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Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control

  • Luciano A. AbriataEmail author
  • Alejandro J. VilaEmail author
  • Matteo Dal Peraro
Original Paper
Part of the following topical collections:
  1. Topical Issue in honor of Ivano Bertini

Abstract

Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a distinct electronic structure compared with those of non-ET-competent copper complexes. The entatic or rack-induced state hypothesis explains these special properties in terms of the strain that the protein matrix exerts on the metal ions. This idea is supported by X-ray structures of apocupredoxins displaying “closed” arrangements of the copper ligands like those observed in the holoproteins; however, it implies completely buried copper-binding atoms, conflicting with the notion that they must be exposed for copper loading. On the other hand, a recent work based on NMR showed that the copper-binding regions of apocupredoxins are flexible in solution. We have explored five cupredoxins in their “closed” apo forms through molecular dynamics simulations. We observed that prearranged ligand conformations are not stable as the X-ray data suggest, although they do form part of the dynamic landscape of the apoproteins. This translates into variable flexibility of the copper-binding regions within a rigid fold, accompanied by fluctuations of the hydrogen bonds around the copper ligands. Major conformations with solvent-exposed copper-binding atoms could allow initial binding of the copper ions. An eventual subsequent incursion to the closed state would result in binding of the remaining ligands, trapping the closed conformation thanks to the additional binding energy and the fastening of noncovalent interactions that make up the rack.

Keywords

Cupredoxins Flexibility Metal ion binding Copper Entatic state 

Notes

Acknowledgments

L.A.A. acknowledges EMBO and the Marie Curie Actions for a Long-Term Fellowship. A.J.V. is a staff member from CONICET, and work at Rosario is funded by ANPCyT (PICT-2012-1285). Dr. María Eugenia Zaballa is acknowledged for manuscript proofreading.

