Energy flow and long-range correlations in guanine-binding riboswitch: A nonequilibrium molecular dynamics study

Journal of Physical Chemistry B

Volumn 113, Issue 27, 2009, Pages 9340-9347

  Nguyen, Phuong H ^a   Derreumaux, Philippe ^b   Stock, Gerhard ^a  

^a GOETHE UNIVERSITY   (Germany)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; DYNAMICS; ENERGY TRANSFER; LIGANDS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; POSITIVE IONS; RNA;

ANISOTROPIC ENERGY; APTAMER; BIO-MOLECULAR; COMPUTATIONAL APPROACH; CONFORMATIONAL CHANGE; CORRELATION FUNCTION; DELAY TIME; ENERGY FLOW; ENERGY SOURCE; EXPLICIT SOLVENTS; IN-LINE; LIGAND COMPLEXES; LINEAR-RESPONSE THEORY; LONG RANGE CORRELATIONS; LONG RANGE INTERACTIONS; MD SIMULATION; MOLECULAR FUNCTION; NON EQUILIBRIUM; NONEQUILIBRIUM MOLECULAR DYNAMICS; RIBOSWITCH; TEMPERATURE-INDUCED;

BINDING ENERGY;

EID: 67650032475     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp902013s     Document Type: Article

References (59)

