Frustration-induced protein intrinsic disorder

Journal of Chemical Physics

Volumn 138, Issue 10, 2013, Pages

  Matsushita, Katsuyoshi ^a   Kikuchi, Macoto ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERIC REGULATION; BIOLOGICAL FUNCTIONS; INTRINSIC DISORDER; INTRINSICALLY DISORDERED PROTEINS; NATIVE STRUCTURES; NEURON-RESTRICTIVE SILENCER FACTORS; PROTEIN INTRINSIC DISORDERS; REGULATION FUNCTIONS;

BINDING ENERGY;

PROTEINS;

RE1 SILENCING TRANSCRIPTION FACTOR; RE1-SILENCING TRANSCRIPTION FACTOR; REPRESSOR PROTEIN;

ANIMAL; ARTICLE; BINDING SITE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOUSE; PROTEIN BINDING; PROTEIN FOLDING; THERMODYNAMICS;

ANIMALS; BINDING SITES; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MICE; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN FOLDING; REPRESSOR PROTEINS; THERMODYNAMICS;

EID: 84875206334     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4794781     Document Type: Article

References (60)

1. E. Fischer, Ber. Dtsch. Chem. Ges. B 27, 2985 (1894). 10.1002/cber.18940270364
2. C. B. Anfinsen, Science 181, 223 (1973). 10.1126/science.181.4096.223
3. N. Go, Annu. Rev. Biophys. Bioeng. 12, 183 (1983). 10.1146/annurev.bb.12. 060183.001151
4. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 7524 (1987). 10.1073/pnas.84.21.7524
5. P. E. Leopold, M. Montal, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 89, 8721 (1992). 10.1073/pnas.89.18.8721
6. J. N. Onuchic, Z. Luthey-Shchulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545 (1997). 10.1146/annurev.physchem.48.1.545
7. F. B. Sheinerman and C. L. Brooks III, J. Mol. Biol. 278, 439 (1998). 10.1006/jmbi.1998.1688
8. B. G. Wensley, S. Batey, F. A. C. Bone, Z. M. Chan, N. R. Tumelty, A. Steward, L. G. Kwa, A. Borgia, and J. Clarke, Nature (London) 463, 685 (2010). 10.1038/nature08743
9. B. G. Wensley, L. G. Kwa, S. L. Shammas, J. M. Rogers, S. Browning, Z. Yang, and J. Clarke, Proc. Natl. Acad. Sci. U.S.A. 109, 17795 (2012). 10.1073/pnas.1201793109
10. A. Kitao, K. Yonekura, S. Maki-Yonekura, F. A. Samatey, K. Imada, and N. Go, Proc. Natl. Acad. Sci. U.S.A. 103, 4894 (2006). 10.1073/pnas.0510285103
11. P. I. Zhuravlev and G. A. Papoian, Q. Rev. Biophys. 43, 295 (2010). 10.1017/S0033583510000119
12. D. U. Ferreiro, J. A. Hegler, E. A. Komives, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 108, 3499 (2011). 10.1073/pnas.1018980108
13. J. Monod, J. Wyman, and J. P. Changeux, J. Mol. Biol. 12, 88 (1965). 10.1016/S0022-2836(65)80285-6
14. D. E. J. Koshland, G. Némethy, and D. Filmer, Biochemistry 5, 365 (1966). 10.1021/bi00865a047
15. A. K. Dunker, E. Garner, S. Guilliot, P. Romero, K. Albrecht, J. Hart, Z. Obradovic, C. Kissinger, and J. E. Villafranca, Pac. Symp. Biocomput. 3, 473 (1998); online at http://www.ncbi.nlm.nih.gov/pubmed/9697205.
16. P. E. Wright and H. J. Dyson, J. Mol. Biol. 293, 321 (1999). 10.1006/jmbi.1999.3110
17. P. Tompa, Structure and Function of Intrinsically Disordered Proteins (Chapman and Hall/CRC, 2009).
18. V. Uversky and S. Longhi, Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation (Wiley-Interscience, 2010).
19. B. A. Shoemeker, J. J. Portman, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 97, 8868 (2000). 10.1073/pnas.160259697
20. A. Soranno, B. Buchli, D. Nettels, R. R. Cheng, S. Muller-Spath, S. H. Pfeil, A. Hoffmann, E. A. Lipman, D. E. Makarov, and B. Schuler, Proc. Natl. Acad. Sci. U.S.A. 109, 17800 (2012). 10.1073/pnas.1117368109
21. H. J. Dyson and P. E. Wright, Curr. Opin. Struct. Biol. 12, 54 (2002). 10.1016/S0959-440X(02)00289-0
22. G. A. Papoian and P. G. Wolynes, Biopolymers 68, 333 (2003). 10.1002/bip.10286
23. K. Sugase, H. J. Dyson, and P. E. Wright, Nature (London) 447, 1021 (2007). 10.1038/nature05858
