Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 7, 2005, Pages 2362-2367

  Liwo, Adam ^a,b   Khalili, Mey ^a   Scheraga, Harold A ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

^b UNIVERSITY OF GDA SK   (Poland)

Author keywords

Langevin dynamics; Mesoscopic models; Restricted free energy

Indexed keywords

POLYPEPTIDE;

AB INITIO CALCULATION; ALPHA HELIX; ARTICLE; ENERGY; ENTROPY; KINETICS; MOLECULAR DYNAMICS; MOLECULAR SIZE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; TECHNIQUE; THERMODYNAMICS;

BIOPHYSICS; COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; THERMODYNAMICS;

EID: 14044266389     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0408885102     Document Type: Article

References (44)

1. Scheraga, H. A., Liwo, A., Ołziej, S., Czaplewski, C., Pillardy, J., Ripoll, D. R., Vila, J. A., Kazmierkiewicz, R., Saunders, J. A., Arnautova, Y. A., et al. (2004) Front. Biosci. 9, 3296-3323.
2. Skolnick, J., Zhang, Y., Arakaki, A. K., Kolinski, A., Boniecki, M., Szilagyi, A. & Kihara, D. (2003) Proteins Struct. Funct. Genet. 53, Suppl. 6, 469-479.
3. Bradley, P., Chivian, D., Meiler, J., Misura, K. M. S., Rohl, C. A., Schief, W. R., Wedemeyer, W. J., Schueler-Furman, O., Murphy, P., Schonbrun, J., et al. (2003) Proteins Struct. Funct. Genet. 53, Suppl. 6, 457-468.
4. Day, R. & Daggett, V. (2003) Adv. Protein Chem. 66, 373-403.
5. Fersht, A. R. & Daggett, V. (2002) Cell 108, 573-582.
6. Kubelka, J., Hofrichter, J. & Eaton, W. A. (2004) Curr. Opin. Struct. Biol. 14, 76-88.
7. Shea, J.-E. & Brooks, C. L., III (2001) Annu. Rev. Phys. Chem. 52, 499-535.
8. Duan, Y. & Kollman, P. A. (1998) Science 282, 740-744.
9. Pande, V. S., Baker, I., Chapman, J., Elmer, S. P., Khaliq, S., Larson, S. M., Rhee, Y. M., Shirts, M. R., Snow, C. D., Sorin, E. J., et al. (2003) Biopolymers 68, 91-109.
10. Elber, R., Ghosh, A. & Cárdenas, A. (2002) Acc. Chem. Res. 35, 396-403.
11. Faradjian, A. K. & Elber, R. (2004) J. Chem. Phys. 120, 10880-10889.
12. Cramer, C. J. & Truhlar, D. G. (1999) Chem. Rev. (Washington, D.C.) 99, 2161-2200.
13. Jang, S., Kim, E., Shin, S. & Pak, Y. (2003) J. Am. Chem. Soc. 125, 14841-14846.
14. Veitshans, T., Klimov, D. & Thirumalai, D. (1996) Folding Des. 2, 1-22.
15. He, S. & Scheraga, H. A. (1998) J. Chem. Phys. 108, 271-286.
16. Cieplak, M., Hoang, T. X. & Robbins, M. O. (2002) Proteins Struct. Funct. Genet. 49, 104-113.
17. Sorenson, J. M & Head-Gordon, T. (2002) Proteins Struct. Funct. Genet. 46, 368-379.
18. Hardin, C., Eastwood, M. P., Prentiss, M., Luthey-Schulten, Z. & Wolynes, P. G. (2002) J. Comput. Chem. 23, 138-146.
19. Fujitsuka, Y., Takada, S., Luthey-Schulten, Z. A. & Wolynes, P. G. (2004) Proteins Struct. Funct. Genet. 54, 88-103.
20. Kolinski, A., Klein, P., Romiszowski, P. & Skolnick, J. (2003) Biophys. J. 85, 3271-3278.
21. Rudnicki, W. R., Bakalarski, G. & Lesyng, B. (2000) J. Biomol. Struct. Dyn. 17, 1097-1108.
22. Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S. & Scheraga, H. A. (1993) Protein Sci. 2, 1715-1731.
23. Liwo, A., Ołdziej, S., Pincus, M. R., Wawak, R. J., Rackovsky, S. & Scheraga, H. A. (1997) J. Comput. Chem. 18, 849-873.
24. Liwo, A., Ołdziej, S., Czaplewski, C., Kozłowska, U. & Scheraga, H. A. (2004) J. Phys. Chem. B 108, 9421-9438.
25. Ołdziej, S., Liwo, A., Czaplewski, C., Pillardy, J. & Scheraga, H. A. (2004) J. Phys. Chem. B 108, 16934-16949.
26. Ołdziej, S. Łagiewka, J., Liwo, A., Czaplewski, C., Chinchio, M., Nanias, M. & Scheraga, H. A. (2004) J. Phys. Chem. B. 108, 16950-16959.
27. Lee, J., Liwo, A., Ripoll, D. R., Pillardy, J. & Scheraga, H. A. (1999) Proteins Struct. Funct. Genet. 3, Suppl., 204-208.
28. Pillardy, J., Czaplewski, C., Liwo, A., Lee, J., Ripoll, D. R., Kazmierkiewicz, R., Oldziej, S., Wedemeyer, W. J., Gibson, K. D., Arnautova, Y. A., et al. (2001) Proc. Natl. Acad. Sci. USA 98, 2329-2333.
29. Maiorov, V. N. & Grippen, G. M. (1992) J. Mol. Biol. 227, 876-888.
30. Fain, B. & Levitt, M. (2003) Proc. Natl. Acad. Sci. USA 100, 10700-10705.
31. Johansson, M. U., de Chateau, M., Wikstrom, M., Forsen, S., Drakenberg, T. & Bjorck, L. (1997) J. Mol. Biol. 266, 859-865.
32. Macias, M. J., Gervais, V., Civera, C. & Oschkinat, H. (2000) Nat. Struct. Biol. 7, 375-379.
33. Bateman, A. & Bycroft, M. (2000) J. Mol. Biol. 299, 1113-1119.
34. Derrick, J. P. & Wigley, D. B. (1994) J. Mol. Biol. 243, 906-918.
35. Ren, P. & Ponder, J. W. (2003) J. Phys. Chem. B 107, 5933-5947.
36. de Gennes, P.-G. (1979) Scaling Concepts in Polymer Physics (Cornell Univ. Press, Ithaca, NY), pp. 198-203.
37. Swope, W. C., Andersen, H. C., Berens, P. H. & Wilson, K. R. (1982) J. Chem. Phys. 76, 637-649.
38. Allen, M. P. (1980) Mol. Phys. 40, 1073-1087.
39. Guarnieri, F. & Still, W. C. (1994) J. Comput. Chem. 15, 1302-1310.
40. Gouda, H., Torigoe, H., Saito, A., Sato, M., Arata, Y. & Shimada, I. (1992) Biochemistry 31, 9665-9672.
41. Dai, Q.-H., Tommos, C., Fuentes, E. J., Blomberg, M. R. A., Dutton, P. L. & Wand, A. J. (2002) J. Am. Chem. Soc. 124, 10952-10953.
42. Svensson, L. A., Thulin, E. & Forsen, S. (1992) J. Mol. Biol. 223, 601-606.
43. Kazmierkiewicz, R., Liwo, A. & Scheraga, H. A. (2002) J. Comput. Chem. 23, 715-723.
44. Kaźmierkiewicz, R., Liwo, A. & Scheraga, H. A. (2003) Biophys. Chem. 100, 261-280.