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Copper coordination to the putative cell binding site of angiogenin: a DFT investigation

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Abstract

We present a DFT study of the structural and spectroscopic properties of the complex formed by Cu2+ with the peptide fragment Ac-PHREN-NH2, which encompasses the putative cell binding domain of angiogenin, as well as with its Ac-PHRQN-NH2 variant. Analysis of structures, energies and spectroscopic parameters has allowed to conclude that the metal coordination environment at pH 8 is formed by a nitrogen atom of His, two deprotonated amide groups, and an oxygen atom from the COO− side chain of Glu, in nice agreement with recent experimental results (La Mendola et al. in Dalton Trans, 39:10678, 2010). Moreover, DFT results allowed to reveal that the Glu side chain of the Ac-PHREN-NH2 peptide is coordinated in equatorial position, in a tetrahedrically distorted square planar arrangement, fully disclosing the effects of Cu2+ binding on the structural properties of this key angiogenin portion. In the Ac-PHRQN-NH2 variant, the carboxylate group is replaced by a H2O molecule in a coordination arrangement similar to that of the wild-type system.

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References

  1. Folkman J (1989) J Natl Cancer Inst 82:4

    Google Scholar 

  2. Bussolino F, Mantovani A, Persico G (1997) Trends Biochem Sci 22:251

    Article  CAS  Google Scholar 

  3. Kishimoto K, Liu S, Tsuji T, Olson KA, Hu G (2005) Oncogene 24:445

    Article  CAS  Google Scholar 

  4. Fett JW, Strydom DJ, Lobb RR, Alderman EM, Bethune JL, Riordan JF, Vallee BL (1985) Biochemistry 24:5486

    Article  Google Scholar 

  5. Gao X, Xu Z (2008) Acta Biochim Biophys Sin 40:619

    Google Scholar 

  6. Badet J, Soncin J, Guitton JD, Lamare O, Cartwright T, Barritault D (1989) Proc Natl Acad Sci USA 86:8427

    Article  CAS  Google Scholar 

  7. McAuslan BR, Reilly W (1980) Exp Cell Res 130:147

    Article  CAS  Google Scholar 

  8. Hu G-F (1998) J Cell Biochem 69:326

    Article  CAS  Google Scholar 

  9. Lequin O, Thuring H, Robin M, Lallemand J-Y (1997) Eur J Biochem 250:712

    Article  CAS  Google Scholar 

  10. Millhauser GL (2007) Annu Rev Phys Chem 58:299

    Article  CAS  Google Scholar 

  11. Solioz M, Vulpe C (1996) Trends Biochem Sci 21:237

    CAS  Google Scholar 

  12. Soncin F, Guitton JD, Cartwright T, Badet J (1997) Biochem Biophys Res Commun 236:604

    Article  CAS  Google Scholar 

  13. Joyce BK, Cohn M (1969) J Biol Chem 244:811

    CAS  Google Scholar 

  14. Acharya KR, Shapiro R, Allen SC, Riordan JF, Vallee BL (1994) Proc Natl Acad Sci USA 91:2915

    Article  CAS  Google Scholar 

  15. Smyth DG, Stein WH, Moore S (1963) J Biol Chem 238:227

    CAS  Google Scholar 

  16. La Mendola D, Magri A, Vagliasindi LI, Hansson O, Bonomo RP, Rizzarelli E (2010) Dalton Trans 39:10678

    Article  Google Scholar 

  17. Halgren TA (1996) J Comput Chem 17:490

    Article  CAS  Google Scholar 

  18. Halgren TA (1999) J Comput Chem 20:720

    Article  CAS  Google Scholar 

  19. Becke AD (1988) Phys Rev A 38:3098

    Article  CAS  Google Scholar 

  20. Perdew JP (1986) Phys Rev B 33:8822

    Article  Google Scholar 

  21. Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Theor Chem Acc 97:119

    Article  CAS  Google Scholar 

  22. Ahlrichs R, Bar M, Haser M, Horn H, Kolmel C (1989) Chem Phys Lett 62:165

    Article  Google Scholar 

  23. Schafer A, Huber C, Ahlrichs R (1994) J Chem Phys 100:5829

    Article  Google Scholar 

  24. Bruschi M, De Gioia L, Mitric R, Bonacic-Koutecky V, Fantucci P (2008) Phys Chem Chem Phys 10:4573

