Recent successes of the energy landscape theory of protein folding and function

Quarterly Reviews of Biophysics

Volumn 38, Issue 4, 2005, Pages 405-410

  Wolynes, P G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; BINDING AFFINITY; CONFERENCE PAPER; ENERGY; HYDROPHILICITY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION;

ALGORITHMS; BIOPHYSICS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN FOLDING; THERMODYNAMICS;

EID: 33748557507     PISSN: 00335835     EISSN: 14698994     Source Type: Journal    
DOI: 10.1017/S0033583505004075     Document Type: Conference Paper

References (22)

1. EASTWOOD, M. & WOLYNES, P. G. (2001). Role of explicitly cooperative interactions in protein folding funnels: a simulation study. Journal of Chemical Physics 114, 4702-4716.
2. EJTEHADI, M. R., AVALL, S. P. & PLOTKIN, S. S. (2004). Three body interactions improve the prediction of rate and mechanisms in protein folding models. Proceedings of the National Academy of Sciences USA 101, 15088-15093.
3. HARDIN, C., LUTHEY-SCHULTEN, Z. & WOLYNES, P. G. (1999). Backbone dynamics, fast folding and secondary structure formation in helical proteins and peptides. Proteins : Structure, Function and Genetics 34, 281-294.
4. KOGA, N. & TAKADA, S. (2001). Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gó-like model. Journal of Molecular Biology 313, 171-180.
5. LEVY, Y., CHO, S. S., SHEN, T., ONUCHIC, J. N. & WOLYNES, P. G. (2005). Symmetry and frustration in protein energy landscapes: a near-degeneracy resolves the ROP dimer folding mystery. Proceedings of the National Academy of Sciences USA 102, 2373-2378.
6. MA, H. R. & GRUEBELE, M. (2005). Kinetisase probe dependent during downhill folding of an engineered lambda (6-85) protein. Proceedings of the National Academy of Sciences USA 102, 2283-2287.
7. MUNSON, M., ANDERSON, K. S. & REGAN, L. (1997). Speeding up protein folding: mutation that increase the rate at which ROP folds and unfolds by four orders of magnitude. Folding & Design 2, 77-87.
8. OLIVEBERG, M. & WOLYNES, P. G. (in press). The experimental survey of protein folding energy landscapes. Quarterly Reviews of Biophysics.
9. ONUCHIC, J. N., LUTHEY-SCHULTEN, Z. & WOLYNES, P. G. (1997). Theory of protein folding: the energy landscape perspective. Annual Review of Physical Chemistry 48, 545-600.
10. PAPOIAN, G. A., ULANDER, J., EASTWOOD, M. P., LUTHEY-SCHULTEN, Z. & WOLYNES, P. G. (2004). Water in protein structure prediction. Proceedings of the National Academy of Sciences USA 101, 3352-3357.
11. PAPOIAN, G. A., ULANDER, J. & WOLYNES, P. G. (2003). The role of water mediated interactions in proteinprotein recognition landscapes. Journal of the American Chemical Society 125, 9170-9178.
12. PLOTKIN, S. S. & ONUCHIC, J. N. (2002a). Understanding protein folding with energy landscape theory. Part I : Basic concepts. Quarterly Reviews of Biophysics 35, 111-167.
13. PLOTKIN, S. S. & ONUCHIC, J. N. (2002b). Understanding protein folding with energy landscape theory. Part II : Quantitative aspects. Quarterly Reviews of Biophysics 35, 205-286.
14. PLOTKIN, S. S. & WOLYNES, P. G. (2003). Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding. Proceedings of the National Academy of Sciences USA 100, 4417-4422.
15. PORTMAN, J. J., TAKADA, S. & WOLYNES, P. G. (1998). Variational theory for site resolved protein folding free energy surfaces. Physical Review Letters 81, 5237-5240.
16. PORTMAN, J. J., TAKADA, S. & WOLYNES, P. G. (2001). Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach. Journal of Chemical Physics 114, 5069-5081.
17. RUMBLEY, J., HOANG, L., MAYNE, L. & ENGLANDER, S. W. (2005). An amino acid code for protein folding. Proceedings of the National Academy of Sciences USA 98, 105-112.
18. SHEN, T., HOFFMAN, C. P., OLIVEBERG, M. & WOLYNES, P. G. (2005). Scanning malleable transition state ensembles : coupling theory and experiment for folding protein U1A. Biochemistry 44, 6433-6439.
19. SHOEMAKER, B. A., PORTMAN, J. J. & WOLYNES, P. G. (2000). Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proceedings of the National Academy of Sciences USA 97, 8868-8873.
20. SHOEMAKER, B. A., WANG, J. & WOLYNES, P. G. (1997). Structural correlations in protein folding funnels. Proceedings of the National Academy of Sciences USA 94, 777-782.
21. TAKETOMI, A., UEDA, Y. & GO, N. (1975). Studies on protein folding, unfolding and fluctuations by computer simulations 1. The effect of specific amino acid sequence represented by specific inter-unit interactions. International Journal of Peptide and Protein Research 7, 445-459.
22. WEINKAM, P., ZONG, C. & WOLYNES, P. (2005). A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proceedings of the National Academy of Sciences USA 102, 12401-12406.