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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Folkman J (1989) J Natl Cancer Inst 82:4
Bussolino F, Mantovani A, Persico G (1997) Trends Biochem Sci 22:251
Kishimoto K, Liu S, Tsuji T, Olson KA, Hu G (2005) Oncogene 24:445
Fett JW, Strydom DJ, Lobb RR, Alderman EM, Bethune JL, Riordan JF, Vallee BL (1985) Biochemistry 24:5486
Gao X, Xu Z (2008) Acta Biochim Biophys Sin 40:619
Badet J, Soncin J, Guitton JD, Lamare O, Cartwright T, Barritault D (1989) Proc Natl Acad Sci USA 86:8427
McAuslan BR, Reilly W (1980) Exp Cell Res 130:147
Hu G-F (1998) J Cell Biochem 69:326
Lequin O, Thuring H, Robin M, Lallemand J-Y (1997) Eur J Biochem 250:712
Millhauser GL (2007) Annu Rev Phys Chem 58:299
Solioz M, Vulpe C (1996) Trends Biochem Sci 21:237
Soncin F, Guitton JD, Cartwright T, Badet J (1997) Biochem Biophys Res Commun 236:604
Joyce BK, Cohn M (1969) J Biol Chem 244:811
Acharya KR, Shapiro R, Allen SC, Riordan JF, Vallee BL (1994) Proc Natl Acad Sci USA 91:2915
Smyth DG, Stein WH, Moore S (1963) J Biol Chem 238:227
La Mendola D, Magri A, Vagliasindi LI, Hansson O, Bonomo RP, Rizzarelli E (2010) Dalton Trans 39:10678
Halgren TA (1996) J Comput Chem 17:490
Halgren TA (1999) J Comput Chem 20:720
Becke AD (1988) Phys Rev A 38:3098
Perdew JP (1986) Phys Rev B 33:8822
Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Theor Chem Acc 97:119
Ahlrichs R, Bar M, Haser M, Horn H, Kolmel C (1989) Chem Phys Lett 62:165
Schafer A, Huber C, Ahlrichs R (1994) J Chem Phys 100:5829
Bruschi M, De Gioia L, Mitric R, Bonacic-Koutecky V, Fantucci P (2008) Phys Chem Chem Phys 10:4573
Schafer A, Horn H, Ahlrichs R (1992) J Chem Phys 97:2571
Kutzelnigg W, Fleischer U, Schindler M (1990) The IGLO-method: Ab initio calculation and interpretation of NMR chemical shifts and magnetic susceptibilities. Springer, Berlin
Hess BA, Marian CM, Walhgren U, Gropen O (1996) Chem Phys Lett 251:365
Kaupp M, Buhl M, Malkin VG (2004) Calculation of NMR and EPR parameters: theory and applications. Wiley-VCH
Neese F (2003) J Chem Phys 117:3939
Marino T, Russo N, Toscano M (2007) J Phys Chem B 111:635
Marino T, Russo N, Toscano M (2011) Int J Quantum Chem 111:1152
Pushie MJ, Rauk A (2003) J Biol Inorg Chem 8:53
Franzini E, De Gioia L, Fantucci P, Zampella G, Bonacic-Koutecky V (2003) Inorg Chem Commun 6:650
Sabolovic J, Tautermann CS, Loerting T, Liedl KR (2003) Inorg Chem 42:2268
Adamo C, Scuseria G, Barone V (1999) J Chem Phys 111:2889
Klamt A (1995) J Phys Chem A 99:2224
Klamt A (1996) J Phys Chem A 100:3349
Klamt A, Schüürmann G (1993) J Chem Soc Perkin Trans 2:799
Hallahan TW (1991) Proc Natl Acad Sci USA 85:5061
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This work was supported by the PRIN Project N 200875WHMR.
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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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DOI: https://doi.org/10.1007/s00214-012-1186-y