Discrete breathers in a realistic coarse-grained model of proteins

Physical Biology

Volumn 8, Issue 4, 2011, Pages

  Luccioli, Stefano ^a,b,c   Imparato, Alberto ^d   Lepri, Stefano ^a,b   Piazza, Francesco ^e   Torcini, Alessandro ^a,b,c,d  

^a ISTITUTO DEI SISTEMI COMPLESSI   (Italy)

^b Centro Interdipartimentale per Lo Studio Delle Dinamiche Complesse   (Italy)

^c INFN SEZIONE DI FIRENZE   (Italy)

^d AARHUS UNIVERSITY   (Denmark)

^e UNIVERSITÉ D'ORLÉANS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; PERIODICITY; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS; VIBRATION;

AMINO ACID SEQUENCE; MOLECULAR DYNAMICS SIMULATION; PERIODICITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS; VIBRATION;

EID: 79961187482     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/8/4/046008     Document Type: Article

References (68)

1. Creighton T E 2002 Proteins: Structures and Molecular Properties (New York: Freeman)
2. Yang L and Bahar I 2005 Structure 13 893-904
3. Bahar I, Erman B, Jernigan R L, Atilgan A R and Covell D G 1999 J. Mol. Biol. 285 1023-37
4. Eisenmesser E Z, Bosco D A, Akke M and Kern D 2002 Science 295 1520-3
5. Kondo J, Urzhumtsev A and Westhof E 2006 Nucleic Acids Res. 34 676-85
6. del Sol A, Tsai C J, Ma B Y and Nussinov R 2009 Structure 17 1042-50
7. Delarue M and Sanejouand Y H 2002 J. Mol. Biol. 320 1011-24
8. Zheng W and Brooks B R 2005 Biophys. J. 88 3109-17
9. Elezgaray J, Marcou G and Sanejouand Y H 2002 Phys. Rev. E 66 31908-15
10. Brooks B R and Karplus M 1985 Proc. Natl Acad. Sci. USA 82 4995-9
11. Marques O and Sanejouand Y H 1995 Proteins 23 557-60
12. Murray J, Hu Q, Navenot J and Peiper S 2002 Biochem. Biophys. Res. Commun. 292 449-55
13. Bahar I, Atilgan A R, Demirel M C and Erman B 1998 Phys. Rev. Lett. 80 2733-6
14. Piazza F and Sanejouand Y H 2008 Phys. Biol. 5 026001
15. Sacquin-Mora S, Laforet E and Lavery R 2007 Proteins 67 350-9
16. Sievers A J and Takeno S 1988 Phys. Rev. Lett. 61 970-3
17. Flach S and Willis C R 1998 Phys. Rep. 295 181-264
18. Flach S and Gorbach A V 2008 Phys. Rep. 467 1-116
19. Trias E, Mazo J J and Orlando T P 2000 Phys. Rev. Lett. 84 741-4
20. Binder P, Abraimov D, Ustinov A V, Flach S and Zolotaryuk Y 2000 Phys. Rev. Lett. 84 745-8
21. Sato M and Sievers A 2009 J. Biol. Phys. 35 57-72
22. Manley M E, Sievers A J, Lynn J W, Kiselev S A, Agladze N I, Chen Y, Llobet A and Alatas A 2009 Phys. Rev. B 79 134304
23. Juanico B, Sanejouand Y H, Piazza F and De Los Rios P 2007 Phys. Rev. Lett. 99 238104
24. Piazza F and Sanejouand Y H 2009 Phys. Biol. 6 046014
25. Piazza F and Sanejouand Y H 2009 Europhys. Lett. 88 68001
26. Piazza F and Sanejouand Y H 2010 Discrete Contin. Dyn. Syst. S 4 1247-66
27. Sitnitsky A E 2006 Physica A 371 481-91
28. Agarwal P K 2005 J. Am. Chem. Soc. 127 15248-56
