Active site modeling in copper azurin molecular dynamics simulations

Journal of Molecular Modeling

Volumn 10, Issue 1, 2004, Pages 25-31

  Rizzuti, Bruno ^a   Swart, Marcel ^b,c   Sportelli, Luigi ^a   Guzzi, Rita ^a  

^a UNIVERSITY OF CALABRIA   (Italy)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Active site; Azurin; Molecular dynamics simulation

Indexed keywords

APOPROTEIN; AZURIN; COORDINATION COMPOUND; COPPER ION; HISTIDINE; LIGAND; METAL; NITROGEN; OXYGEN; POLYPEPTIDE; COPPER; GLYCINE; ION; METALLOPROTEIN;

ARTICLE; ATOM; CHEMICAL BOND; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; ELECTRICITY; GEOMETRY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; REDUCTION; ROOM TEMPERATURE; SURFACE CHARGE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; TEMPERATURE; TIME;

AZURIN; BINDING SITES; COPPER; ELECTROSTATICS; GLYCINE; IONS; LIGANDS; METALLOPROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; TEMPERATURE; TIME FACTORS;

EID: 2942700186     PISSN: 16102940     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00894-003-0165-6     Document Type: Article

References (46)

1. Shen J, Wong CF, Subramanian S, Albright TA, McCammon JA (1990) J Comput Chem 11:346-350
2. Fields BA, Guss JM, Freeman HC (1991) J Mol Biol 222:1053-1065
3. Banci L, Carloni P, La Penna G, Orioli PL (1992) J Am Chem Soc 114:6994-7001
4. Wang CX, Bizzarri AR, Xu YW, Cannistraro S (1994) Chem Phys 183:155-166
5. Mark AE, van Gunsteren WF (1994) J Mol Biol 240:167-176
6. Falconi M, Gallimbeni R, Paci E (1996) J Comput Aided Mol Design 10:490-498
7. Ungar LW, Scherer NF, Voth GA (1997) Biophys J 72:5-17
8. Subramanian V, Shankaranarayanan C, Nair BU, Kanthimathi M, Manickkavachagam R, Ramasami T (1997) Chem Phys Lett 274:275-280
9. De Kerpel JO, Ryde U (1999) Proteins 36:157-174
10. Gray HB, Malmström BG (2000) J Biol Inorg Chem 5:551-559
11. Arcangeli C, Bizzarri AR, Cannistraro S (1999) Biophys Chem 78:247-257
12. Luise A, Falconi M, Desideri A (2000) Proteins 39:56-67
13. Arcangeli C, Bizzarri AR, Cannistraro S (2001) Biophys Chem 90:45-56
14. Romero C, Moratal JM, Donaire A (1998) FEBS Lett 440:93-98
15. De Beer S, Wittung-Stafshede P, Leckner J, Karlsson BG, Winkler JR, Gray HB, Malmström BG, Solomon EI, Hedman B, Hodgson KO (2000) Inorg Chim Acta 297:278-282
16. Swart M (2002) Density functional theory applied to copper proteins. PhD thesis, Rijksuniversiteit Groningen, Groningen
17. te Velde G, Bickelhaupt FM, Baerends EJ, Fonseca Guerra C, van Gisbergen SJA, Snijders JG, Ziegler T (2001) J Comput Chem 22:931-967
18. Swart M, van den Bosch M, Berendsen HJC, Canters GW, Mark AE, Snijders JG (2003) in preparation
19. Canters GW, Kalverda AP, Hoitink CW (1993) Structure and activity of type I Cu sites. In: Welch AJ, Chapman SK (eds) The chemistry of the copper and zinc triads. The Royal Society of Chemistry, Cambridge, pp 30-37
20. Pozdnyakova I, Guidry J, Wittung-Stafshede P (2000) J Am Chem Soc 122:6337-6338
21. Pozdnyakova I, Guidry J, Wittung-Stafshede P (2001) J Biol Inorg Chem 6:182-188
22. Berendsen HJC, van der Spoel D, van Drunen R (1995) Comput Phys Comm 91:43-56
23. Lindahl E, Hess B, van der Spoel D (2001) J Mol Mod 7:306-317
24. van Gunsteren WF, Billeter FR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG (1996) Biomolecular simulation: the GROMOS96 manual and user guide. Vdf Hochschulverlag AG an der ETH Zürich, Zürich
25. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235-242
26. Nar H, Messerschmidt A, Huber R, van de Kamp M, Canters GW (1991) J Mol Biol 218:427-447
27. Nar H, Messerschmidt A, Huber R, van de Kamp M, Canters GW (1991) J Mol Biol 221:765-772
28. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. Reidel, Dordrecht, pp 331-342
29. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) J Comp Chem 18:1463-1472
30. Miyamoto S, Kollman PA (1992) J Comp Chem 13:952-962
31. Berendsen HJC, Postma JPM, Di Nola A, Haak JR (1984) J Chem Phys 81:3684-3690
32. Hol WGJ, van Duijnen PT, Berendsen HJC (1978) Nature 273:443-446
33. Matthews BW (1993) Curr Opin Struct Biol 3:589-593
34. Kalverda AP, Ubbink M, Gilardi G, Wijmenga SS, Crawford A, Jeuken LJC, Canters GW (1999) Biochemistry 38:12690-12697
35. Holm RH, Kennepohl P, Solomon EI (1996) Chem Rev 96:2239-2314
36. La Croix LB, Shadle SE, Wang Y, Averill BA, Hedman B, Hodgson KO, Solomon EI (1996) J Am Chem Soc 118:7755-7768
37. Guckert JA, Lowery MD, Solomon EI (1995) J Am Chem Soc 117:2817-2844
38. Gray HB, Malmström BG (1983) Comments Inorg Chem 2:203-209
39. Malmström BG (1994) Eur J Biochem 223:207-216
40. Williams RJP (1995) Eur J Biochem 234:363-381
41. Ryde U, Olsson MHM, Pierloot K, Roos BO (1996) J Mol Biol 261:586-596
42. Olsson MHM, Ryde U, Roos BO, Pierloot K (1998) J Biol Inorg Chem 3:109-125
43. Pierloot K, De Kerpel JO, Ryde U, Olsson MHM, Roos BO (1998) J Am Chem Soc 120:13156-13166
44. Ryde U, Olsson MHM (2001) Int J Quantum Chem 81:335-347
45. Swart M, van den Bosch M, Berendsen HJC, Canters GW, Snijders JG (2003) in preparation
46. Koradi R, Billeter M, Wüthrich K (1996) J Mol Graphics 14:51-55