S.; Hecht, M. H. Biochemistry 2000, 39, 4603-4607
10. Wei, Y.; Kim, S.; Fela, D.; Baum, J.; Hecht, M. H. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13270-13273
11. Go, A.; Kim, S.; Baum, J.; Hecht, M. H. Protein Sci. 2008, 17, 821-832
12. Patel, S. C.; Bradley, L. H.; Jinadasa, S. P.; Hecht, M. H. Protein Sci. 2009, 18, 1388-1400
13. Fisher, M. A.; McKinley, K. L.; Bradley, L. H.; Viola, S. R.; Hecht, M. H. PLoS One 2011, 6, e15364
14. Wang, A. F. Senior Thesis, Princeton University, NJ, 2006.
15. Platt, J. M. Senior Thesis, Princeton University, NJ, 2007.
16. Hendrickson, W. A. Science 1991, 254, 51-58
17. LeMaster, D. M.; Richards, F. M. Biochemistry 1985, 24, 7263-7268
18. Johnson, B. H.; Hecht, M. H. Bio/Technology 1994, 12, 1357-1360
19. Otwinowski, Z.; Minor, W. Methods Enzymol. 1997, 276, 307-326
20. Terwilliger, T. C.; Berendzen, J. Acta Crystallogr., Sect. D 1999, 55, 849-861
21. Terwilliger, T. C. Acta Crystallogr., Sect. D 2002, 58, 1937-1940
22. Emsley, P.; Lohkamp, B.; Scott, W. G.; Cowtan, K. Acta Crystallogr., Sect. D 2010, 66, 486-501
23. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallogr., Sect. D 1997, 53, 240-255
24. Murshudov, G. N.; Skubak, P.; Lebedev, A. A.; Pannu, N. S.; Steiner, R. A.; Nicholls, R. A.; Winn, M. D.; Long, F.; Vagin, A. A. Acta Crystallogr., Sect. D 2011, 67, 355-367
25. Collaborative Computational Project, Acta Crystallogr., Sect. D 1994, 50, 760-763.
26. Laskowski, R. A.; Macarthur, M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283-291
27. Chen, V. B.; Arendall, W. B., 3rd; Headd, J. J.; Keedy, D. A.; Immormino, R. M.; Kapral, G. J.; Murray, L. W.; Richardson, J. S.; Richardson, D. C. Acta Crystallogr., Sect. D 2010, 66, 12-21
28. Davis, I. W.; Leaver-Fay, A.; Chen, V. B.; Block, J. N.; Kapral, G. J.; Wang, X.; Murray, L. W.; Arendall, W. B., 3rd; Snoeyink, J.; Richardson, J. S.; Richardson, D. C. Nucleic Acids Res. 2007, 35, W375-383
29. Lovell, S. C.; Davis, I. W.; Arendall, W. B., 3rd; de Bakker, P. I.; Word, J. M.; Prisant, M. G.; Richardson, J. S.; Richardson, D. C. Proteins 2003, 50, 437-450
30. Orthaber, D.; Bergmann, A.; Glatter, O. J. Appl. Crystallogr. 2000, 33, 218-225
31. Glatter, O. Acta Phys. Austriaca 1980, 52, 243-256
32. Glatter, O. J. Appl. Crystallogr. 1980, 13, 577-584
33. Glatter, O.; Kratky, O. Small-Angle X-Ray Scattering; Academic Press: New York, 1982.
34. Vedadi, M.; Niesen, F. H.; Allali-Hassani, A.; Fedorov, O. Y.; Finerty, P. J., Jr.; Wasney, G. A.; Yeung, R.; Arrowsmith, C.; Ball, L. J.; Berglund, H.; Hui, R.; Marsden, B. D.; Nordlund, P.; Sundstrom, M.; Weigelt, J.; Edwards, A. M. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 15835-15840
35. Niesen, F. H.; Berglund, H.; Vedadi, M. Nat. Protoc. 2007, 2, 2212-2221
36. Harding, M. M. Acta Crystallogr., Sect. D 2002, 58, 872-874
37. Bennett, M. J.; Choe, S.; Eisenberg, D. Protein Sci. 1994, 3, 1444-1463
38. Liu, Y.; Eisenberg, D. Protein Sci. 2002, 11, 1285-1299
39. Mason, J. M.; Arndt, K. M. ChemBioChem 2004, 5, 170-176
40. Crick, F. H. C. Acta Crystallogr. 1953, 6, 689-697
41. Lederer, F.; Glatigny, A.; Bethge, P. H.; Bellamy, H. D.; Matthew, F. S. J. Mol. Biol. 1981, 148, 427-448
42. Sato, T.; Shimozawa, T.; Fukasawa, T.; Ohtaki, M.; Aramaki, K.; Wakabayashi, K.; Ishiwata, S. Biophysics 2010, 6, 1-11
43. Reedy, C. J.; Gibney, B. R. Chem. Rev. 2004, 104, 617-649
44. Finzel, B. C.; Weber, P. C.; Hardman, K. D.; Salemme, F. R. J. Mol. Biol. 1985, 186, 627-643
45. Hendlich, M.; Rippmann, F.; Barnickel, G. J. Mol. Graphics Modell. 1997, 15, 359-363
46. Beneš, P.; Chovancová, E.; Kozlíková, B.; Pavelka, A.; Strnad, O.; Brezovský, J.; Šustr, V.; Klvaňa, M.; Szabó, T.; Gora, A.; Zamborský, M.; Biedermannová, L.; Medek, P.; Damborský, J.; Sochor, J. CAVER 2.1 Software; Masaryk University: Brno, Czech Republic, 2010.
47. Das, A.; Wei, Y.; Pelczer, I.; Hecht, M. H. Protein Sci. 2011, 20, 702-711
48. Fujinaga, M.; Cherney, M. M.; Oyama, H.; Oda, K.; James, M. N. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3364-3369
49. Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. Protein Eng. 1995, 8, 127-134