Structural ensemble of an intrinsically disordered polypeptide

Journal of Physical Chemistry B

Volumn 117, Issue 1, 2013, Pages 118-124

  Mittal, Jeetain ^a   Yoo, Tae Hyeon ^b   Georgiou, George ^c,d   Truskett, Thomas M ^c  

^a Lehigh University   (United States)

^b Ajou University   (South Korea)

^c The University of Texas at Austin   (United States)

^d UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; PROTEINS;

BOUND STRUCTURE; CELL SIGNALING; CLUSTERING METHODS; CONFORMATIONAL ENSEMBLE; DISORDERED PROTEINS; EXPERIMENTAL VALIDATIONS; EXPLICIT SOLVENTS; FREE-ENERGY LANDSCAPE; MOLECULAR SIMULATIONS; ORDERED STRUCTURES; PROTEIN MODELS; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; SOLUTION STRUCTURES; SPATIO-TEMPORAL RESOLUTION; STRUCTURAL CHANGE; STRUCTURAL SIMILARITY; TERTIARY STRUCTURES; WILD TYPES;

LIGANDS;

EID: 84872323081     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp308984e     Document Type: Article

References (68)

1. Dyson, H. J.; Wright, P. E. Nat. Rev. Mol. Cell Biol. 2005, 6, 197-208
2. Tompa, P. FEBS Lett. 2005, 579, 3346-3354
3. Uversky, V. N. Protein Sci. 2002, 11, 739-756
4. Cheng, Y.; LeGall, T.; Oldfield, C. J.; Mueller, J. P.; Van, Y.-Y. J.; Romero, P.; Cortese, M. S.; Uversky, V. N.; Dunker, A. K. Trends Biotechnol. 2006, 24, 435-442
5. Ward, J.; Sodhi, J.; McGuffin, L.; Buxton, B.; Jones, D. J. Mol. Biol. 2004, 337, 635-645
6. Tompa, P.; Fuxreiter, M. Trends Biochem. Sci. 2008, 33, 2-8
7. Cheng, Y.; LeGall, T.; Oldfield, C.; Dunker, A. K.; Uversky, V. N. Biochemistry 2006, 45, 10448-10460
8. Iakoucheva, L.; Brown, C.; Lawson, J.; Obradovic, Z.; Dunker, A. K. J. Mol. Biol. 2002, 323, 573-584
9. Bracken, C.; Iakoucheva, L.; Romero, P.; Dunker, K. A. Curr. Opin. Struct. Biol. 2004, 14, 570-576
10. Radivojac, P.; Iakoucheva, L. M.; Oldfield, C. J.; Obradovic, Z.; Uversky, V. N.; Dunker, A. K. Biophys. J. 2007, 92, 1439-1456
11. Receveur-Bréchot, V.; Bourhis, J.; Uversky, V. N.; Canard, B.; Longhi, S. Proteins 2006, 62, 24-45
12. Müller-Späth, S.; Soranno, A.; Hirschfeld, V.; Hofmann, H.; Rüegger, S.; Reymond, L.; Nettels, D.; Schuler, B. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 14609
13. Mao, A. H.; Crick, S. L.; Vitalis, A.; Chicoine, C. L.; Pappu, R. V. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 8183
14. Sgourakis, N. G.; Yan, Y. L.; McCallum, S. A.; Wang, C. Y.; Garcia, A. E. J. Mol. Biol. 2007, 368, 1448
15. Sgourakis, N. G.; Merced-Serrano, M.; Boutsidis, C.; Drineas, P.; Du, Z.; Wang, C.; Garcia, A. E. J. Mol. Biol. 2011, 405, 570
16. Click, T. H.; Ganguly, D.; Chen, J. Int. J. Mol. Sci. 2010, 11, 5292-5309
17. Chen, J. Arch. Biochem. Biophys. 2012, 524, 123-131
18. Jha, A.; Colubri, A.; Freed, K. F.; Sosnick, T. R. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13099-13104
19. Wells, M.; Tidow, H.; Rutherford, T. J.; Markwick, T. J.; Jensen, M. R.; Mylonas, E.; Svergun, D. I.; Blackledge, M.; Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 5762
20. Mittag, T.; Forman-Kay, J. Curr. Opin. Struct. Biol. 2007, 17, 3-14
21. Ringkjobing Jensen, M.; Markwick, P. R. L.; Meier, S.; Griesinger, C.; Zweckstetter, M.; Grzesiek, S.; Bernado, P.; Blackledge, M. Structure 2009, 17, 1169-1185
22. Fisher, C.; Stultz, C. Curr. Opin. Struct. Biol. 2011, 21, 426-431
23. Ashbaugh, H. S.; Hatch, H. W. J. Am. Chem. Soc. 2008, 130, 9536
24. Dedmon, M. M.; Lindorff-Larsen, K.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. J. Am. Chem. Soc. 2005, 127, 476-477
25. Francis, C. J.; Lindorff-Larsen, K.; Best, R. B.; Vendruscolo, M. Proteins 2006, 65, 145-152
26. Lowry, D.; Stancik, A.; Shrestha, R.; Daughdrill, G. Proteins 2008, 71, 587-598
27. Huang, J.; Grzesiek, S. J. Am. Chem. Soc. 2009, 132, 694-705
