Targeting metastable coiled-coil domains by computational design

Journal of the American Chemical Society

Volumn 130, Issue 36, 2008, Pages 12038-12044

  Barth, Patrick ^a,b   Schoeffler, Allyn ^a   Alber, Tom ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; CENTRIFUGATION; COMPUTATIONAL METHODS; DICHROISM; INTEGRAL EQUATIONS; OPTICAL PROPERTIES; STABILITY; STRUCTURAL DESIGN;

COILED-COIL DOMAINS; COMPUTATIONAL DESIGN; PEPTIDE INHIBITORS;

STRUCTURAL OPTIMIZATION;

SEPTIN;

ARTICLE; BINDING AFFINITY; CALCULATION; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; GENOME; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; ULTRACENTRIFUGATION;

CELL CYCLE PROTEINS; CYTOSKELETAL PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE PROTEINS; THERMODYNAMICS;

EID: 51749124224     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja802447e     Document Type: Article

References (38)

1. Wolf, E.; Kim, P. S.; Berger, B. Protein Sci. 1997, 6, 1179-1189.
2. O'Shea, E. K.; Klemm, J. D.; Kim, P. S.; Alber, T. Science 1991, 254, 539-544.
3. Sharma, V. A.; Logan, J.; King, D. S.; White, R.; Alber, T. Curr. Biol. 1998, 8, 823-830.
4. Arndt, K. M.; Pelletier, J. N.; Muller, K. M.; Alber, T.; Michnick, S. W.; Pluckthun, A. J. Mol. Biol. 2000, 295, 627-639.
5. Harbury, P. B.; Zhang, T.; Kim, P. S.; Alber, T. Science 1993, 262, 1401-1407.
6. Gonzalez, L., Jr.; Plecs, J. J.; Alber, T. Nat. Struct. Biol. 1996, 3, 510-515.
7. Zhou, N. E.; Zhu, B. Y.; Kay, C. M.; Hodges, R. S. Biopolymers 1992, 32, 419-426.
8. Harbury, P. B.; Plecs, J. J.; Tidor, B.; Alber, T.; Kim, P. S. Science 1998, 282, 1462-1467.
9. Keating, A. E.; Malashkevich, V. N.; Tidor, B.; Kim, P. S. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14825-14830.
10. Havranek, J. J.; Harbury, P. B. Nat. Struct. Biol. 2003, 10, 45-52.
11. Grigoryan, G.; Keating, A. E. J. Mol. Biol. 2006, 355, 1125-1142.
12. Pandya, M. J.; Spooner, G. M.; Sunde, M.; Thorpe, J. R.; Rodger, A.; Woolfson, D. N. Biochemistry 2000, 39, 8728-8734.
13. Papapostolou, D.; Smith, A. M.; Atkins, E. D.; Oliver, S. J.; Ryadnov, M. G.; Serpell, L. C.; Woolfson, D. N. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 10853-10858.
14. Li, Y.; Brown, J. H.; Reshetnikova, L.; Blazsek, A.; Farkas, L.; Nyitray, L.; Cohen, C. Nature 2003, 424, 341-345.
15. Shimizu, T.; Ihara, K.; Maesaki, R.; Amano, M.; Kaibuchi, K.; Hakoshima, T. J. Biol. Chem. 2003, 278, 46046-46051.
16. Hicks, M. R.; Holberton, D. V.; Kowalczyk, C.; Woolfson, D. N. Fold Des. 1997, 2, 149-158.
17. Hicks, M. R.; Walshaw, J.; Woolfson, D. N. J. Struct. Biol. 2002, 137, 73-81.
18. Dyson, H. J.; Wright, P. E. Nat. Rev. Mol. Cell. Biol. 2005, 6, 197-208.
19. Haynes, C.; Oldfield, C. J.; Ji, F.; Klitgord, N.; Cusick, M. E.; Radivojac, P.; Uversky, V. N.; Vidal, M.; Iakoucheva, L. M. PLoS Comput. Biol. 2006, 2, e100.
20. Shifman, J. M.; Mayo, S. L. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13274-13279,
21. Kortemme, T.; Joachimiak, L. A.; Bullock, A. N.; Schuler, A. D.; Stoddard, B. L.; Baker, D. Nat. Struct. Mol. Biol. 2004, 11, 371-379.
22. Weirich, C. S.; Erzberger, J. P.; Barral, Y. Nat. Rev. Mol. Cell. Biol. 2008, 9 (6), 478-489.
23. Harbury, P. B.; Tidor, B.; Kim, P. S. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 8408-8412.
24. Koehl, P.; Delarue, M. J. Mol. Biol. 1994, 239, 249-275.
25. Jorgensen, W. L.; Tiradorives, J. J. Am. Chem. Soc. 1988, 110, 1666-1671.
26. Havranek, J. J.; Harbury, P. B. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11145-11150.
27. Lacroix, E.; Viguera, A. R.; Serrano, L. J. Mol. Biol. 1998, 284, 173- 191.
28. Lovell, S. C.; Word, J. M.; Richardson, J. S.; Richardson, D. C. Proteins 2000, 40, 389-408.
29. Barth, P.; Alber, T.; Harbury, P. B. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4898-4903.
30. Edelhoch, H. Biochemistry 1967, 6, 1948-1954.
31. Woolfson, D. N. Adv. Protein Chem. 2005, 70, 79-112.
32. Versele, M.; Gullbrand, B.; Shulewitz, M. J.; Cid, V. J.; Bahmanyar, S.; Chen, R. E.; Barth, P.; Alber, T.; Thorner, J. Mol. Biol. Cell 2004, 15, 4568-4583.
33. Mason, J. M.; Schmitz, M. A.; Muller, K. M.; Arndt, K. M. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 8989-8994.
34. Mason, J. M.; Muller, K. M.; Arndt, K. M. Biochemistry 2007, 46, 4804-4814.
35. Schueler-Furman, O.; Wang, C.; Bradley, P.; Misura, K.; Baker, D. Science 2005, 310, 638-642.
36. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Science 2003, 302, 1364-1368.
37. Bertin, A.; McMurray, M. A.; Grob, P.; Park, S.-S.; Garcia, G.; Patanwala, I.; Ng, H.-L.; Alber, T.; Thorner, J.; Nogales, E. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8274-8279.
38. Sirajuddin, M.; Farkasovsky, M.; Hauer, F.; Kuhlmann, D.; Macara, I. G.; Weyand, M.; Stark, H.; Wittinghofer, A. Nature 2007, 449, 311-315.