Journal of Molecular Modeling

, Volume 10, Issue 1, pp 25–31 | Cite as

Active site modeling in copper azurin molecular dynamics simulations

  • Bruno Rizzuti
  • Marcel Swart
  • Luigi Sportelli
  • Rita Guzzi
Original Paper

Abstract

Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the polypeptide chain, using for the ligand residues a set of charges that is modified with respect to the apo form of the protein by the presence of the copper ion.

The results show that the different charge values do not lead to relevant effects on the geometry of the active site of the protein, as long as bond distance constraints are used for all the five ligand atoms. The distance constraint on the O atom of Gly45 can be removed without altering the active site geometry. The coordination between Cu and the other axial ligand Met121 is outlined as being flexible. Differences are found between the bonds of the copper ion with the two apparently equivalent Nδ1 atoms of His46 and His117.

The overall findings are discussed in connection with the issue of determining a model for the active site of azurin suitable to be used in molecular dynamics simulations under unfolding conditions.

Figure Model of azurin active site. Copper ligand residues are cut off at Cα position except Gly45, for which the portion of backbone connecting it to His46 is shown. Only polar H atoms are shown. All atoms are in standard colors (Cu in violet), and the five ligands are labeled

Keywords

Azurin Active site Molecular dynamics simulation 

References

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

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Bruno Rizzuti
    • 1
  • Marcel Swart
    • 2
    • 3
  • Luigi Sportelli
    • 1
  • Rita Guzzi
    • 1
  1. 1.Dipartimento di Fisica and Unità INFM, Laboratorio di Biofisica MolecolareUniversità della CalabriaRende CSItaly
  2. 2.Theoretische Chemie (MSC)Rijksuniversiteit GroningenGroningenThe Netherlands
  3. 3.Organische en Anorganische ChemieVrije Universiteit AmsterdamAmsterdamThe Netherlands

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