Statistical mechanical model for helix-sheet-coil transitions in homopolypeptides

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 78, Issue 5, 2008, Pages

  Hong, Liu ^a   Lei, Jinzhi ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PAPER SHEETING;

COIL TRANSITIONS; CONFORMATION TRANSITIONS; CORRECTION FACTORS; INITIATION FACTORS; MECHANICAL MODELS; PARTITION FUNCTIONS; PROPAGATION FACTORS; RANDOM COILS;

MODEL STRUCTURES;

EID: 56649084841     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.78.051904     Document Type: Article

References (65)

1. C. Branden and J. Tooze, Introduction to Protein Structure (Garland, London, 1998).
2. R. H. Pain, Mechanisms of Protein Folding (Oxford University Press, Oxford, 2000).
3. S. B. Prusiner, Science 10.1126/science.1675487 252, 1515 (1991).
4. P. J. Flory, Statistical Mechanics of Chain Molecules (Hanser, Munich, 1988).
5. B. H. Zimm and J. K. Bragg, J. Chem. Phys. 10.1063/1.1730390 31, 526 (1959).
6. S. Lifson and A. Roig, J. Chem. Phys. 10.1063/1.1731802 34, 1963 (1961).
7. D. Poland and H. A. Scheraga, Theory of Helix-coil Transitions in Biopolymers (Academic Press, New York, 1970).
8. A. Y. Grosberg and A. R. Khokhlov, Statistical Physics of Macromolecules (AIP, New York, 1994).
9. T. M. Birstein and O. B. Ptitsyn, Conformations of Macromolecules (Interscience, London, 1966).
10. H. Qian and J. A. Schellman, J. Phys. Chem. 10.1021/j100189a015 96, 3987 (1992).
11. A. J. Doig, Biophys. Chem. 10.1016/S0301-4622(02)00170-9 101, 281 (2002).
12. C. A. Rohl and R. L. Baldwin, Biochemistry 10.1021/bi9706677 36, 8435 (1997).
13. W. Shalongo, L. Dugad, and E. Stellwagen, J. Am. Chem. Soc. 10.1021/ja00085a034 116, 2500 (1994).
14. A. V. Finkelstein, Protein Eng. 8, 207 (1995). 10.1093/protein/8.2.207
15. A. J. Doig, A. Chakrabartty, T. M. Klingler, and R. L. Baldwin, Biochemistry 33, 3396 (1994). 10.1021/bi00177a033
16. A. Chakrabartty, A. J. Doig, and R. L. Baldwin, Proc. Natl. Acad. Sci. U.S.A. 90, 11332 (1993). 10.1073/pnas.90.23.11332
17. A. J. Doig and R. L. Baldwin, Protein Sci. 4, 1325 (1995).
18. N. H. Andersen and H. Tong, Protein Sci. 6, 1920 (1997).
19. D. A. E. Cochran, S. Penel, and A. J. Doig, Protein Sci. 10, 463 (2001). 10.1110/ps.31001
20. D. A. E. Cochran and A. J. Doig, Protein Sci. 10, 1305 (2001). 10.1110/ps.50701
21. M. Petukhov, V. Munoz, N. Yumoto, S. Yoshikawa, and L. Serrano, J. Mol. Biol. 278, 279289 (1998). 10.1006/jmbi.1998.1682
22. M. Petukhov, K. Uegaki, N. Yumoto, S. Yoshikawa, and L. Serrano, Protein Sci. 8, 2144 (1999).
23. E. T. Harper and G. D. Rose, Biochemistry 32, 7605 (1993). 10.1021/bi00081a001
24. J. M. Scholtz, H. Qian, V. H. Robbins, and R. L. Baldwin, Biochemistry 10.1021/bi00088a019 32, 9668 (1993).
25. W. Shalongo and E. Stellwagen, Protein Sci. 4, 1161 (1995).
26. B. J. Stapley, C. A. Rohl, and A. J. Doig, Protein Sci. 4, 2383 (1995).
27. M. Vasquez and H. A. Scheraga, Biopolymers 10.1002/bip.360270104 27, 41 (1988).
28. C. H. Roberts, Biopolymers 10.1002/bip.360300311 30, 335 (1990).
29. P. J. Gans, P. C. Lyu, P. C. Manning, R. W. Woody, and N. R. Kallenbach, Biopolymers 10.1002/bip.360311315 31, 1605 (1991).
30. H. Qian, Biophys. J. 67, 349 (1994).
31. A. Mitsutake and Y. Okamoto, J. Chem. Phys. 10.1063/1.481697 112, 10638 (2000).
32. Y. Peng, U. H. E. Hansmann, and N. A. Alves, J. Chem. Phys. 10.1063/1.1532348 118, 2374 (2003).
