Prediction of hydrodynamic and other solution properties of partially disordered proteins with a simple, coarse-grained model

Journal of Chemical Theory and Computation

Volumn 9, Issue 3, 2013, Pages 1678-1685

  Amoros D ^a   Ortega, A ^a   De La Torre, J García ^a  

^a UNIVERSITY OF MURCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84874909420     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300948u     Document Type: Article

References (56)

1. Tompa, P. Trends Biochem. Sci. 2002, 27, 527-533
2. Fink, A. Curr. Opin. Struct. Biol 2005, 15, 35-41
3. Structure and Function of Intrinsically Disordered Proteins; Tompa, P., Ed.; CRC Press: Boca Raton, FL, 2010.
4. Wright, P.; Dyson, H. J. Mol. Biol. 1999, 293, 321-331
5. Dyson, H. J.; Wright, P. E. Chem. Rev. 2004, 104, 3607-3622
6. Serdyuk, I. N.; Zaccai, N. R.; Zaccai, J. Methods in Molecular Biophysics; Cambridge University Press: New York, 2008; Vol. 1, p 1.
7. van Holde, K.; Johnson, W.; Ho, P. Principles of Physical Biochemistry, 2 nd ed.; Prentice Hall: Upper Saddle River, NJ, 1998.
8. García de la Torre, J.; Huertas, M.; Carrasco, B. Biophys. J. 2000, 78, 719-730
9. García de la Torre, J.; Huertas, M.; Carrasco, B. J. Magn. Reson. 2000, 147, 138-146
10. Ortega, A.; Garcia de la Torre, J. J. Am. Chem. Soc. 2005, 127, 12764-12765
11. Ortega, A.; Amorós, D.; Garcia de la Torre, J. Biophys. J. 2011, 101, 892-898
12. Bae, S. H.; Dyson, H.; Wright, P. J. Am. Chem. Soc. 2009, 131, 6814-6821
13. Garcia de la Torre, J.; Hernandez Cifre, J. G.; Ortega, A.; Rodriguez Schmidt, R.; Fernandes, M.; Sánchez, H. E. P.; Pamies, R. J. Chem. Theory Comput. 2009, 5, 2606-2618
14. Coarse-Graining of Condensed Phase and Biomolecular Systems; Voth, G., Ed.; CRC Press: Boca Raton, FL, 2010.
15. del Rio Echenique, G.; Rodriguez Schmidt, R.; Freire, J.; Hernandez Cifre, J. G.; García de la Torre, J. J. Am. Chem. Soc. 2009, 131, 8548-8556
16. Tozzini, V.; Rocchia, W.; Cammon, J. M. J. Chem. Theory Comput. 2006, 2, 667-673
17. Tozzini, V.; McCammon, J. A. In Coarse-Graining of Condensed Phase and Biomolecular Systems; Voth, G. A., Ed.; CRC Press: Boca Raton, FL, 2009.
18. Frembgen-Kesner, T.; Elcock, A. J. Chem. Theory Comput. 2009, 5, 242-256
19. Amorós, D.; Ortega, A.; García de la Torre, J. Macromolecules 2011, 44, 5788-5797
20. Kleywegt, G. J. J. Mol. Biol. 1997, 273, 371-376
21. Hobohm, U.; Sander, C. Protein Sci. 1994, 3, 522-524
22. Amorós, D.; Ortega, A.; Garcia de la Torre, J. In preparation.
23. Clementi, C.; Nyemeyer, H.; Onuchic, J. J. Mol. Biol. 2000, 298, 937-53
24. Frembgen-Kesner, T.; Elcock, A. H. J. Chem. Theory Comput. 2009, 5 (2) 242-256
25. Sobolev, V.; Sorokine, A.; Prilusky, J.; Abola, E. E.; Edelman, M. Bioinformatics 1999, 15, 327-332
26. Gallagher, T.; Alexander, P.; Bryan, P.; Gilliland, G. Biochemistry 1994, 33, 4721-4729
27. Syvitsky, R.; Burton, I.; Mattatall, N.; Douglas, S.; Jakeman, D. Biochemistry 2005, 44, 7282-7293
