A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants(272 views) Barone V, De Rienzo F, Langella E, Menziani MC, Rega N, Sola M
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jan 1; 62(1): 262-269.
Dipartimento di Chimica, Università Federico II di Napoli, Complesso Universitario Monte S. Angela, Napoli, Italy
S3-INFM, Modena, Italy
References: Grunwald, E., Thermodynamic properties of nonpolar solutes in water and the structure of hydrophobic hydration shells (1986) J Am Chem Soc, 108, pp. 5726-573
Liu, L., Guo, Q.-X., Isokinetic relationship, isoequilibrium relationship, and enthalpy-entropy compensation (2001) Chem Rev, 101, pp. 673-695
Battistuzzi, G., Borsari, M., Di Rocco, G., Ranieri, A., Sola, M., Enthalpy/entropy compensation phenomena in the reduction thermodynamics of electron transport metalloproteins (2004) J Biol Inorg Chem, 9, pp. 23-26
Baker, E.N., Structure of azurin from Alcaligenes denitrificans refinement at 1.8 Å resolution and comparison of the two crystallographically independent molecules (1988) J Mol Biol, 203, pp. 1071-1095
Kalverda, A.P., Ubbink, M., Gilardi, G., Wijmenga, S.S., Crawford, A., Jeuken, L.J.C., Canters, G.W., Backbone dynamics of azurin in solution: Slow conformational change associated with deprotonation of histidine 35 (1999) Biochemistry, 38, pp. 12690-12697
Fraser, E.D., Zelda, H.L.A., Robert, R.E., Hasnain, S.S., Structures of oxidized and reduced azurin II from Alcaligenes xylosoxidans at 1.75 Å resolution (2000) Acta Crystallogr D, 56, pp. 690-696
Cheung, K.C., Strange, R.W., Hasnain, S.S., 3D EXAFS refinement of the Cu site of azurin sheds light on the nature of structural change at the metal centre in an oxidation-reduction process: An integrated approach combining EXAFS and crystallography (2000) Acta Crystallogr D, 56, pp. 697-704
Nar, H., Messerschmidt, A., Huber, R., Van De Kamp, M., Canters, G.W., Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip (1991) J Mol Biol, 221, pp. 765-772
Battistuzzi, G., Bellei, M., Borsari, M., Canters, G.W., De Waal, E., Jeuken, L.J.C., Ranieri, A., Sola, M., Control of metalloprotein reduction potential: Compensation phenomena in the reduction thermodynamics of blue copper proteins (2003) Biochemistry, 42, pp. 9214-9220
Olsson, M.H.M., Ryde, U., The influence of axial ligands on the reduction potential of blue copper proteins (1999) J Biol Inorg Chem, 4, pp. 654-663
Li, H., Webb, P.S., Ivanic, J., Jensen, J.H., Determinants of the relative reduction potentials of type-1 copper sites in proteins (2004) J Am Chem Soc, 126, pp. 8010-8019
Olsson, M.H.M., Hong, G.Y., Warshel, A., Frozen density functional free energy simulations of redox proteins: Computational studies of the reduction potential of plastocyanin and rusticyanin (2003) J Am Chem Soc, 125, pp. 5025-5039
Datta, S.N., Sudhamsu, J., Pandey, A., Theoretical determination of the standard reduction potential of Plastocyanin in vitro (2004) J Phys Chem, 108, pp. 8007-8016
Van Den Bosch, M., Swart, M., Snijders, J.G., Berendsen, H.J.C., Mark, A.E., Oostenbrink, C., Van Gunsteren, W.F., Canters, G.W., Calculation of the redox potential of the protein azurin and some mutants (2005) Chem Biol Chem, 6, pp. 738-746
Kolczak, U., Dennison, C., Messerschmidt, A., Canters, G.W., (2001) Handbook of Metalloproteins, 2, pp. 1170-1194. , New York: Wiley
Jeuken, L.J.C., (2001), PhD Thesis, University of Leiden, The NetherlandsSvensson, M., Humbel, S., Froese, R.D.J., Mastubara, T., Sieber, S., Morokuma, K., ONIOM: A multilayered integrated MO + MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 Oxidative addition (1996) J Phys Chem, 100, pp. 19357-19363
Dapprich, S., Komaromi, I., Byun, K.S., Morokuma, K., Frisch, M.J., A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives (1999) Theochem, 461-462, pp. 1-21
Cossi, M., Rega, N., Scalmani, G., Barone, V., New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution (2002) J Chem Phys, 117, pp. 43-54
Miertus, S., Scrocco, E., Tomasi, J., Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular (1981) Chem Phys, 55, p. 117
Tomasi, J., Persico, M., Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent (1994) Chem Rev, 94, pp. 2027-2094