28. Esteban-MartiIÌn, S.; Fenwick, R.; Salvatella, X. J. Am. Chem. Soc. 2010, 132, 4626-4632
29. Fisher, C.; Huang, A.; Stultz, C. J. Am. Chem. Soc. 2010, 132, 14919-14927
30. Marsh, J.; Forman-Kay, J. Proteins 2012, 80, 556-572
31. Ytreberg, F. M.; Zuckerman, D. M. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 7982-7987
32. Daughdrill, G. W.; Kashtanov, S.; Stancik, A.; Hill, S. E.; Helms, G.; Muschol, M.; Receveur-Brechot, V.; Ytreberg, F. M. Molecular BioSystems 2012, 8, 308
33. Vousden, K.; Lane, D. Nat. Rev. Mol. Cell Biol. 2007, 8, 275-283
34. Brooks, C.; Gu, W. Mol. Cell 2006, 21, 307-315
35. Toledo, F.; Wahl, G. Nat. Rev. Canc. 2006, 6, 909-923
36. CheÌne, P. Nat. Rev. Cancer 2003, 3, 102-109
37. Joerger, A.; Fersht, A. Annu. Rev. Biochem. 2008, 77, 557-582
38. Kussie, P.; Kussie, P.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, I.; Levine, A. I.; Pavletich, N. P. Science 1996, 274, 948-953
39. Issaeva, N.; Bozko, P.; Enge, M.; Protopopova, M.; Verhoef, L. G.; Masucci, M.; Pramanik, A.; Selivanova, G. Nat. Med. 2004, 10, 1321-1328
40. Shangary, S.; Qin, D.; McEachern, D.; Liu, M.; Miller, R. S.; Qiu, S.; Nikolovska-Coleska, Z.; Ding, K.; Wang, G.; Chen, J.; Bernard, D.; Zhang, J.; Lu, Y.; Gu, Q.; Shah, R. B.; Pienta, K. J.; Ling, X.; Kang, S.; Guo, M.; Sun, Y.; Yang, D.; Wang, S. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 3933
41. Vassilev, L.; Vu, B. T.; Graves, B.; Carvajal, D.; Podlaski, F.; Filipovic, Z.; Kong, N.; Kammlott, U.; Lukacs, C.; Klein, C.; Fotouhi, N.; Liu, E. A. Science 2004, 303, 844
42. Best, R. B.; Mittal, J. J. Phys. Chem. B 2010, 114, 14916
43. Abascal, J. L. F.; Vega, C. J. Chem. Phys. 2005, 123, 234505
44. Barbas, C. F.; Burton, D. R.; Scott, J. K.; Silvermann, G. J. Phage Display: A Laboratory Manual; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001.
45. Zondlo, S.; Lee, A.; Zondlo, N. Biochemistry 2006, 45, 11945-11957
46. Dastidar, S.; Lane, D.; Verma, C. J. Am. Chem. Soc. 2008, 130, 13514-13515
47. Nick Pace, C.; Martin Scholtz, J. Biophys. J. 1998, 75, 422-427
48. Paschek, D.; Hempel, S.; Garcia, A. E. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 17754
49. Freddolino, P.; Harrison, C.; Liu, Y.; Schulten, K. Nature Physics 2010, 6, 751-758
50. Mittal, J.; Best, R. B. Biophys. J. 2010, 98, 1-3
51. Piana, S.; Lindorff-Larsen, K.; Shaw, D. E. Biophys. J. 2011, 100, 47
52. Nettels, D.; Muller-Spath, S.; Kuster, F.; Hofmann, H.; Haenni, D.; Ruegger, S.; Reymond, L.; Hoffmann, A.; Kubelka, J.; Heinz, B.; Gast, K.; Best, R. B.; Schuler, B. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 20740
53. Earl, D. J.; Deem, M. W. Phys. Chem. Chem. Phys. 2005, 7, 3910
54. Best, R. B.; Mittal, J. J. Phys. Chem. B 2010, 114, 8790
55. Day, R.; Paschek, D.; Garcia, A. E. Proteins 2010, 78, 1889
56. Lin, E.; Shell, M. S. J. Chem. Theory Comput. 2009, 5, 2062
57. Shen, Y.; Bax, A. J. Biomol. NMR 2010, 48, 13-22
58. Lee, H.; Hun Mok, K.; Muhandiram, R.; Park, K.-H.; Suk, J.-E.; Kim, D.-H.; Chang, J.; Chul Sung, Y.; Choi, K. Y.; Han, K.-H. J. Biol. Chem. 2000, 275, 29426-29432
59. Spera, S.; Bax, A. J. Am. Chem. Soc. 1991, 113, 5490-5492
60. Wishart, D.; Sykes, B.; Richards, F. J. Mol. Biol. 1991, 222, 311-333
61. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew. Chem., Int. Ed. 1999, 38, 236-240
62. Boehr, D.; Nussinov, R.; Wright, P. Nat. Chem. Biol. 2009, 5, 789-796
63. Shoemaker, B. A.; Portman, J. J.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8868
64. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. J. Comput. Chem. 2003, 24, 1999-2012
65. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151
66. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577
67. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56
68. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447