28. Hammel, M.; Fierobe, H.-P.; Czjzek, M.; Kurkal, V.; Smith, J. C.; Bayer, E. A.; Finet, S.; Reveceur-Bréchot, V. J. Biol. Chem. 2005, 280, 38562-38568
29. Mosyak, L.; Zhang, Y.; Glasfeld, E.; Haney, S.; Stahl, M.; Seehra, J.; Somers, W. EMBO J. 2000, 19, 3179-3191
30. Ohashi, T.; Hale, C.; de Boer, P.; Erikson, H. J. Bacteriol. 2002, 184, 4313-4315
31. Blanchard, L.; Tarbouriech, N.; Blackledge, M.; Timmins, P.; Burmeister, W. P.; Ruigrok, R. W. H.; Marion, D. Virology 2004, 319, 201-211
32. Bernadó, P.; Blanchard, L.; Timmins, P.; Marion, D.; Ruigrok, R. W. H.; Blackledge, M. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 17002-17007
33. Rotkiewicz, P.; Skolnick, J. J. Comput. Chem. 2008, 29, 1460-1465
34. Houben, K.; Blanchard, L.; Blackledge, M.; Marion, D. Biophys. J. 2007, 93, 2830-2844
35. Bertini, I.; Calderone, V.; Fragai, M.; Jaiswal, R.; Luchinat, C.; Melikian, M.; Mylonas, E.; Svergun, D. I. J. Am. Chem. Soc. 2008, 130, 7011-7021
36. Hyvonen, M.; Saraste, M. EMBO J. 1997, 16, 3396-3404
37. Hansson, H.; Mattsson, P.; Allard, P.; Haapaniemi, P.; Vihinen, M.; Smith, C.; Hard, T. Biochemistry 1998, 37, 2912-2924
38. Huang, K.-C.; Cheng, H.-T.; Pai, M.-T.; Tzeng, S.-R.; Cheng, J.-W. J. Biomol. NMR 2006, 36, 73-78
39. Mao, C.; Zhou, M.; Uckun, F. J. Biol. Chem. 2001, 276, 41435-41443
40. Marquez, J. A.; Smith, C. I.; Petoukhov, M. V.; Surdo, P. L.; Mattsson, P. T.; Knekt, M.; Westlund, A.; Scheffzek, K.; Saraste, M.; Svergun, D. I. EMBO J. 2003, 22, 4616-4624
41. Bernadó, P.; Mylonas, E.; Petoukhov, M. V.; Blackledge, M.; Svergun, D. I. J. Am. Chem. Soc. 2007, 129, 5656-5664
42. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546-4559
43. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4559-4570
44. Zimm, B. Macromolecules 1980, 13, 592-602
45. Hagerman, P.; Zimm, B. Biopolymers 1981, 20, 1481-1502
46. García de la Torre, J.; Jiménez, A.; Freire, J. Macromolecules 1982, 15, 148-154
47. García de la Torre, J.; del Rio Echenique, G.; Ortega, A. J. Phys. Chem. B 2007, 111, 955-961
48. García de la Torre, J.; López Martinez, M. C.; Tirado, M.; Freire, J. Macromolecules 1984, 17, 2715-2722
49. García Bernal, J.; Tirado, M.; García de la Torre, J. Macromolecules 1991, 24, 593-598
50. García de la Torre, J.; Ortega, A.; Perez Sánchez, H. E.; Hernandez Cifre, J. G. Biophys. Chem. 2005, 116, 121-128
51. Frembgen-Kesner, T.; Elcock, A. H. Biophys. J. 2010, 99, L75-L77
52. Rossky, P.; Doll, J.; Friedman, H. J. Chem. Phys. 1978, 69, 4628-4633
53. Laue, T. M.; Shah, B. D.; Ridgeway, T. M.; Pelletier, S. L. In Analytical Ultracentrifugation in Biochemistry and Polymer Science; Harding, S.; Rowe, A.; Horton, J., Eds.; Royal Society of Chemistry: Cambridge, U. K., 1992; pp 90-125.
54. Eswar, N.; Marti-Renom, M. A.; Webb, B.; Madhusudhan, M. S.; Eramian, D.; Shen, M.; Pieper, U.; Sali, A. Curr. Protoc. Bioinf. 2006, 15, 5.6.1-5.6.30.
55. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38
56. Svergun, D. I.; C., C. B.; Koch, M. H. J. J. Appl. Crystallogr. 1995, 28, 768-773