Competition for hydrogen-bond formation in the helix-coil transition and protein folding

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

Volumn 83, Issue 5, 2011, Pages

  Badasyan, A V ^a   Tonoyan, Sh A ^b   Mamasakhlisov, Y Sh ^b   Giacometti, Achille ^a   Benight, A S ^c   Morozov, V F ^a  

^a CA' FOSCARI UNIVERSITY OF VENICE   (Italy)

^b YEREVAN STATE UNIVERSITY   (Armenia)

^c PORTLAND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPLICIT SOLVENTS; EXTERNAL INFLUENCES; GENERALIZED MODEL OF POLYPEPTIDE CHAINS; HELIX-COIL TRANSITIONS; HYDROGEN-BOND FORMATION; MECHANICAL FORCE; OSMOTIC STRESS; POLYNUCLEOTIDES;

COMPETITION; HYDROGEN; NUCLEIC ACIDS; POLYMERS; POLYPEPTIDES; PROTEIN FOLDING; STRESSES;

HYDROGEN BONDS;

EID: 79961050462     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.83.051903     Document Type: Article

References (74)

1. C. Cantor and T. Shimmel, Biophysical Chemistry (Freeman and Co., San Francisco, 1980).
2. B. Alberts, D. Bray, J. Lewis, K. Roberts, and D. Watson, Molecular Biology of the Cell, Vol. 1 (Garland Publications, New York, 1983).
3. P. Flory, Statistical Mechanics of Chain Molecules (Interscience, New York, 1969).
4. W. L. Mattice and U. W. Suter, Conformational Theory of Large Molecules (Wiley Interscience, New York, 1994).
5. A. Grosberg and A. Khokhlov, Statistical Physics of Macromolecules (AIP Press, New York, 1994).
6. R. E. Goldstein, Phys. Lett. A PYLAAG 0375-9601 10.1016/0375-9601(84) 90072-0 104, 285 (1984).
7. N. Ananikian, L. Ananikyan, R. Artuso, and K. Sargsyan, Physica A PHYADX 0378-4371 10.1016/j.physa.2008.05.020 387, 5433 (2008).
8. A. V. Badasyan, A. Giacometti, Y. S. Mamasakhlisov, V. F. Morozov, and A. S. Benight, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.81.021921 81, 021921 (2010).
9. N. Ananikyan, Sh. Hayryan, E. Mamasakhlisov, and V. Morozov, Biopolymers BIPMAA 0006-3525 10.1002/bip.360300313 30, 357 (1990).
10. Sh. Hayryan, E. Mamasakhlisov, and V. Morozov, Biopolymers BIPMAA 0006-3525 10.1002/bip.360350108 35, 75 (1995).
11. V. Morozov, E. Mamasakhlisov, Sh. Hayryan, and Hu Chin-Kun, Physica A PHYADX 0378-4371 10.1016/S0378-4371(00)00054-6 281, 51 (2000).
12. M. I. Marques, J. M. Borreguero, H. E. Stanley, and N. V. Dokholyan, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.91.138103 91, 138103 (2003).
13. B. H. Zimm and J. K. Bragg, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1730390 31, 526 (1959).
14. S. Lifson and A. Roig, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1731802 34, 1963 (1961).
15. D. Poland and H. Scheraga, The Theory of Helix-Coil Transition (Academic Press, New York, 1970).
16. K. Sastry, M. G. Mazza, H. E. Stanley, and G. Franzese, Proc. Nat. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0912756107 107, 1301 (2010).
17. J. S. Walker and C. A. Vause, Phys. Lett. A 0375-9601 10.1016/0375-9601(80)90281-9 79, 421 (1980);
18. R. E. Goldstein and J. S. Walker, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.444839 78, 1492 (1983).
19. S. Sastry, F. Sciortino, and H. E. Stanley, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.464365 98, 9863 (1993);
20. S. S. Borick, P. G. Debenedetti, and S. Sastry, J. Chem. Phys. JPCHAX 0022-3654 10.1021/j100011a054 99, 3781 (1995);
21. S. Sastry, P. G. Debenedetti, F. Sciortino, and H. E. Stanley, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.53.6144 53, 6144 (1996).