References

  1. 1.
    Gray HB, Malmström BG, Williams RJ (2000) J Biol Inorg Chem 5:551–559PubMedCrossRefGoogle Scholar
  2. 2.
    Randall DW, Gamelin DR, LaCroix LB, Solomon EI (2000) J Biol Inorg Chem 5:16–29PubMedGoogle Scholar
  3. 3.
    Malmström BG (1994) Eur J Biochem 223:711–718PubMedCrossRefGoogle Scholar
  4. 4.
    Ryde U, Olsson MH, Roos BO et al (2000) J Biol Inorg Chem 5:565–574PubMedCrossRefGoogle Scholar
  5. 5.
    Marcus RA, Sutin N (1985) Biochim Biophys Acta 811:265–322CrossRefGoogle Scholar
  6. 6.
    Gray HB, Winkler JR (1996) Annu Rev Biochem 65:537–561PubMedCrossRefGoogle Scholar
  7. 7.
    Di Bilio AJ, Hill MG, Bonander N et al (1997) J Am Chem Soc 119:9921–9922CrossRefGoogle Scholar
  8. 8.
    Farver O, Lu Y, Ang MC, Pecht I (1999) Proc Natl Acad Sci USA 96:899–902PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Abriata LA, Álvarez-Paggi D, Ledesma GN et al (2012) Proc Natl Acad Sci USA 109:17348–17353PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Warren JJ, Lancaster KM, Richards JH, Gray HB (2012) J Inorg Biochem 115:119–126PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Abriata LA (2012) Acta Crystallogr Sect D 68:1223–1231CrossRefGoogle Scholar
  12. 12.
    Sato K, Li C, Salard I et al (2009) Proc Natl Acad Sci USA 106:5616–5621PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Velarde M, Huber R, Yanagisawa S et al (2007) Biochemistry 46:9981–9991PubMedCrossRefGoogle Scholar
  14. 14.
    Battistuzzi G, Borsari M, Dennison C et al (2009) Biochim Biophys Acta 1794:995–1000PubMedCrossRefGoogle Scholar
  15. 15.
    Buning C, Canters GW, Comba P et al (2000) J Am Chem Soc 122:204–211CrossRefGoogle Scholar
  16. 16.
    Li C, Banfield MJ, Dennison C (2007) J Am Chem Soc 129:709–718PubMedCrossRefGoogle Scholar
  17. 17.
    Yanagisawa S, Dennison C (2004) J Am Chem Soc 126:15711–15719PubMedCrossRefGoogle Scholar
  18. 18.
    Lancaster KM, Zaballa M-E, Sproules S et al (2012) J Am Chem Soc 134:8241–8253PubMedCrossRefGoogle Scholar
  19. 19.
    Machczynski MC, Gray HB, Richards JH (2002) J Inorg Biochem 88:375–380PubMedCrossRefGoogle Scholar
  20. 20.
    Paltrinieri L, Borsari M, Battistuzzi G et al (2013) Biochemistry 52:7397–7404PubMedCrossRefGoogle Scholar
  21. 21.
    Sinnecker S, Neese F (2006) J Comput Chem 27:1463–1475PubMedCrossRefGoogle Scholar
  22. 22.
    Lancaster KM, Farver O, Wherland S et al (2011) J Am Chem Soc 133:4865–4873PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Nar H, Messerschmidt A, Huber R et al (1992) FEBS Lett 306:119–124PubMedCrossRefGoogle Scholar
  24. 24.
    Baker EN, Anderson BF, Blackwell KE et al (1991) J Inorg Biochem 43:162CrossRefGoogle Scholar
  25. 25.
    Garrett TP, Clingeleffer DJ, Guss JM et al (1984) J Biol Chem 259:2822–2825PubMedGoogle Scholar
  26. 26.
    Petratos K, Papadovasilaki M, Dauter Z (1995) FEBS Lett 368:432–434PubMedCrossRefGoogle Scholar
  27. 27.
    Durley R, Chen L, Lim LW et al (1993) Protein Sci 2:739–752PubMedCentralPubMedCrossRefGoogle Scholar
  28. 28.
    Abriata LA, Banci L, Bertini I et al (2008) Nat Chem Biol 4:599–601PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Zaballa M-E, Abriata LA, Donaire A, Vila AJ (2012) Proc Natl Acad Sci USA 109:9254–9259PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Hass MAS, Vlasie MD, Ubbink M, Led JJ (2009) Biochemistry 48:50–58PubMedCrossRefGoogle Scholar
  31. 31.
    Alvarez-Paggi D, Abriata LA, Murgida DH, Vila AJ (2013) Chem Commun 49:5381–5383CrossRefGoogle Scholar
  32. 32.
    Bai Y, Chung J, Dyson HJ, Wright PE (2001) Protein Sci 10:1056–1066PubMedCentralPubMedCrossRefGoogle Scholar
  33. 33.
    Williams PA, Blackburn NJ, Sanders D et al (1999) Nat Struct Biol 6:509–516PubMedCrossRefGoogle Scholar
  34. 34.
    Phillips JC, Braun R, Wang W et al (2005) J Comput Chem 26:1781–1802PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Hornak V, Abel R, Okur A et al (2006) Proteins 65:712–725PubMedCrossRefGoogle Scholar
  36. 36.
    Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) J Chem Phys 79:926–935CrossRefGoogle Scholar
  37. 37.
    Piana S, Lindorff-Larsen K, Dirks RM et al (2012) PLoS One 7:e39918. doi: 10.1371/journal.pone.0039918 PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Humphrey W, Dalke A, Schulten K (1996) J Mol Graphics 14:33–38CrossRefGoogle Scholar
  39. 39.
    Caliandro R, Rossetti G, Carloni P (2012) J Chem Theory Comput 8:4775–4785CrossRefGoogle Scholar
  40. 40.
    Abriata LA, Ledesma GN, Pierattelli R, Vila AJ (2009) J Am Chem Soc 131:1939–1946PubMedCentralPubMedCrossRefGoogle Scholar
  41. 41.
    Rizzuti B, Sportelli L, Guzzi R (2009) Proteins 74:961–971PubMedCrossRefGoogle Scholar
  42. 42.
    Rizzuti B, Sportelli L, Guzzi R (2007) Biophys Chem 125:532–539PubMedCrossRefGoogle Scholar
  43. 43.
    Gorelsky SI, Xie X, Chen Y et al (2006) J Am Chem Soc 128:16452–16453PubMedCrossRefGoogle Scholar
  44. 44.
    Hadt RG, Sun N, Marshall NM et al (2012) J Am Chem Soc 134:16701–16716PubMedCentralPubMedCrossRefGoogle Scholar
  45. 45.
    Abriata LA, Vila AJ (2013) J Inorg Biochem. doi: 10.1016/j.jinorgbio.2013.07.032 PubMedGoogle Scholar
  46. 46.
    Blaszak JA, McMillin DR, Thornton AT, Tennent DL (1983) J Biol Chem 258:9886–9892PubMedGoogle Scholar
  47. 47.
    Chacón KN, Blackburn NJ (2012) J Am Chem Soc 134:16401–16412PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© SBIC 2014

Authors and Affiliations

  1. 1.Laboratory of Biomolecular Modeling, School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
  2. 2.Swiss Institute of BioinformaticsLausanneSwitzerland
  3. 3.Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina

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