A new twist on the helix-coil transition: A non-biological helix with protein-like intermediates and traps

Journal of Physical Chemistry B

Volumn 105, Issue 2, 2001, Pages 482-485

  Elmer, Sidney ^a   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; COMPUTER SIMULATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS;

NONBIOLOGICAL HELIX; POLYPHENYLACETYLENE;

PROTEINS;

EID: 0035132373     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0019761     Document Type: Article

References (19)

1. Zimm, B. H.; Bragg, J. K. J. Chem. Phys. 1959, 31, 526-535.
2. Lifson, S.; Roig, A. J. Chem. Phys. 1961, 34, 1963-1974.
3. Clarke, D. T.; Doig, A. J.; Stapley, B. J.; Jones, G. R. Proc. Natl. Acad. Sci. 1999, pp 7232-7237.
4. Yang, W. Y.; Prince, R. B.; Sabelko, J.; Moore, J. S.; Gruebele, M. J. Am. Chem. Soc. 2000, 122, 3248-3249.
5. Nelson, J. C; Saven, J. G.; Moore, J. S.; Wolynes, P. G. Science 1997, 277, 1793-1796.
6. 18 We added values for the dihedral angle potential between rings (important for the different isomers of this polymer). For this angle dihredral potential, we used values from ref 15.
7. 10-13
8. drag = -γv, where v is the velocity. We have set γ = 1/ps for the results reported in the paper. We also find a linear dependence of folding time on viscosity (data not shown), which is reasonable because small changes in γ likely changes the microscopic time at which dynamics occurs, rather than the underlying mechanism.
9. Kai, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312.
10. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins: Struct. Funct. Genet. 1995,21, 167-195.
11. Chan, H. S.; Dill, K. A. Nat. Struct. Biol. 1997, 4, 10-19.
12. Shakhnovich, E. I. Curr. Opin. Struct. Biol. 1997, 7, 29-40.
13. Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Rokhsar, D. S. Curr. Opin. Struct. Biol. 1998, 8, 68-79.
14. Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, E. I. J. Chem. Phys. 1998, 108, 334-350.
15. Okuyama, K.; Hasegawa, T.; Ito, M.; Mikami, N. J. Chcm. Phys. 1984, 88, 1711-1716.
16. Pande, V. S.; Rokhsar, D. S. Proc. Nail. Acad. Sci. 1999, 96(16).
17. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Nail Acad. Sci. 1999, 96, 9068-9073.
18. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Cliem. 1983, 4, 187-217.
19. We thank Jeff Moore and Martin Gruebele for their insightful comments and review of our manuscript. Some calculations were run on the T3E at the National Energy Resources Supercomputer Center (NERSC).