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Pesce, A.; Nardini, M.; Dewilde, S.; Capece, L.; Martí, M.A.; Congia, S.; Salter, M.D.; Blouin, G.C.; Estrin, D.A.; Ascenzi, P.; Moens, L.; Bolognesi, M.; Olson, J.S. "Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin" (2011) Journal of Biological Chemistry. 286(7):5347-5358
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Abstract:

The large apolar tunnel traversing the mini-hemoglobin from Cerebratulus lacteus (CerHb) has been examined by xray crystallography, ligand binding kinetics, and molecular dynamic simulations. The addition of 10 atm of xenon causes loss of diffraction in wild-type (wt) CerHbO2 crystals, but Leu-86(G12)Ala CerHbO2, which has an increased tunnel volume, stably accommodates two discrete xenon atoms: one adjacent to Leu-86(G12) and another near Ala-55(E18). Molecular dynamics simulations of ligand migration in wt CerHb show a low energy pathway through the apolar tunnel when Leu or Ala, but not Phe or Trp, is present at the 86(G12) position. The addition of 10-15 atm of xenon to solutions of wt CerHbCO and L86A CerHbCO causes 2-3-fold increases in the fraction of geminate ligand recombination, indicating that the bound xenon blocks CO escape. This idea was confirmed by L86F and L86W mutations, which cause even larger increases in the fraction of geminate CO rebinding, 2-5-fold decreases in the bimolecular rate constants for ligand entry, and large increases in the computed energy barriers for ligand movement through the apolar tunnel. Both the addition of xenon to the L86A mutant and oxidation of wt CerHb heme iron cause the appearance of an out Gln-44(E7) conformer, in which the amide side chain points out toward the solvent and appears to lower the barrier for ligand escape through the E7 gate. However, the observed kinetics suggest little entry and escape (≤25%) through the E7 pathway, presumably because the in Gln- 44(E7) conformer is thermodynamically favored. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Registro:

Documento: Artículo
Título:Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin
Autor:Pesce, A.; Nardini, M.; Dewilde, S.; Capece, L.; Martí, M.A.; Congia, S.; Salter, M.D.; Blouin, G.C.; Estrin, D.A.; Ascenzi, P.; Moens, L.; Bolognesi, M.; Olson, J.S.
Filiación:Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy
Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita' di Milano, Via Celoria 26, 20133 Milano, Italy
Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
Departamento de Quimica Inorganica, Analitica Y Quimica Fisica/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
Dept. of Biochemistry and Cell Biology, Rice University, 6100 Main St., Houston, TX 77005-1892, United States
Department of Biology, Interdepartmental Laboratory for Electron Microscopy, University Roma Tre, Viale Guglielmo Marconi 446, 00146 Roma, Italy
Dept. of Neuroscience and Brain Technologies, Italian Institute of Technology, Genova, Italy
Optical Technology Division, Biophysics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899-1070, United States
Palabras clave:Amide side chain; Bimolecular rate constants; CO Rebinding; Heme iron; Ligand binding; Ligand movement; Low energies; Molecular dynamic simulations; Molecular dynamics simulations; Wild types; Xenon atoms; Amides; Computer simulation; Crystallography; Hemoglobin; Internet protocols; Molecular dynamics; Porphyrins; Rate constants; Ligands; ligand; article; binding kinetics; cell migration; Cerebratulus lacteus; controlled study; crystallization; dissociation; equilibrium constant; gene mutation; genetic recombination; hydrogen bond; ligand binding; molecular dynamics; Nemertea; nonhuman; oxidation; photolysis; priority journal; protein conformation; thermodynamics; X ray crystallography; X ray diffraction; Animals; Computer Simulation; Crystallography, X-Ray; Heme; Hemoglobins; Invertebrates; Iron; Kinetics; Ligands; Models, Molecular; Mutation, Missense; Protein Structure, Tertiary; Thermodynamics; Xenon; Cerebratulus lacteus
Año:2011
Volumen:286
Número:7
Página de inicio:5347
Página de fin:5358
DOI: http://dx.doi.org/10.1074/jbc.M110.169045
Título revista:Journal of Biological Chemistry
Título revista abreviado:J. Biol. Chem.
ISSN:00219258
CODEN:JBCHA
CAS:Heme, 14875-96-8; Hemoglobins; Iron, 7439-89-6; Ligands; Xenon, 7440-63-3
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219258_v286_n7_p5347_Pesce

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Citas:

---------- APA ----------
Pesce, A., Nardini, M., Dewilde, S., Capece, L., Martí, M.A., Congia, S., Salter, M.D.,..., Olson, J.S. (2011) . Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin. Journal of Biological Chemistry, 286(7), 5347-5358.
http://dx.doi.org/10.1074/jbc.M110.169045
---------- CHICAGO ----------
Pesce, A., Nardini, M., Dewilde, S., Capece, L., Martí, M.A., Congia, S., et al. "Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin" . Journal of Biological Chemistry 286, no. 7 (2011) : 5347-5358.
http://dx.doi.org/10.1074/jbc.M110.169045
---------- MLA ----------
Pesce, A., Nardini, M., Dewilde, S., Capece, L., Martí, M.A., Congia, S., et al. "Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin" . Journal of Biological Chemistry, vol. 286, no. 7, 2011, pp. 5347-5358.
http://dx.doi.org/10.1074/jbc.M110.169045
---------- VANCOUVER ----------
Pesce, A., Nardini, M., Dewilde, S., Capece, L., Martí, M.A., Congia, S., et al. Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin. J. Biol. Chem. 2011;286(7):5347-5358.
http://dx.doi.org/10.1074/jbc.M110.169045