Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of α/β proteins

Journal of the American Chemical Society

Volumn 128, Issue 15, 2006, Pages 5168-5176

  Zong, Chenghang ^a   Papoian, Garegin A ^b   Ulander, Johan ^c   Wolynes, Peter G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of North Carolina at Chapel Hill   (United States)

^c ASTRAZENECA R AND D   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANNEALING; COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; MORPHOLOGY; SURFACE ROUGHNESS; WATER;

PROTEIN ENERGY LANDSCAPES; PROTEIN MORPHOLOGY; SECONDARY STRUCTURES;

PROTEINS;

BETA PROTEIN; PROTEIN; UNCLASSIFIED DRUG; WATER;

ANALYTICAL PARAMETERS; ARTICLE; BETA SHEET; COMPUTER SIMULATION; ENERGY; MODEL; MOLECULAR INTERACTION; NONADDITIVE INTERACTION; PREDICTION; PROTEIN FOLDING; PROTEIN POLYMORPHISM; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; TOPOLOGY;

PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS; WATER;

EID: 33646161965     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja058589v     Document Type: Article

References (22)

1. Schueler-Furman, O.; Wang, C.; Bradley, P.; Misura, K.; Baker, D. Science 2005, 310, 638.
2. Chivian, D. et al. Proteins: Structure, Function, and Bioinformatics 2005, 61, 157.
3. Fujitsuka, Y.; Takada, G. C. S. Proteins: Structure, Function, and Bioinformatics 2006, 62, 381.
4. Guo, C.; Levine, H.; Kessler, P. PRL 2000, 84, 3490.
5. Papoian, G. A.; Ulander, J.; Eastwood, M. P.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3352.
6. Friedrichs, M. S.; Wolynes, P. G. Science 1989, 246, 371.
7. Hardin, C.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14235.
8. Hardin, C.; Eastwood, M. P.; Premiss, M. C.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679.
9. Kimura, T. et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2748.
10. Munoz, V.; Thompson, P.; Hofrichter, J.; Eaton, W. Nature 1997, 390, 196.
11. de la Cruz, X.; Hutchinson, E.; Shepherd, A.; Thornton, J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11157.
12. Takagi, F.; Koga, N.; Takada, S. Proc. Natl. Acad. Sci. U.S.A. 2003, 14, 892.
13. Chikenji, G.; Fujitsuka, Y.; Takada, S. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 3145.
14. Wu, Y.; Chen, M.; Lu, M.; Wang, Q.; Ma, J. J. Mol. Biol. 2005, 350, 571.
15. Eastwood, M. P.; Hardin, C.; Luthey-Schulten, Z.; Wolynes, P. G. IBM J. Res. Dev. 2001, 45, 475.
16. Cuff, A. J.; Clamp, E. M.; Siddiqui, S. A.; Finlay, M.; Barton, G. J. Bioinformatics 1998, 14, 892.
17. Zemla, A. Nucleic Acids Research 2003, 31, 3370.
18. Chahine, J.; Nymeyer, H.; Socci, V. L. N.; Onuchic, J. PRL 2002, 88, 168101.
19. Luthey-Schulten, Z.; Ramirez, B. E.; Wolynes, P. G. J. Phys. Chem. 1995, 99, 2177.
20. Goldstein, R. A.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4918.
21. Shindyalov, I.; Bourne, P. Protein Eng. 1998, 11, 739.
22. Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 6170.