Insights into MAPK p38α DFG flip mechanism by accelerated molecular dynamics

Bioorganic and Medicinal Chemistry

Volumn 18, Issue 18, 2010, Pages 6805-6812

  Filomia, Federico ^a   De Rienzo, Francesca ^a,b   Menziani, M Cristina ^a  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^b CNR   (Italy)

Author keywords

Allosteric inhibitors; Conformational change; DFG loop; Mechanism; Molecular dynamics simulation; p38 MAPKinase

Indexed keywords

ASPARTIC ACID; GLYCINE; MITOGEN ACTIVATED PROTEIN KINASE 14; PHENYLALANINE; DFG PEPTIDE; OLIGOPEPTIDE;

ARTICLE; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; HUMAN; HYDROGEN BOND; MOLECULAR DYNAMICS; PROTEIN MOTIF; SEQUENCE ANALYSIS; ALLOSTERISM; CHEMISTRY; GENETICS; METABOLISM; PROTEIN TERTIARY STRUCTURE; SITE DIRECTED MUTAGENESIS;

ALLOSTERIC REGULATION; AMINO ACID MOTIFS; CATALYTIC DOMAIN; MITOGEN-ACTIVATED PROTEIN KINASE 14; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS, SITE-DIRECTED; OLIGOPEPTIDES; PROTEIN STRUCTURE, TERTIARY;

EID: 77956339455     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2010.07.047     Document Type: Article

References (32)

1. J. Adams, A. Badger, S. Kumar, and J. Lee Prog. Med. Chem. 38 2001 1
2. G. Pearson, F. Robinson, T. Beers Gibson, B. Xu, M. Karandikar, K. Berman, and M. Cobb Endocr. Rev. 22 2001 153
3. J. Subramanian, S. Sharma, and C. B-Rao ChemMedChem 3 2008 336
4. A. Kornev, N. Haste, S. Taylor, and L. Ten Eyck Proc. Natl. Acad. Sci. U.S.A. 103 2006 17783
5. F. Bernstein, T. Koetzle, G. Williams, and E. Meyer Arch. Biochem. Biophys. 185 1978 584
6. K. Wilson, P. McCaffrey, K. Hsiao, S. Pazhanisamy, V. Galullo, G. Bemis, M. Fitzgibbon, P. Caron, M. Murcko, and M. Su Chem. Biol. 4 1997 423
7. A. Gill, M. Frederickson, A. Cleasby, S. Woodhead, M. Carr, A. Woodhead, M. Walker, M. Congreve, L. Devine, and D. Tisi J. Med. Chem. 48 2005 414
8. F. Zuccotto, E. Ardini, E. Casale, and M. Angiolini J. Med. Chem. 53 2010 2681
9. I. Kufareva, and R. Abagyan J. Med. Chem. 51 2008 7921
10. J. Simard, M. Getlik, C. Grutter, R. Schneider, S. Wulfert, and D. Rauh J. Am. Chem. Soc. 132 2010 4152
11. T. Zhou, L. Commodore, W. Huang, Y. Wang, T. Sawyer, W. Shakespeare, T. Clackson, X. Zhu, and D. Dalgarno Chem. Biol. Drug Des. 75 2010 18
12. Y. Liu, and N. Gray Nat. Chem. Biol. 2 2007 358
13. B. Okram, A. Nagle, F. Adrián, C. Lee, P. Ren, X. Wang, T. Sim, Y. Xie, X. Wang, G. Xia, G. Spraggon, M. Warmuth, Y. Liu, and N. Gray Chem. Biol. 13 2006 779
14. R. Angell, T. Angell, P. Bamborough, M. Bamford, C. Chung, S. Cockerill, S. Flack, K. Jones, D. Laine, and T. Longstaff Bioorg. Med. Chem. Lett. 18 2008 4433
15. M. Vogtherr, K. Saxena, S. Hoelder, S. Grimme, M. Betz, U. Schieborr, B. Pescatore, M. Robin, L. Delarbre, T. Langer, K.U. Wendt, and H. Schwalbe Angew. Chem., Int. Ed. 45 2006 993
16. T. Frembgen-Kesner, and A. Elcock J. Mol. Biol. 359 2006 202
17. Y. Shana, M.A. Seeliger, F. Eastwood, M.P. Frank, H. Xua, M.O. Jensena, R.O. Drora, J. Kuriyan, and D. Shaw Proc. Natl. Acad. Sci. U.S.A. 106 2009 139
18. M. Bukhtiyarova, M. Karpusas, K. Northrop, H.V.M. Namboodiri, and E.B. Springman Biochemistry 46 2007 5687
19. J. Sullivan, G. Holdgate, D. Campbell, D. Timms, S. Gerhardt, J. Breed, A. Breeze, A. Bermingham, R. Pauptit, and R. Norman Biochemistry 44 2005 16475
20. J. Simard, M. Getlik, C. Grutter, V. Pawar, S. Wulfert, M. Rabiller, and D. Rauh J. Am. Chem. Soc. 131 2009 13286
21. J. Simard, C. Grutter, V. Pawar, B. Aust, A. Wolf, M. Rabiller, S. Wulfert, A. Robubi, S. Kluter, and C. Ottmann J. Am. Chem. Soc. 131 2009 18478
22. E. Lindahl, B. Hess, and D. van der Spoel J. Mol. Model. 7 2001 306
23. H. Berendsen, D. Van der Spoel, and R. Van Drunen Comp. Phys. Commun. 91 1995 43
24. van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meu-lenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual Version. http://www.gromacs.org, 2005.
25. Url = http://accelrys.com/products/quanta/index.html, 2006.
26. B. Hess, H. Bekker, H. Berendsen, and J. Fraaije J. Comp. Chem. 18 1997 1463
27. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus J. Comp. Chem. 4 1983 187
28. Url = http://accelrys.com/products/discovery-studio, 2007.
29. F. Costanzo, R. Della Valle, and V. Barone J. Phys. Chem. B 109 2005 23016
30. J.S. Rao, H. Zipse, and G.N. Sastry J. Phys. Chem. B 113 2009 7225
31. D. Dougherty J. Nutr. 137 2007 1504S
32. W. Humphrey, A. Dalke, and K. Schulten J. Mol. Graphics 14 1996 33