    Article  CAS  Google Scholar 

  25. Schafer A, Horn H, Ahlrichs R (1992) J Chem Phys 97:2571

    Article  Google Scholar 

  26. Kutzelnigg W, Fleischer U, Schindler M (1990) The IGLO-method: Ab initio calculation and interpretation of NMR chemical shifts and magnetic susceptibilities. Springer, Berlin

    Google Scholar 

  27. Hess BA, Marian CM, Walhgren U, Gropen O (1996) Chem Phys Lett 251:365

    Article  CAS  Google Scholar 

  28. Kaupp M, Buhl M, Malkin VG (2004) Calculation of NMR and EPR parameters: theory and applications. Wiley-VCH

  29. Neese F (2003) J Chem Phys 117:3939

    Article  Google Scholar 

  30. Marino T, Russo N, Toscano M (2007) J Phys Chem B 111:635

    Article  CAS  Google Scholar 

  31. Marino T, Russo N, Toscano M (2011) Int J Quantum Chem 111:1152

    Article  CAS  Google Scholar 

  32. Pushie MJ, Rauk A (2003) J Biol Inorg Chem 8:53

    Article  CAS  Google Scholar 

  33. Franzini E, De Gioia L, Fantucci P, Zampella G, Bonacic-Koutecky V (2003) Inorg Chem Commun 6:650

    Article  CAS  Google Scholar 

  34. Sabolovic J, Tautermann CS, Loerting T, Liedl KR (2003) Inorg Chem 42:2268

    Article  CAS  Google Scholar 

  35. Adamo C, Scuseria G, Barone V (1999) J Chem Phys 111:2889

    Article  CAS  Google Scholar 

  36. Klamt A (1995) J Phys Chem A 99:2224

    CAS  Google Scholar 

  37. Klamt A (1996) J Phys Chem A 100:3349

    CAS  Google Scholar 

  38. Klamt A, Schüürmann G (1993) J Chem Soc Perkin Trans 2:799

    Google Scholar 

  39. Hallahan TW (1991) Proc Natl Acad Sci USA 85:5061

    Google Scholar 

Download references

Acknowledgments

This work was supported by the PRIN Project N 200875WHMR.

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Authors and Affiliations

  1. Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano Bicocca, Piazza della Scienza, 2, 20126, Milan, Italy

    Luca Bertini, Marco Romaniello, Giuseppe Zampella, Matteo Tiberti, Valentina Barbieri, Claudio Greco, Piercarlo Fantucci & Luca De Gioia

  2. Dipartimento di Scienze Ambientali, Università degli Studi di Milano Bicocca, Piazza della Scienza, 1, 20126, Milan, Italy

    Maurizio Bruschi

  3. Istituto di Biostrutture e Bioimmagini, CNR, Viale A. Doria 6, 95125, Catania, Italy

    Diego La Mendola

  4. Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy

    Raffaele P. Bonomo

Authors
  1. Luca Bertini
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  2. Maurizio Bruschi
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  3. Marco Romaniello
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  4. Giuseppe Zampella
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  6. Valentina Barbieri
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  7. Claudio Greco
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  8. Diego La Mendola
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  9. Raffaele P. Bonomo
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  10. Piercarlo Fantucci
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  11. Luca De Gioia
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Correspondence to Luca De Gioia.

Additional information

Dedicated to Professor Vincenzo Barone and published as part of the special collection of articles celebrating his 60th birthday.

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Bertini, L., Bruschi, M., Romaniello, M. et al. Copper coordination to the putative cell binding site of angiogenin: a DFT investigation. Theor Chem Acc 131, 1186 (2012). https://doi.org/10.1007/s00214-012-1186-y

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