29. Hennig D, Schimansky-Geier L and Hänggi P 2007 Europhys. Lett. 78 20002
30. Salerno M and Kivshar Y S 1994 Phys. Lett. A 193 263-6
31. Archilla J F R, Gaididei Y B, Christiansen P L and Cuevas J 2002 J. Phys. A: Math. Gen. 35 8885-902
32. Snchez-Rey B, Archilla J F R, Palmero F and Romero F R 2002 Phys. Rev. E 66 017601
33. Honeycutt J D and Thirumalai D 1990 Proc. Natl Acad. Sci. USA 87 3526-9
34. Berry R S, Elmaci N, Rose J P and Vekhter B 1997 Proc. Natl Acad. Sci. USA 94 9520-4
35. Guo Z and Thirumalai D 1995 Biopolymers 36 83-102
36. Guo Z and Brooks C L 1997 Biopolymers 42 745-57
37. Veitshans T, Klimov D and Thirumalai D 1997 Fold. Des. 2 1-22
38. Evans D A and Wales D J 2003 J. Chem. Phys. 118 3891-7
39. Kim J, Straub J E and Keyes T 2006 Phys. Rev. Lett. 97 050601
40. Kim J M and Keyes T 2007 J. Phys. Chem. B 111 2647
41. Li F Y, Yuan J M and Mou C Y 2001 Phys. Rev. E 63 021905
42. Lacks D J 2005 Biophys. J. 88 3494-501
43. Imparato A, Luccioli S and Torcini A 2007 Phys. Rev. Lett. 99 168101
44. Luccioli S, Imparato A and Torcini A 2008 Phys. Rev. E 78 031907
45. Imparato A, Luccioli S and Torcini A 2010 Prog. Theor. Phys. Suppl. 184 339-50
46. Luccioli S, Imparato A, Mitternacht S, Irbäck A and Torcini A 2010 Phys. Rev. E 81 010902
47. Blondel A and Karplus M 1996 J. Comput. Chem. 17 1132-41
48. Rampioni A 2005 Caratterizzazione del panorama energetico di piccoli peptidi al variare della loro lunghezza PhD Thesis University of Florence, Italy
49. Atela P and McLachlan R I 1992 Nonlinearity 5 541
50. Wales D J 2003 Energy Landscapes (Cambridge: Cambridge University Press)
51. Aoki H 1983 J. Phys. C: Solid State Phys. 16 L205
52. Forinash K, Peyrard M and Malomed B 1994 Phys. Rev. E 49 3400-11
53. Kopidakis G and Aubry S 2000 Physica D 139 247-75
54. Kopidakis G and Aubry S 1999 Physica D 130 155-86
55. Bickham S R, Kiselev S A and Sievers A J 1993 Phys. Rev. B 47 14206
56. Cretegny T, Dauxois T, Ruffo S and Torcini A 1998 Physica D 121 109-26
57. Kosevich Y and Lepri S 2000 Phys. Rev. B 61 299-307
58. Kabsch W 1976 Acta Crystallogr. A 32 922-3
59. Tsironis G P and Aubry S 1996 Phys. Rev. Lett. 77 5225-8
60. Piazza F, Lepri S and Livi R 2003 Chaos 13 637
61. Moritsugu K, Miyashita O and Kidera A 2003 J. Phys. Chem. B 107 3309-17
62. Moritsugu K, Miyashita O and Kidera A 2000 Phys. Rev. Lett. 85 3970-3
63. Lazarides N, Tsironis G P and Kivshar Y S 2008 Phys. Rev. E 77 065601
64. Mirny L and Shakhnovich E 2001 J. Mol. Biol. 308 123-9
65. Tsai C J, Del Sol A and Nussinov R 2009 Mol. Biosyst. 5 207-16
66. Gunasekaran K, Ma B and Nussinov R 2004 Proteins: Struct. Funct. Bioinformatics 57 433-43
67. Miller M A and Wales D J 1999 J. Chem. Phys. 111 6610-6
68. Wales D J and Dewsbury P E J 2004 J. Chem. Phys. 121 10284-90