Free-energy landscapes of protein domain movements upon ligand binding

Journal of Physical Chemistry B

Volumn 115, Issue 23, 2011, Pages 7629-7636

  Kondo, Hiroko X ^a,b   Okimoto, Noriaki ^a   Morimoto, Gentaro ^a   Taiji, Makoto ^a,b  

^a RIKEN   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DYNAMICS; FREE ENERGY; LIGANDS; PROTEINS; X RAY CRYSTALLOGRAPHY;

APO-STATE; CONFORMATIONAL CHANGE; CONFORMATIONAL DIFFERENCES; CONFORMATIONAL TRANSITIONS; CRYSTALLOGRAPHIC STUDIES; ENERGY PROFILE; EQUILIBRIUM DYNAMICS; FREE-ENERGY LANDSCAPE; HOLOPROTEINS; LIGAND BINDING; MEDICINAL CHEMISTRY; MOLECULAR SIMULATIONS; PROTEIN DOMAINS; PROTEIN-LIGAND INTERACTIONS; STRUCTURAL BIOLOGY; TARGET PROTEINS;

BINDING ENERGY;

EID: 79958863650     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp111902t     Document Type: Article

References (38)

1. Koshland, D. E. Proc. Natl. Acad. Sci. U.S.A. 1958, 44, 98
2. Monod, J.; Wyman, J.; Changeux, J. P. J. Mol. Biol. 1965, 12, 88
3. Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R. Protein Sci. 1999, 8, 1181
4. Henzler-Wildman, K. A.; Thai, V.; Lei, M.; Ott, M.; Wolf-Watz, M.; Fenn, T.; Pozharski, E.; Wilson, M. A.; Petsko, G. A.; Karplus, M.; Hubner, C. G.; Kern, D. Nature 2007, 450, 838
5. Xu, Y.; Colletier, J. P.; Jiang, H.; Silman, I.; Sussman, J. L.; Weik, M. Protein Sci. 2008, 17, 601
6. Hammes, G. G.; Chang, Y. C.; Oas, T. G. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 13737
7. Okazaki, K.; Takada, S. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11182
8. Miller, D. W.; Dill, K. A. Protein Sci. 1997, 6, 2166
9. Boehr, D. D.; Nussinov, R.; Wright, P. E. Nat. Chem. Biol. 2009, 5, 789
10. Davidson, A. L. J. Bacteriol. 2002, 184, 1225
11. Manson, M. D. Adv. Microb. Physiol. 1992, 33, 277
12. Oh, B. H.; Pandit, J.; Kang, C. H.; Nikaido, K.; Gokcen, S.; Ames, G. F.; Kim, S. H. J. Biol. Chem. 1993, 268, 11348
13. Millet, O.; Hudson, R. P.; Kay, L. E. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12700
14. Evenas, J.; Tugarinov, V.; Skrynnikov, N. R.; Goto, N. K.; Muhandiram, R.; Kay, L. E. J. Mol. Biol. 2001, 309, 961
15. Medintz, I. L.; Deschamps, J. R. Curr. Opin. Biotechnol. 2006, 17, 17
16. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187
17. Kitao, A.; Hirata, F.; Go, N. Chem. Phys. 1991, 158, 447
18. Kitao, A.; Go, N. Curr. Opin. Struct. Biol. 1999, 9, 164
19. Sharff, A. J.; Rodseth, L. E.; Spurlino, J. C.; Quiocho, F. A. Biochemistry 1992, 31, 10657
20. Quiocho, F. A.; Spurlino, J. C.; Rodseth, L. E. Structure 1997, 5, 997
21. Jones, G.; Willett, P.; Glen, R. C. J. Mol. Biol. 1995, 245, 43
22. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J. Mol. Biol. 1997, 267, 727
23. Case, D. A.; Darden, T. A.; Cheatham, T. E. r.; 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. A. AMBER, version 8.0; University of California: San Francisco, CA, 2004.
24. Narumi, T.; Ohno, Y.; Okimoto, N.; Koishi, T.; Suenaga, A.; Futatsugi, N.; Yanai, R.; Himeno, R.; Fujikawa, S.; Ikei, M.; Taiji, M. A 185 Tflops simulation of amyloid-forming peptides from Yeast Prion Sup35 with the special-purpose computer System MD-GRAPE3. Proc. Supercomputing [CD-ROM] 2006.
25. Taiji, M. MDGRAPE-3 chip: a 165 Gflops application specific LSI for molecular dynamics simulations. Proc. Hot Chips [CD-ROM] 2004, 16.
26. Taiji, M.; Narumi, T.; Ohno, Y.; Futatsugi, N.; Suenaga, A.; Takada, N.; Konagaya, A. Protein explorer: a petaflops special-purpose computer system or molecular dynamics simulations. Proc. Supercomputing [CD-ROM] 2003.
27. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
28. 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
29. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327
30. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
31. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684
32. Chen, J.; Lu, G.; Lin, J.; Davidson, A. L.; Quiocho, F. A. Mol. Cell 2003, 12, 651
33. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1992, 13, 1011
34. Tang, C.; Schwieters, C. D.; Clore, G. M. Nature 2007, 449, 1078
35. Hall, J. A.; Ganesan, A. K.; Chen, J.; Nikaido, H. J. Biol. Chem. 1997, 272, 17615
36. Sharff, A. J.; Rodseth, L. E.; Quiocho, F. A. Biochemistry 1993, 32, 10553
37. Skrynnikov, N. R.; Goto, N. K.; Yang, D.; Choy, W. Y.; Tolman, J. R.; Mueller, G. A.; Kay, L. E. J. Mol. Biol. 2000, 295, 1265
38. Xu, Y.; Zheng, Y.; Fan, J. S.; Yang, D. Nat. Methods 2006, 3, 931