Role of secondary motifs in fast folding polymers: A dynamical variational principle

Physical Review Letters

Volumn 84, Issue 13, 2000, Pages

  Maritan, Amos ^a,b   Micheletti, Cristian ^a,b   Banavar, Jayanth R ^c  

^a INFM   (Italy)

^b ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMORPHOUS GLASSES; HELIX-COLI TRANSITION MODELS; NONBIOLOGICAL OLIGOMERS; PACKING DENSITY;

AMORPHOUS MATERIALS; BIOCHEMISTRY; CONFORMATIONS; CRYSTALLIZATION; MONOMERS; OLIGOMERS; PROTEINS; TARGETS; THERMODYNAMICS;

POLYMERS;

POLYMER;

CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; KINETICS; PHYSICS; PROCEDURES; THEORETICAL MODEL;

KINETICS; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR CONFORMATION; PHYSICS; POLYMERS;

EID: 0034719580     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.84.3009     Document Type: Article

References (29)

1. C. Levinthal, J. Chim. Phys. 65, 44 (1968).
2. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 7524-7528 (1987); J. D. Bryngelson, J. N. Onuchic, J. N. Socci, and P. G. Wolynes, Proteins: Struct. Fund. Genet. 21, 167-195 (1995).
3. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 7524-7528 (1987); J. D. Bryngelson, J. N. Onuchic, J. N. Socci, and P. G. Wolynes, Proteins: Struct. Fund. Genet. 21, 167-195 (1995).
4. P. E. Leopold, M. Montai, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 89, 8721-8725 (1992); P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science 267, 1619-1620 (1995); J. N. Onuchic, Z. Luthey Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545-600 (1997); K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10-19 (1997).
5. P. E. Leopold, M. Montai, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 89, 8721-8725 (1992); P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science 267, 1619-1620 (1995); J. N. Onuchic, Z. Luthey Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545-600 (1997); K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10-19 (1997).
6. P. E. Leopold, M. Montai, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 89, 8721-8725 (1992); P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science 267, 1619-1620 (1995); J. N. Onuchic, Z. Luthey Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545-600 (1997); K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10-19 (1997).
7. P. E. Leopold, M. Montai, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 89, 8721-8725 (1992); P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science 267, 1619-1620 (1995); J. N. Onuchic, Z. Luthey Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545-600 (1997); K. A. Dill and H. S. Chan, Nat. Struct. Biol. 4, 10-19 (1997).
8. H. Li, R. Helling, C. Tang, and N. Wingreen, Science 273, 666-669 (1996); N. E. G. Buchler and R. A. Goldstein, Proteins: Struct. Funct. Genet. 34, 113-124 (1999); C. Micheletti, J. R. Banavar, A. Maritan, and F. Seno, Phys. Rev. Lett. 80, 5683 (1998); C. Micheletti, A. Maritan, and J. R. Banavar, J. Chem. Phys. 110, 9730 (1999).
9. H. Li, R. Helling, C. Tang, and N. Wingreen, Science 273, 666-669 (1996); N. E. G. Buchler and R. A. Goldstein, Proteins: Struct. Funct. Genet. 34, 113-124 (1999); C. Micheletti, J. R. Banavar, A. Maritan, and F. Seno, Phys. Rev. Lett. 80, 5683 (1998); C. Micheletti, A. Maritan, and J. R. Banavar, J. Chem. Phys. 110, 9730 (1999).
10. H. Li, R. Helling, C. Tang, and N. Wingreen, Science 273, 666-669 (1996); N. E. G. Buchler and R. A. Goldstein, Proteins: Struct. Funct. Genet. 34, 113-124 (1999); C. Micheletti, J. R. Banavar, A. Maritan, and F. Seno, Phys. Rev. Lett. 80, 5683 (1998); C. Micheletti, A. Maritan, and J. R. Banavar, J. Chem. Phys. 110, 9730 (1999).
11. H. Li, R. Helling, C. Tang, and N. Wingreen, Science 273, 666-669 (1996); N. E. G. Buchler and R. A. Goldstein, Proteins: Struct. Funct. Genet. 34, 113-124 (1999); C. Micheletti, J. R. Banavar, A. Maritan, and F. Seno, Phys. Rev. Lett. 80, 5683 (1998); C. Micheletti, A. Maritan, and J. R. Banavar, J. Chem. Phys. 110, 9730 (1999).
12. C. Micheletti, J. R. Banavar, A. Maritan, and F. Seno, Phys. Rev. Lett. 82, 3372-3375 (1999).
13. L. Pauling, R. B. Corey, and H. R. Branson, Proc. Natl. Acad. Sci. U.S.A. 37, 205-208 (1951).
14. B. H. Zimm and J. Bragg, J. Chem. Phys. 31, 526 (1959); O. B. Ptitsyn and A. M. Skvortsov, Biophys. 10, 1007 (1965); I. M. Lifshitz, A. Y. Grosberg, and A. R. Khokhlov, Rev. Mod. Phys. 50, 683 (1978).
15. B. H. Zimm and J. Bragg, J. Chem. Phys. 31, 526 (1959); O. B. Ptitsyn and A. M. Skvortsov, Biophys. 10, 1007 (1965); I. M. Lifshitz, A. Y. Grosberg, and A. R. Khokhlov, Rev. Mod. Phys. 50, 683 (1978).
16. B. H. Zimm and J. Bragg, J. Chem. Phys. 31, 526 (1959); O. B. Ptitsyn and A. M. Skvortsov, Biophys. 10, 1007 (1965); I. M. Lifshitz, A. Y. Grosberg, and A. R. Khokhlov, Rev. Mod. Phys. 50, 683 (1978).
17. N. G. Hunt, L. M. Gregoret, and F. E. Cohen, J. Mol. Biol. 241, 214-225 (1994).
18. R. Aurora, T. P. Creamer, R. Srinivasan, and G. D. Rose, J. Mol. Biol. 272, 1413-1416 (1997).
19. J. C. Nelson, J. G. Saven, J. S. Moore, and P. G. Wolynes, Science 277, 1793-1796 (1997).
20. D. P. Yee, H. S. Chan, T. F. Havel, and K. A. Dill, J. Mol. Biol. 241, 557-573 (1994).
21. N. D. Socci, W. S. Bialek, and J. N. Onuchic, Phys. Rev. E 49, 3440-3443 (1994).
22. A. Halperin and P. M. Goldbart, cond-mat/9905306 [Phys. Rev. E (to be published)].
23. N. Go, Macromolecules 9, 535-541 (1976).
24. D. G. Covell and R. Jernigan, Biochemistry 29, 3287 (1990).
25. The native state structures of monomeric proteins of length between 50 and 200 show an excellent correlation of this form, when two nonconsecutive amino acids along the sequence are defined to be in contact when they are within 6.5 Å of each other.
26. J. H. Holland, Adaptation in Natural and Artificial Systems (MIT Press, Cambridge, MA, 1992).
27. K. M. Plaxco, K. T. Simons, and D. Baker, J. Mol. Biol. 277, 985-994 (1998).
28. A. P. Capaldi and S. E. Radford, Curr. Opin. Struct. Biol. 8, 86-92 (1998).
29. V. Muñoz, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 95, 5872 (1998).