22. C. E. Fiore, M. M. Szortyka, M. C. Barbosa, and V. B. Henriques, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3253297 131, 164506 (2009).
23. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, Berlin, 1984), p. 368 -384.
24. V. A. Bloomfield, D. M. Crothers, and I. Tinoco Jr., Nucleic Acids: Structures, Properties, and Functions (University Science Books, Sausalito, CA, 2000), p. 475 -534.
25. J. S. Walker and C. A. Vause, Mol. Cryst. Liq. Cryst. JCPSA6 1542-1406 10.1080/00268948408074516 110, 349 (1984).
26. A. Hansen, M. H. Jensen, K. Sneppen, and G. Zocchi, Eur. Phys. J. B EPJBFY 1434-6028 10.1007/s100510050537 6, 157 (1998).
27. A. Bakk, P. G. Dommersnes, A. Hansen, J. S. Hoye, K. Sneppen, and M. H. Jensen, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/S0010-4655(02)00293-X 147, 307 (2002). (Pubitemid 34822718)
28. P. De Los Rios and G. Caldarelli, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.62.8449 62, 8449 (2000); (Pubitemid 32087907)
29. P. De Los Rios and G. Caldarelli, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.63.031802 63, 031802 (2001).
30. S. A. Hawley, Biochemistry CPHCBZ 0006-2960 10.1021/bi00789a002 10, 2436 (1971).
31. D. N. Dubins, A. Lee, R. B. Macgregor, and T. V. Chalikian, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja004309u 14, 9254 (2001). (Pubitemid 32900297)
32. E. Ascolese and G. Graziano, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2008.10.078 467, 150 (2008);
33. A. Riccio, E. Ascolese, and G. Graziano, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2009.12.088 486, 65 (2010).
34. H. S. Chan and K. Dill, Proteins 18PLAF 0887-3585 10.1002/(SICI)1097- 0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R 30, 2 (1998). (Pubitemid 28036107)
35. E. Nordmeier, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100182a086 96, 1494 (1992).
36. G. Rayan and R. B. Macgregor, Biophys. Chem. BICIAZ 0301-4622 10.1016/j.bpc.2009.06.007 144, 62 (2009);
37. G. Rayan and R. B. Macgregor, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp050899c 109, 15558 (2005). (Pubitemid 41260806)
38. I. Rouzina and V. Bloomfield, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(01)76067-5 80, 882 (2001);
39. I. Rouzina and V. Bloomfield, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(01)76068-7 80, 894 (2001).
40. M. C. Williams, J. R. Wenner, I. Rouzina, and V. Bloomfield, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(01)76163-2 80, 1932 (2001);
41. M. C. Williams, I. Rouzina, and V. Bloomfield, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar010045k 35, 159 (2002).
42. V. Morozov, A. Badasyan, A. Grigoryan, M. Sahakyan, and E. Mamasakhlisov, Biopolymers BIPMAA 0006-3525 10.1002/bip.20143 75, 434 (2004). (Pubitemid 39611431)
43. V. Morozov, A. Badasyan, A. Grigoryan, M. Sahakyan, and E. Mamasakhlisov, Mod. Phys. Lett. B MPLBET 0217-9849 10.1142/S0217984905008062 19, 79 (2005). (Pubitemid 40522243)
44. A. V. Badasyan, A. V. Grigoryan, E. Sh. Mamasakhlisov, A. S. Benight, and V. F. Morozov, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2107507 123, 194701 (2005). (Pubitemid 41636811)
45. E. Mamasakhlisov, A. V. Badasyan, A. V. Tsarukyan, A. V. Grigoryan, and V. F. Morozov, Abdus Salam ICTP preprint IC2005037 (2005).
46. A. Grigoryan, E. Mamasakhlisov, T. Buryakina, A. Tsarukyan, A. Benight, and V. Morozov, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2727456 126, 165101 (2007). (Pubitemid 46685480)