1. Proteins: Energy, Heat and Signal Flow (Computation in Chemistry); Leitner, D.; Straub, J., Eds.; Taylor and Francis/CRC Press: London, 2009.
2. Botan, V.; Backus, E.; Pfister, R.; Moretto, A.; Crisma, M.; Toniolo, C.; Nguyen, P. H.; Stock, G.; Hamm, P. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 12749-12754.
3. Yu, X.; Leitner, D. M. J. Phys. Chem. B 2003, 107, 1698-1707.
4. Yu, X.; Leitner, D. M. J. Chem. Phys. 2005, 122, 054902.
5. Fujisaki, H.; Straub, J. E. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6726-6731.
6. Fujisaki, H.; Straub, J. J. Phys. Chem. B 2007, 111, 12017-12023.
7. Moritsugu, K.; Miyashita, O.; Kidera, A. Phys. Rev. Lett. 2000, 85, 3970-3973.
8. Henry, E. R.; Eaton, W. A.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 8982-8986.
9. Sagnella, D. E.; Straub, J. E. J. Phys. Chem. B 2001, 105, 7057-7063.
10. Moritsugu, K.; Miyashita, O.; Kidera, A. J. Phys. Chem. B 2003, 107, 3309-3317.
11. Ota, N.; Agard, D. A. J. Mol. Biol. 2005, 351, 345-354.
12. Sharp, K.; Skinner, J. J. Proteins 2006, 65, 347-361.
13. Kong, Y.; Karplus, M. Proteins 2009, 74, 145-154.
14. Ishikura, T.; Yamato, T. Chem. Phys. Lett. 2006, 432, 533-537.
15. Ghosh, A.; Vishveshwara, S. Proc. Natl. Acad. Sci. U.S.A. 2006, 104, 15711-15716.
16. Seth, A.; Eargle, J.; Black, A. A.; Luthey-Schulten, Z. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6620-6625.
17. Nguyen, P. H.; Stock, G. J. Chem. Phys. 2003, 119, 11350.
18. Nguyen, P. H.; Stock, G. Chem. Phys. 2006, 323, 36-44.
19. Bahar, I.; Chennubhotla, C.; Tobi, D. Curr. Opin. Struct. Biol 2007, 17, 633-640.
20. Changeux, J.-P.; Edelstein, S. J. Science 200, 308, 1424-1428.
21. Lockless, S. W.; Ranganathan, R. Science 1999, 286, 295-299.
22. Shulman, A. I.; Larson, C.; Mangelsdorf, D. J.; Ranganathan, R. Cell 2004, 116, 417-429.
23. Suel, G. M.; Lockless, S. W.; Wall, M. A.; Ranganathan, R. Nat. Struct. Biol. 2003, 10, 59-69.
24. Zhang, Q.; Sun, X.; Watt, E. D.; Al-Hashimi, H. M. Science 2006, 311 (5761), 653-656.
25. Hall, K. B. Curr. Opin. Chem. Biol. 2008, 12, 612-618.
26. Edwards, T. E.; Klein, D. J.; Ferre-d'Amare, A. R. Curr. Opin. Struct. Biol. 2007, 17, 273-279.
27. Schwalbe, H.; Buck, J.; Fürtig, B.; Noeske, J.; Wöhnert, J. Angew. Chem., Int. Ed. 2007, 46, 1212-1219.
28. Montange, R. K.; Batey, R. T. Annu. Rev. Biochem. 2008, 37, 117-133.
29. Mandal, M.; Boese, B.; Barrick, J. E.; Winkler, W. C.; Breaker, R. R. Cell 2003, 113, 577-586.
30. Batey, R. T.; Gilbert, S. D.; Montange, R. K. Nature 2004, 432, 411-415.
31. Serganov, A.; Yuan, Y.; Pikovskaya, O.; Polonskaia, A.; Malinina, L.; Phan, A. T.; Hobartner, C.; Micura, R.; Breaker, R. R.; Patel, D. J. Chem. Biol. 2004, 11, 1729-1741.
32. Gilbert, S. D.; Stoddard, C. D.; Wise, S. J.; Batey, R. T. J. Mol. Biol. 2006, 359, 754-768.
33. Lemay, J.-F.; Penedo, J. C.; Tremblay, R.; Lilley, D. M. J.; Lafontaine, D. A. Chem. Biol. 2006, 13, 857-868.
34. Rieder, R.; Lang, K.; Graber, D.; Micura, R. ChemBioChem 2007, 8, 896-902.
35. Noeske, J.; Richter, C.; Grundl, M. A.; Nasiri, H. R.; Schwalbe, H.; Wöhnert, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 1372-1377.
36. Noeske, J.; Buck, J.; Fürtig, B.; Schwalbe, H.; Wöhnert, J. Nucleic Acids Res. 2007, 35, 572-582.
37. Stoddard, C. D.; Gilbert, S. D.; Batey, R. T. RNA 2008, 14, 675-684.
38. Villa, A.; Wöhnert, J.; Stock, G. Nucl. Acids Res. 2009, in press.
39. Buck, J.; Fürtig, B.; Noeske, J.; Wöhnert, J.; Schwalbe, H. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 15699-15704.
40. Nguyen, P. H.; Hamm, P.; Stock, G. In Proteins: Energy, Heat and Signal Flow (Computation in Chemistry); Leitner, D.; Straub, J., Eds., Taylor and Francis/CRC Press: London, 2009.
41. Ikeguchi, M.; Ueno, J. M. S.; Kidera, A. Phys. Rev. Lett. 2005, 94, 078102.
42. Zacharias, M. Curr. Opin. Struct. Biol. 2000, 10, 311-317.
43. Mu, Y.; Stock, G. Biophys. J. 2006, 90, 391-399.
44. Rázga, F.; Zacharias, M.; Réblová, K.; Koča, J.; S ̌poner, J. Structure 2006, 14, 825-835.
45. Kormos, B. L.; Baranger, A. M.; Beveridge, D. L. J. Am. Chem. Soc. 2006, 128, 8992-8993.
46. Auffinger, P.; Hashem, Y. Curr. Opin. Struct. Biol. 2007, 17, 325-333.
47. Hashem, Y.; Westhof, E.; Auffinger, P. In Computational Structural Biology; Schwede, T.; Peitsch, M. C., Eds.; World Scientific: New York, 2008.
48. Chen, S.-J. Annu. Rev. Biophys. 2008, 37, 197-214.
49. Villa, A.; Widjajakusuma, E.; Stock, G. J. Phys. Chem. B 2008, 112, 134-142.
50. Wang, J.; Cieplak, P.; Kollman, P. J. Comput. Chem. 2000, 21, 1049.
51. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. J. Chem. Phys. 1983, 79, 926.
52. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43.
53. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718.
54. Darden, T.; York, D.; Petersen, L. J. Chem. Phys. 1993, 98, 10089.
55. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
56. Backus, E.; Nguyen, P. H.; Botan, V.; Pfister, R.; Moretto, A.; Crisma, M.; Toniolo, C.; Stock, G.; Hamm, P. J. Phys. Chem. B 2008, 112, 9091-9099.
57. Backus, E.; Nguyen, P. H.; Botan, V.; Pfister, R.; Moretto, A.; Crisma, M.; Toniolo, C.; Stock, G.; Hamm, P. J. Phys. Chem. B 2008, 112, 15487-15492.
58. Chennubhotla, C.; Bahar, I. PLoS Comput. Biol. 2007, 9, 1716.
59. Zwanzig, R. Nonequilibrium Statistical Mechanics; Oxford University: Oxford, 2001.