The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment

Chemical Physics Letters

Volumn 456, Issue 4-6, 2008, Pages 236-242

  Mollica, Luca ^a,b   Curioni, Alessandro ^b   Andreoni, Wanda ^b   Bianchi, Marco E ^a,c   Musco, Giovanna ^a,c  

^a DULBECCO TELETHON INSTITUTE   (Italy)

^b IBM RESEARCH ZURICH   (Switzerland)

^c VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR MODELING; PROTEINS;

BINDING DOMAIN; CARBENOXOLONE; PRO-INFLAMMATORY ACTIVITY;

ENZYME INHIBITION;

EID: 42249094359     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2008.03.022     Document Type: Article

References (35)

1. Wang H., et al. Science 285 (1999) 248
2. Sakamoto R., Okano M., Takena H., and Ohtsuki K. Biol. Pharm. Bull. 24 (2001) 906
3. Scaffidi P., Misteli T., and Bianchi M.E. Nature 418 (2002) 191
4. Yang H., et al. Proc. Natl. Acad. Sci. USA 101 (2004) 296
5. Knapp S., Muller S., Digilio G., Bonaldi T., Bianchi M.E., and Musco G. Biochemistry 43 (2004) 11992
6. Bianchi M.E., and Manfredi A. Biochim. Biophys. Acta 1677 (2004) 181
7. Yang H., Wang H., Czura C.J., and Tracey K.J. J. Leukocyte Biol. 78 (2005) 1
8. Lotze M.T., and Tracey T.J. Nat. Rev. 5 (2005) 331
9. Qin S., et al. J. Exp. Med. 203 (2006) 1637
10. Bell C.W., Jiang W.W., Reich C.F., and Pisetsky D.S. Am. J. Physiol.-Cell Physiol. 291 (2006) C1318
11. Sitia G., Iannacone M., Müller S., Bianchi M.E., and Guidotti L.G. J. Leukocyte Biol. 81 (2007) 100
12. Mollica L., et al. Chem. Biol. 14 (2007) 431
13. Hardman C.H., Broadhurst R.W., Raine A.R., Grasser K.D., Thomas J.O., and Laue E.D. Biochemistry 34 (1995) 16596
14. Weir H.M., Kraulis P.J., Hill C.S., Raine A.R., Laue E.D., and Thomas J.O. EMBO J. 12 (1993) 1311
15. van Gunsteren W.F., et al. Biomolecular Simulation: The GROMOS96 Manual and User Guide. vdF: Hochschulverlag AG an der ETH Zürich (1996), Zurich Switzerland, & BIOMOS b.v. Groningen, The Netherlands
16. Schuttelkopf A.W., and van Aalten D.M. Acta Crystallogr. D 60 (2004) 1355
17. Curioni A., Mordasini T., and Andreoni W. J. Comput. Aid. Mol. Des. 18 (2004) 773
18. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. J. Comput. Chem. 19 (1998) 1639
19. Berendsen H.J.C., van der Spoel D., and van Drunen R. Comp. Phys. Commun. 91 (1995) 43
20. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Di Nola A A., and Haak J.R. J. Chem. Phys. 81 (1984) 3684
21. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J. J. Comput. Chem. 18 (1997) 1463
22. Darden T., York D., and Pedersen L. J. Chem. Phys. 98 (1993) 10089
23. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. In: Pullman B. (Ed). Intermolecular Forces (1981), Reidel, Dordrecht, The Netherlands 331
24. van Gunsteren W.F., et al. CHIMIA 55 (2001) 856
25. Mordasini T., Curioni A., Bursi R., and Andreoni W. Chem BioChem 4 (2003) 155
26. CPMD V3.11, Copyright IBM Corporation 1990-2008; MPI für Festkörperforschung, Stuttgart, Germany, 1997-2001.
27. Becke A.D. Phys. Rev. A 38 (1988) 3098
28. Lee C., Yang W., and Parr R.G. Phys. Rev. B 37 (1988) 785
29. Troullier N., and Martins J.L. Phys. Rev. B 43 (1991) 1993
30. Ghosh D., Erman M., Wawrzak Z., Duax W.I., and Pangborn W. Str. Form. Funct. Mod. Biol. 2 (1994) 973
31. Ferrara Ph., et al. J. Chem. Inf. Model 46 (2006) 254
32. Sugita Y., and Okamoto Y. Chem. Phys. Lett. 314 (1999) 141
33. Meyer M., and Meyer B. Angew. Chem. Int. Ed. 38 (1999) 1784
34. Neuhaus D., and Williamson M.P. The Nuclear Overhauser Effect in Structural and Conformational Analysis (2000), John Wiley & Sons, New York
35. Zagrovic B., and van Gunsteren W.F. PROTEINS: Struct. Funct. Bioinform. 63 (2006) 210