Vreven, T., Mennucci, B., Da Silva, C.O., Morokuma, K., Tomasi, J., The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution (2001) J Chem Phys, 115, pp. 62-72
Improta, R., Rega, N., Aleman, C., Barone, V., Conformational behavior of macromolecules in solution by the polarizable continuum model in quantum mechanical and molecular mechanical frames. Homopolypeptides of a-aminoisobutyrric acid as test cases (2001) Macromolecules, 34, pp. 7550-7559
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz Jr., K.M., Ferguson, D.M., Spellmeyer, D.C., Kollman, P.A., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (1995) J Am Chem Soc, 117, pp. 5179-5197
Van De Kamp, M., Silvestrini, M.C., Brunori, M., Van Beeumen, J., Hali, F.C., Canters, G.W., Involvement of the hydrophobic patch of azurin in the electron-transfer reactions with cytochrome C551 and nitrite reductase (1990) Eur J Biochem, 194, pp. 109-118
De Rienzo, F., Gabdoulline, R.R., Menziani, M.C., Wade, R.C., Blue copper proteins: A comparative analysis of their molecular interaction properties (2000) Protein Sci, 9, pp. 1439-1454
Liu, L., Guo, Q. -X., Isokinetic relationship, isoequilibrium relationship, and enthalpy-entropy compensation (2001) Chem Rev, 101, pp. 673-695
Baker, E. N., Structure of azurin from Alcaligenes denitrificans refinement at 1. 8 resolution and comparison of the two crystallographically independent molecules (1988) J Mol Biol, 203, pp. 1071-1095
Kalverda, A. P., Ubbink, M., Gilardi, G., Wijmenga, S. S., Crawford, A., Jeuken, L. J. C., Canters, G. W., Backbone dynamics of azurin in solution: Slow conformational change associated with deprotonation of histidine 35 (1999) Biochemistry, 38, pp. 12690-12697
Fraser, E. D., Zelda, H. L. A., Robert, R. E., Hasnain, S. S., Structures of oxidized and reduced azurin II from Alcaligenes xylosoxidans at 1. 75 resolution (2000) Acta Crystallogr D, 56, pp. 690-696
Cheung, K. C., Strange, R. W., Hasnain, S. S., 3D EXAFS refinement of the Cu site of azurin sheds light on the nature of structural change at the metal centre in an oxidation-reduction process: An integrated approach combining EXAFS and crystallography (2000) Acta Crystallogr D, 56, pp. 697-704
Olsson, M. H. M., Ryde, U., The influence of axial ligands on the reduction potential of blue copper proteins (1999) J Biol Inorg Chem, 4, pp. 654-663
Li, H., Webb, P. S., Ivanic, J., Jensen, J. H., Determinants of the relative reduction potentials of type-1 copper sites in proteins (2004) J Am Chem Soc, 126, pp. 8010-8019
Olsson, M. H. M., Hong, G. Y., Warshel, A., Frozen density functional free energy simulations of redox proteins: Computational studies of the reduction potential of plastocyanin and rusticyanin (2003) J Am Chem Soc, 125, pp. 5025-5039
Datta, S. N., Sudhamsu, J., Pandey, A., Theoretical determination of the standard reduction potential of Plastocyanin in vitro (2004) J Phys Chem, 108, pp. 8007-8016
Jeuken, L. J. C., (2001), PhD Thesis, University of Leiden, The NetherlandsSvensson, M., Humbel, S., Froese, R. D. J., Mastubara, T., Sieber, S., Morokuma, K., ONIOM: A multilayered integrated MO + MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt (P (t-Bu) 3) 2 + H2 Oxidative addition (1996) J Phys Chem, 100, pp. 19357-19363
Frisch, M. J., Trucks, G. W., Schlegel, H. B., (2004) Gaussian03 Rel. B. 05, , Wallingford, CT: Gaussian Inc
Foresman, J. B., Frisch, A. E., (1996) Exploring Chemistry with Electronic Structure Methods, 2nd Ed., , Pittsburgh, PA: Gaussian Inc
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz Jr., K. M., Ferguson, D. M., Spellmeyer, D. C., Kollman, P. A., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (1995) J Am Chem Soc, 117, pp. 5179-5197
A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants
Kállay C, Dávid A, Timári S, Nagy EM, Sanna D, Garribba E, Micera G, De Bona P, Pappalardo G, Rizzarelli E, Sóvágó I * Copper(II) complexes of rat amylin fragments(357 views) Dalton T (ISSN: 1477-9234, 1477-9226, 1477-9234electronic), 2011 Oct 14; 40(38): 9711-9721. Impact Factor:3.838 ViewExport to BibTeXExport to EndNote