Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface

Biopolymers

Volumn 81, Issue 4, 2006, Pages 256-269

  Zhao, Ying ^a   Kormos, Bethany L ^a   Beveridge, David L ^a   Baranger, Anne M ^a  

^a WESLEYAN UNIVERSITY   (United States)

Author keywords

Design; Molecular dynamics; RNA recognition motif; RNA binding protein; U1A

Indexed keywords

AMINO ACIDS; BINDING ENERGY; COMPUTER SIMULATION; CONFORMATIONS; MOLECULAR DYNAMICS; RNA; SYNTHESIS (CHEMICAL);

MOLECULAR DYNAMICS SIMULATION; PROTEIN RNA COMPLEX; RNA RECOGNITION MOTIF; RNA-BINDING PROTEIN; U1A;

PROTEINS;

AROMATIC AMINO ACID; RNA BINDING PROTEIN;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN; PROTEIN MOTIF; PROTEIN RNA BINDING; RNA DEGRADATION; RNA EDITING; RNA PROCESSING; RNA STRUCTURE; SIMULATION; WILD TYPE;

COMPUTER SIMULATION; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN FOLDING; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RIBONUCLEOPROTEINS; RNA-BINDING PROTEINS;

EID: 33645077057     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20408     Document Type: Article

References (49)

1. Maris, C.; Dominguez, C.; Allain, F. H. T. FEBS J 2005, 272, 2118.
2. Zhao, Y.; Baranger, A. M. J Am Chem Soc 2003, 125, 2480-2488.
3. Oubridge, C.; Ito, N.; Evans, P. R.; Teo, C. H.; Nagai, K. Nature 1994, 372, 432-438.
4. Allain, F. H. T.; Howe, P. W. A.; Neuhaus, D.; Varani, G. EMBO J 1997, 16, 5764-5774.
5. Allain, R. H. T.; Bouvet, P.; Dieckmann, T.; Feigon, J. EMBO J 2000, 19, 6870-6881.
6. Varani, L.; Gunderson, S. I.; Mattaj, I. W.; Kay, L. E.; Neuhaus, D.; Varani, G. Nature Struct Biol 2000, 7, 329-335.
7. Johansson, C.; Finger, L.; Trantirek, L.; Mueller, T.; Kim, S.; Laird-Offringa, I.; Feigon, J. J Mol Biol 2004, 337, 799-816.
8. Handa, N.; Nureki, O.; Kuimoto, K.; Kim, I.; Sakamoto, H.; Shimura, Y.; Muto, Y.; Yokoyama, S. Nature 1999, 398, 579-585.
9. Price, S. R.; Evans, P. R.; Nagai, K. Nature 1998, 394, 645-650.
10. Deo, R. C.; Bonanno, J. B.; Sonenberg, N.; Burley, S. K. Cell 1999, 98, 835-845.
11. Ding, J.; Hayashi, M. K.; Zhang, Y.; Manche, L.; Krainer, A. R.; Xu, R. J. Genes Dev 1999, 13, 1102-1115.
12. Wang, X.; Tanaka Hall, T. M. Nature Struct Biol 2001, 8, 141-145.
13. Mazza, C.; Segref, A.; Mattaj, I.; Cusack, S. EMBO J 2002, 21, 5548-5557.
14. Green, M. R. Annu Rev Cell Biol 1991, 7, 559-599.
15. Stark, H.; Dube, P.; Lührmann, R.; Kastner, B. Nature 2001, 409, 539-542.
16. Tsai, D. E.; Harper, D. S.; Keene, J. D. Nucleic Acids Res 1991, 19, 4931-4936.
17. Hall, K. B. Biochemistry 1994, 33, 10076-10088.
18. Nolan, S. J.; Shiels, J. C.; Tuite, J. B.; Cecere, K. L.; Baranger, A. M. J Am Chem Soc 1999, 121, 8951-8952.
19. Shiels, J. C.; Tuite, J. B.; Nolan, S. J.; Baranger, A. M. Nucleic Acids Res 2002, 30, 550-558.
20. Cramer, C. J. Essentials of Computational Chemistry; Wiley: New York, 2002.
21. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; Wiley: New York, 1986.
22. Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry; McGraw-Hill: New York, 1982.
23. Hariharan, P. C.; Pople, J. A. Theor Chim Acta 1973, 28, 213-222.
24. Hehre, W. J.; Ditchfield, R.; Pople, J. A. J Chem Phys 1972, 56, 2257-2261.
25. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J Phys Chem 1993, 97, 10269-10280.
26. Cieplak, P.; Cornell, W. D.; Bayly, C. I.; Kollman, P. A. J Comput Chem 1995, 16, 1357-1377.
27. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J Am Chem Soc 1993, 115, 9620-9631.
28. Pitici, F.; Beveridge, D. L.; Baranger, A. M. Biopolymers 2002, 65, 424-435.
29. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C.; Darden, T.; Merz, K. M.; Stanton, R. V.; Cheng, A.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. AMBER 6.0 University of California: San Francisco, 1999.
30. Ravishanker, G.; Wang, W.; Beveridge, D. Molecular Dynamics Tool Chest 2.0; Wesleyan University, Middletown, CT, 1998.
31. Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Nucleic Acids Res 1997, 25, 4940-4945.
32. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. AMBER 8.0 University of California: San Francisco, 2004.
33. Gohlke, H.; Case, D. A. J Comput Chem 2004, 25, 238-250.
34. Ajay, A.; Murcko, M. A. J Med Chem 1995, 38, 4953-4967.
35. Jayaram, B.; McConnell, K.; Dixit, S. B.; Beveridge, D. L. J Comput Phys 1999, 151, 333-357.
36. Jayaram, B.; McConnell, K.; Dixit, S. B.; Das, A.; Beveridge, D. L. J Comput Chem 2002, 23, 1-14.
37. Kombo, D. C.; Jayaram, B.; McConnell, K. J.; Beveridge, D. L. Molecular Simulation 2002, 28, 187-211.
38. Swanson, J. M.; Henchman, R. H.; McCammon, J. A. Biophys J 2004, 86, 67-74.
39. Onufriev, A.; Bashford, D.; Case, D. A. J Phys Chem B 2000, 104, 3712-3720.
40. Onufriev, A.; Bashford, D.; Case, D. A. Proteins 2004, 55, 383-394.
41. Sitkoff, D.; Sharp, K. A.; Honig, B. J Phys Chem 1994, 98, 1978-1988.
42. Connolly, M. L. J Appl Cryst 1983, 16, 548-558.
43. Kranz, J. K.; Lu, J. R.; Hall, K. B. Protein Sci 1996, 5, 1567-1583.
44. Tang, Y.; Nilsson, L. Biophys J 1999, 77, 1284-1305.
45. Reyes, C. M.; Kollman, P. A. J Mol Biol 2000, 297, 1145-1158.
46. Williams, D. J.; Hall, K. B. J Mol Biol 1996, 257, 265-275.
47. Harvey, S. C.; Prabhakaran, M. J Am Chem Soc 1986, 108, 6128-6136.
48. Altona, C.; Sundaral, M. J Am Chem Soc 1972, 94, 8205-8212.
49. Duarte, C. M.; Pyle, A. M. J Mol Biol 1998, 284, 1465-1478.