33. H. Wako, N. Saito, and H. A. Scheraga, J. Protein Chem. 10.1007/BF01025356 2, 221 (1983).
34. C. A. Rohl and A. J. Doig, Protein Sci. 5, 1687 (1996).
35. V. Munoz, E. R. Henry, J. Hofrichter, and W. A. Eaton, Nature (London) 10.1038/36626 390, 196 (1998).
36. D. K. Klimov and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.97.6.2544 97, 2544 (2000).
37. A. R. Dinner, T. Lazaridis, and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.96.16.9068 96, 9068 (1999).
38. W. L. Mattice, Annu. Rev. Biophys. Biophys. Chem. 10.1146/annurev.bb.18. 060189.000521 18, 93 (1989).
39. C. W. David and R. Schor, J. Chem. Phys. 42, 2156 (1965). 10.1063/1.1697101
40. C. W. David, H. B. Haukaas, J. G. Kalnins, and R. Schor, Biophys. J. 7, 505 (1967).
41. R. Schor, H. B. Haukaas, and C. W. David, J. Chem. Phys. 10.1063/1.1669946 49, 4726 (1968).
42. V. Munoz, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.95.11.5872 95, 5872 (1998).
43. W. L. Mattice and H. A. Scheraga, Biopolymers 10.1002/bip.360230907 23, 1701 (1984).
44. W. L. Mattice and H. A. Scheraga, Biopolymers 10.1002/bip.360231212 23, 2879 (1984).
45. W. L. Mattice and H. A. Scheraga, Biopolymers 10.1002/bip.360240310 24, 565 (1985).
46. S. J. Chen and K. A. Dill, J. Chem. Phys. 10.1063/1.470461 103, 5802 (1995).
47. S. J. Chen and K. A. Dill, J. Chem. Phys. 10.1063/1.477065 109, 4602 (1998).
48. J. K. Sun and A. J. Doig, J. Phys. Chem. B 10.1021/jp9918555 104, 1826 (2000).
49. D. L. Minor Jr and P. S. Kim, Nature (London) 10.1038/367660a0 367, 660 (1994).
50. D. L. Minor Jr and P. S. Kim, Nature (London) 10.1038/371264a0 371, 264 (2002).
51. G. D. Fasman, Prediction of Protein Structure and the Principles of Protein Conformation (Plenum, New York, 1989).
52. A. M. Lesk, Introduction to Protein Architecture (Oxford University Press, Oxford, 2003).
53. K. Janek, S. Rothemund, K. Gast, M. Beyermann, J. Zipper, H. Fabian, M. Bienert, E. Krause, and E. Krause, Biochemistry 40, 5457 (2001). 10.1021/bi002005e
54. R. A. Brualdi, Introductory Combinatorics (Pearson/Prentice Hall, New York, 2004).
55. A. Chakrabartty, T. Kortemme, and R. L. Baldwin, Protein Sci. 3, 843 (1994).
56. L. Wang, T. O. Connell, A. Tropsha, and J. Hermans, Proc. Natl. Acad. Sci. U.S.A. 92, 10924 (1995). 10.1073/pnas.92.24.10924
57. S. Patel, P. V. Balaji, and Y. U. Sasidhar, J. Pept. Res. 13, 314 (2007). 10.1002/psc.843
58. J. A. Vila, R. L. Williams, J. A. Grant, J. Wojcik, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.89.16.7821 89, 7821 (1992).
59. H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.240455797 97, 13075 (2000).
60. J. A. Vila, D. R. Ripoll, and H. A. Scheraga, Biopolymers 58, 235 (2001). 10.1002/1097-0282(200103)58:3<235::AID-BIP1001>3.0.CO;2-T
61. J. Wojcik, K. H. Altman, and H. A. Scheraga, Biopolymers 10.1002/bip.360300113 30, 121 (1990).
62. H. A. Scheraga, J. A. Vila, and D. R. Ripoll, Biophys. Chem. 101-102, 255 (2002). 10.1016/S0301-4622(02)00175-8
63. H. A. Scheraga, in Perspectives in Structure Biology, edited by, M. Vijayan, N. Y. athindra and, A. S. Kolaskar, (Indian Academy of Sciences, Bangalore, 1999), pp. 275-292.
64. P. Y. Chou and G. D. Fasman, Biochemistry 10.1021/bi00699a001 13, 211 (1974).
65. Srinivas Aluru, Handbook of Computational Molecular Biology (CRC Press, Boca Raton, FL, 2006).