Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

Chemical Physics Letters

Volumn 559, Issue , 2013, Pages 94-98

  Takemura, Kazuhiro ^a   Burri, Raghunadha Reddy ^a,b   Ishikawa, Takeshi ^b,c   Ishikura, Takakazu ^c   Sakuraba, Shun ^d,e   Matubayasi, Nobuyuki ^b,d   Kuwata, Kazuo ^b,c   Kitao, Akio ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c GIFU UNIVERSITY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; CRYSTAL STRUCTURE; ENZYMES; FREE ENERGY; MOLECULAR DYNAMICS;

BINDING FREE ENERGY; ENERGY REPRESENTATIONS; FREE ENERGY ANALYSIS; HEN EGG WHITE LYSOZYME; MOLECULAR DYNAMICS SIMULATIONS; N-ACETYL-D-GLUCOSAMINE; PROTEIN-LIGAND COMPLEXES; SOLUTION THEORY;

BINDING ENERGY;

EID: 84873704422     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2012.12.063     Document Type: Article

References (35)

1. P. Kollman Chem. Rev. 93 1993 2395
2. M.R. Shirts, D.L. Mobley, and J.D. Chodera Annu. Rep. Comput. Chem. 3 2007 41
3. J.D. Chodera, D.L. Mobley, M.R. Shirts, R.W. Dixon, K. Branson, and V.S. Pande Curr. Opin. Struct. Biol. 21 2011 150
4. R.W. Zwanzig J. Chem. Phys. 22 1954 1420
5. J. Qvist, C. Medina, and J.E. Samuelsson Protein Eng. 7 1994 385
6. N. Matubayasi, and M. Nakahara J. Chem. Phys. 113 2000 6070
7. N. Matubayasi, and M. Nakahara J. Chem. Phys. 117 2002 3605 (J. Chem. Phys. 118 (2003) 2446 (erratum))
8. N. Matubayasi, and M. Nakahara J. Chem. Phys. 119 2003 9686
9. Y. Karino, M.V. Fedorov, and N. Matubayasi Chem. Phys. Lett. 496 2010 351
10. R. Wolfenden, L. Andersson, P.M. Cullis, and C.C.B. Southgate Biochemistry (Mosc.) 20 1981 849
11. M.R. Shirts, and V.S. Pande J. Chem. Phys. 122 2005
12. K. Maenaka, M. Matsushima, H. Song, F. Sunada, K. Watanabe, and I. Kumagai J. Mol. Biol. 247 1995 281
13. N. Kamiya, Y. Yonezawa, H. Nakamura, and J. Higo Proteins-Struct., Funct., Bioinf. 70 2008 41
14. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson J. Comput. Chem. 19 1998 1639
15. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor J. Mol. Biol. 267 1997 727
16. R. Thomsen, and M.H. Christensen J. Med. Chem. 49 2006 3315
17. J.C. Cheetham, P.J. Artymiuk, and D.C. Phillips J. Mol. Biol. 224 1992 613
18. D.A. McQuarrie Statistical Mechanics 2000 University Science Books Sausalito
19. M. Karplus, and J.N. Kushick Macromolecules 14 1981 325
20. A. Kitao, F. Hirata, and N. Go Chem. Phys. 158 1991 447
21. J. Schlitter Chem. Phys. Lett. 215 1993 617
22. I. Andricioaei, and M. Karplus J. Chem. Phys. 115 2001 6289
23. R. Baron, W.F. van Gunsteren, and P.H. Hünenberger Trends Phys. Chem. 11 2006 87
24. J. Numata, M. Wan, and E.-W. Knapp Genome Inform. 18 2007 191
25. H. Saito, N. Matubayasi, K. Nishikawa, and H. Nagao Chem. Phys. Lett. 497 2010 218
26. Y. Karino, and N. Matubayasi J. Chem. Phys. 134 2011
27. K. Takemura, H. Guo, S. Sakuraba, N. Matubayasi, and A. Kitao J. Chem. Phys. 137 2012 215105
28. N. Matubayasi, W. Shinoda, and M. Nakahara J. Chem. Phys. 128 2008 195107
29. M.C. Vaney, S. Maignan, M. RiesKautt, and A. Ducruix Acta Crystallogr. D: Biol. Crystallogr. 52 1996 505
30. J.C. Phillips J. Comput. Chem. 26 2005 1781
31. A.D. MacKerell J. Phys. Chem. B 102 1998 3586
32. A.D. Mackerell Jr., M. Feig, and C.L. Brooks 3rd J. Comput. Chem. 25 2004 1400
33. O. Guvench J. Chem. Theory Comput. 7 2011 3162
34. T. Wiseman, S. Williston, J.F. Brandts, and L.N. Lin Anal. Biochem. 179 1989 131
35. W. Humphrey, A. Dalke, and K. Schulten J. Mol. Graph. Model. 14 1996 33