47. P. Bruscolini and A. Pelizzola, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.88.258101 88, 258101 (2002).
48. A. Imparato, A. Pelizzola, and M. Zamparo, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.148102 98, 148102 (2007). (Pubitemid 46557426)
49. A. V. Badasyan, A. V. Grigoryan, E. Sh. Mamasakhlisov, A. V. Tsarukyan, and V. F. Morozov, J. C. Phys. (NAS of Armenia) 40, 148 (2005).
50. R. M. Wartell and A. S. Benight, Phys. Rep. PRPLCM 0370-1573 10.1016/0370-1573(85)90060-2 126, 67 (1985).
51. A. Schellman, Compt. rend. trav. Lab. Carlsberg. Ser. chim. 29, 223 (1955)
52. A. Schellman, Compt. rend. trav. Lab. Carlsberg. Ser. chim. 29, 230 (1955).
53. S. A. Hawley and R. M. Macleod, Biopolymers BIPMAA 0006-3525 10.1002/bip.1974.360130712 13, 1417 (1974).
54. L. Smeller, Biochim. Biophys. Acta BIPMAA 0167-4838 10.1016/S0167- 4838(01)00332-6 1595, 11 (2002). (Pubitemid 34442633)
55. S. Kunugi and N. Tanaka, Biochim. Biophys. Acta BIPMAA 0167-4838 10.1016/S0167-4838(01)00354-5 1595, 329 (2002). (Pubitemid 34442654)
56. P. Privalov, Crit. Rev. Biochem. Mol. Biol. CRBBEJ 1040-9238 10.3109/10409239009090612 25, 281 (1990).
57. M. Rubinstein and R. H. Colby, Polymer Physics (Oxford University Press, Oxford, 2003).
58. C. Nakamoto, T. Kitada, and E. Katob, Polym. Gels Netw. PGNEEI 0966-7822 10.1016/0966-7822(96)00022-6 4, 17 (1996). (Pubitemid 126411826)
59. F. G. Hopkins, Nature (London) NATUAS 0028-0836 10.1038/126383a0 126, 383 (1930).
60. W. K. Lim, J. Rosgen, and S. W. Englander, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0812588106 106, 2595 (2009).
61. A. Zipp and W. Kauzmann, Biochemistry PNASA6 0006-2960 10.1021/bi00745a028 12, 4217 (1973).
62. C. B. Stanley and H. H. Strey, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.107.122705 94, 4427 (2008).
63. A. Hanke, M. G. Ochoa, and R. Metzler, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.018106 100, 018106 (2008). (Pubitemid 351388336)
64. Y. Z. Chen and E. W. Prohofsky, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.47.2100 47, 2100 (1993).
65. D. Marenduzzo, A. Trovato, and A. Maritan, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.64.031901 64, 031901 (2001);
66. E. Orlandini, S. M. Bhattacharjee, D. Marenduzzo, A. Maritan, and F. Seno, J. Phys. A JPHAC5 0305-4470 10.1088/0305-4470/34/50/104 34, L751 (2001). (Pubitemid 33579076)
67. E. Orlandini, S. M. Bhattacharjee, D. Marenduzzo, A. Maritan, and F. Seno J. Phys. A: Math. Gen. JPHAC5 0305-4470 10.1088/0305-4470/34/50/104 34, L751 (2001). (Pubitemid 33579076)
68. J. Rudnick and T. Kuriabova Phys. Rev. E JPHAC5 1539-3755 10.1103/PhysRevE.77.051903 77, 051903 (2008). (Pubitemid 351668279)
69. S. J. Rahi, M. P. Hertzberg, and M. Kardar, Phys. Rev. E JPHAC5 1539-3755 10.1103/PhysRevE.78.051910 78, 051910 (2008).
70. A. Buhot and A. Halperin, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.84.2160 84, 2160 (2000).
71. M. N. Tamashiro and P. Pincus, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.63.021909 63, 021909 (2001).
72. A. Buhot and A. Halperin, Macromolecules MAMOBX 0024-9297 10.1021/ma011631w 35, 3238 (2002). (Pubitemid 34586551)
73. S. Courty, J. L. Gornall, and E. M. Terentjev, Proc. Natl. Acad. Sci. USA. PNASA6 0027-8424 10.1073/pnas.0506864102 102, 13457 (2005); (Pubitemid 41420869)
74. Y. Seol, G. M. Skinner, K. Visscher, A. Buhot, and A. Halperin, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.158103 98, 158103 (2007). (Pubitemid 46582689)