24. P. E. Wright and H. J. Dyson, Curr. Opin. Struct. Biol. 19, 31 (2009). 10.1016/j.sbi.2008.12.003
25. M. Nomura, H. Uda-Tochio, K. Murai, N. Mori, and Y. Nishimura, J. Mol. Biol. 354, 903 (2005). 10.1016/j.jmb.2005.10.008
26. S. J. Demarest, M. Martinez-Yamout, J. Chung, H. Chen, W. Xu, H. J. Dyson, R. M. Evans, and P. E. Wright, Nature (London) 415, 549 (2002). 10.1038/415549a
27. G. M. Verkhiviker, D. Bouzida, D. K. Gehlhaar, P. A. Rejto, S. T. Freer, and P. W. Rose, Proc. Natl. Acad. Sci. U.S.A. 100, 5148 (2003). 10.1073/pnas.0531373100
28. N. Gupta and A. Irbäck, J. Chem. Phys. 120, 3983 (2004). 10.1063/1.1643900
29. V. H. Hilser and E. B. Tompson, Proc. Natl. Acad. Sci. U.S.A. 104, 8311 (2007). 10.1073/pnas.0700329104
30. A. D. Turjanski, J. S. Gutkind, R. B. Best, and G. Hummer, PLoS ONE 4, e1000060 (2008). 10.1371/journal.pcbi.1000060
31. H.-F. Chen, PLoS ONE 4, e6516 (2009). 10.1371/journal.pone.0006516
32. Y. Houng and Z. Liu, J. Mol. Bio. 393, 1143 (2009). 10.1016/j.jmb.2009. 09.010
33. J. Higo, Y. Nishimura, and H. Nakamura, J. Am. Chem. Soc. 133, 10448 (2011). 10.1021/ja110338e
34. J. A. Chong, J. Tapia-Ramirez, S. Kim, J. J. Toledo-Aral, M. C. B. Yingcong Zheng, Y. M. Altshuller, M. A. Frohman, S. D. Kraner, and G. Mandel, Cell 80, 949 (1995). 10.1016/0092-8674(95)90298-8
35. C. J. Schoenherr and D. J. Anderson, Science 267, 1360 (1995). 10.1126/science.7871435
36. H. Wako and N. Saitô, J. Phys. Soc. Jpn. 44, 1931 (1978). 10.1143/JPSJ.44.1931
37. H. Wako and N. Saitô, J. Phys. Soc. Jpn. 44, 1939 (1978). 10.1143/JPSJ.44.1939
38. N. Saitô and M. Oonuki, J. Phys. Soc. Jpn 29, 69 (1970). 10.1143/JPSJ.29.69
39. V. Muñoz, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 95, 5872 (1998). 10.1073/pnas.95.11.5872
40. V. Muñoz and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 96, 11311 (1999). 10.1073/pnas.96.20.11311
41. D. A. Wolf-Gladrow, Lattice-Gas Cellular Automata and Lattice Boltzmann Models (Springer, 2000).
42. B. H. Zimm and J. K. Bragg, J. Chem. Phys. 31, 526 (1959). 10.1063/1.1730390
43. K. Itoh and M. Sasai, Proc. Natl. Acad. Sci. U.S.A. 101, 14736 (2004). 10.1073/pnas.0402978101
44. P. Bruscolini and A. Pelizzola, Phys. Rev. Lett. 88, 258101 (2002). 10.1103/PhysRevLett.88.258101
45. K. Itoh and M. Sasai, Proc. Natl. Acad. Sci. U.S.A. 103, 7298 (2006). 10.1073/pnas.0510324103
46. M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006). 10.1103/PhysRevLett.97.068106
47. P. Bruscolini, A. Pelizzola, and M. Zamparo, Phys. Rev. Lett. 99, 038103 (2007). 10.1103/PhysRevLett.99.038103
48. A. Imparato, A. Pelizzola, and M. Zamparo, Phys. Rev. Lett. 98, 148102 (2007). 10.1103/PhysRevLett.98.148102
49. E. D. Nelson and N. V. Grishin, Proc. Natl. Acad. Sci. U.S.A. 105, 1489 (2008). 10.1073/pnas.0705707105
50. W. Yu, K. Chung, M. Cheon, M. Heo, K.-H. Han, and S. Ham, Proc. Natl. Acad. Sci. U.S.A. 105, 2397 (2008). 10.1073/pnas.0708480105
51. K. Itoh and M. Sasai, Proc. Natl. Acad. Sci. U.S.A. 107, 7775 (2010). 10.1073/pnas.0912978107
52. M. Zamparo, Phys. Rev. Lett. 105, 108102 (2010). 10.1103/PhysRevLett.105. 108102
53. M. Caraglio and A. Pelizzola, Phys. Biol. 9, 016006 (2012). 10.1088/1478-3975/9/1/016006
54. K. A. Dill, Biochemistry 24, 1501 (1985). 10.1021/bi00327a032
55. K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989). 10.1021/ma00200a030
56. M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996). 10.1103/PhysRevLett.77. 1905
57. C. Clementi, H. Nymeyer, and J. N. Onuchic, J. Mol. Biol. 298, 937 (2000). 10.1006/jmbi.2000.3693
58. N. Koga and S. Takada, J. Mol. Biol. 313, 171 (2001). 10.1006/jmbi.2001.5037
59. J. A. McCammon, Models for Protein Dynamics (CECAM, Orsay, France, 1976), p. 137.
60. J. A. McCammon, B. R. Gelin, and M. Karplus, Nature (London) 267, 585 (1977). 10.1038/267585a0