Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case

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Truncated hemoglobins (trHbs) are heme proteins present in bacteria, unicellular eukaryotes, and higher plants. Their tertiary structure consists in a 2-over-2 helical sandwich, which display typically an inner tunnel/cavity system for ligand migration and/or storage. The microorganism Bacillus subt...

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Detalles Bibliográficos
Autor principal: Boechi, L.
Otros Autores: Mañez, P.A, Javier Luque, F., Marti, M.A, Estrin, D.A
Formato: Capítulo de libro
Lenguaje:Inglés
Publicado: 2010
Acceso en línea:Registro en Scopus
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Registro en la Biblioteca Digital
Aporte de:Registro referencial: Solicitar el recurso aquí
Biblioteca Central Dr. Luis F. Leloir (FCEN) de Universidad de Buenos Aires
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024 7 |2 scopus  |a 2-s2.0-77949317319 
024 7 |2 cas  |a carbon monoxide, 630-08-0; oxygen, 7782-44-7; Bacterial Proteins; Carbon Monoxide, 630-08-0; Oxygen, 7782-44-7; Truncated Hemoglobins 
040 |a Scopus  |b spa  |c AR-BaUEN  |d AR-BaUEN 
100 1 |a Boechi, L. 
245 1 0 |a Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case 
260 |c 2010 
270 1 0 |m Boechi, L.; Departamento de Química Inorgánica, Analítica y Quimica Fisica/Inquimae-Conicet, Universidad de Buenos Aires, Pabellón 2, Buenos Aires, C1428EHA, Argentina; email: lboechi@qi.fcen.uba.ar 
506 |2 openaire  |e Política editorial 
504 |a Milani, M., Pesce, A., Nardini, M., Ouellet, H., Ouellet, Y., Dewilde, S., Bocedi, A., Bolognesi, M., Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins (2005) J Inorg Biochem, 1, pp. 97-109 
504 |a Wittenberg, J.B., Bolognesi, M., Wittenberg, B.A., Guertin, M., Truncated hemoglobins: A new family of hemoglobins widely distributed in bacteria, unicellular eukaryotes, and plants (2002) J Biol Chem, 277, pp. 871-874 
504 |a Pesce, A., Nardini, M., Milani, M., Bolognesi, M., Protein fold and structure in the truncated (2/2) globin family (2007) Gene, 398, pp. 2-11 
504 |a Pathania, R., Navani, N.K., Rajamohan, G., Dikshit, K.L., Mycobacterium tuberculosis hemoglobin HbO associates with membranes and stimulates cellular respiration of recombinant Escherichia coli (2002) J Biol Chem, 277, pp. 15293-15302 
504 |a Couture, M., Yeh, S.R., Wittenberg, B.A., Wittenberg, J.B., Ouellet, Y., Rousseau, D.L., Guertin, M., A cooperative oxygen-binding hemoglobin from Mycobacterium tuberculosis (1999) Proc Natl Acad Sci USA, 96, pp. 11223-11228 
504 |a Vuletich, D.A., Lecomte, J.T., A phyiogenetic and structural analysis of truncated hemoglobins (2006) J Mol Evol, 62, pp. 196-210 
504 |a Crespo, A., Marti, M.A., Kalko, S.G., Morreale, A., Orozco, M., Gelpi, J.L., Luque, F.J., Estrin, D.A., Theoretical study of the truncated hemoglobin HbN: Exploring the molecular basis of the NO detoxification mechanism (2005) J Am Chem Soc, 127, pp. 4433-4444 
504 |a Ouellet, H., Milani, M., Labarre, M., Bolognesi, M., Couture, M., Guertin, M., The roles of Tyr(CD1) and Trp(G8) in Mycobacterium tuberculosis truncated hemoglobin O in ligand binding and on the heme distal site architecture (2007) Biochemistry, 46, pp. 11440-11450 
504 |a Boechi, L., Martí, M.A., Milani, M., Bolognesi, M., Luque, F.J., Estrin, D.A., Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O (2008) Proteins, 73, pp. 372-379 
504 |a Bidon-Chanal, A., Martí, M.A., Crespo, A., Milani, M., Orozco, M., Bolognesi, M., Luque, F.J., Estrin, D.A., Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N (2006) Proteins, 64, pp. 457-464 
504 |a Milani, M., Pesce, A., Ouellet, Y., Ascenzi, P., Guertin, M., Bolognesi, M., Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O 2 diffusion to the heme (2001) EMBO J, 20, pp. 3902-3909 
504 |a Giangiacomo, L., Ilari, A., Boffi, A., Morea, V., Chiancone, E., The truncated oxygen-avid hemoglobin from Bacillus subtilis: X-ray structure and ligand binding properties (2005) J Biol Chem, 280, pp. 9192-9202 
504 |a Jorgensen, W.L., Chandrasekar, J., Madura, J., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) J Chem Phys, 79, pp. 926-935 
504 |a Luty, B.A., Tironi, I.G., Van Gunsteren, W.F., Lattice-sum methods for calculating electrostatic interactions in molecular simulations (1995) J Chem Phys, 103, pp. 3014-3021 
504 |a Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Debolt, S., Ferguson, D., Kollman, P., AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules (1995) Comput Phys Commun, 91, pp. 1-41 
504 |a Jarzynski, C., Nonequilibrium equality for free energy differences (1997) Phys Rev Lett, 78, pp. 2690-2693 
504 |a Crespo, A., Marti, M.A., Estrin, D.A., Roitberg, A.E., Multiple-steering QM-MM calculation of the free energy profile in chorismate mutas (2005) J Am Chem Soc, 127, pp. 6940-6941 
504 |a Lu, C., Egawa, T., Mukai, M., Poole, R.K., Yeh, S.R., Hemoglobins from Mycobacterium tuberculosis and Campylobacter jejuni: A comparative study with resonance Raman spectroscopy (2008) Methods Enzymol, 437, pp. 255-286 
504 |a Di Lella, S., Ma, L., Ricci, J.C., Rabinovich, G.A., Asher, S.A., Alvarez, R.M., Critical role of the solvent environment in galectin-1 binding to the disaccharide lactose (2009) Biochemistry, 48, pp. 786-791 
504 |a Feis, A., Lapini, A., Catacchio, B., Brogioni, S., Foggi, P., Chiancone, E., Boffi, A., Smulevich, G., Unusually strong H-bonding to the heme ligand and fast geminate recombination dynamics of the carbon monoxide complex of Bacillus subtilis truncated hemoglobin (2008) Biochemistry, 47, pp. 902-910 
520 3 |a Truncated hemoglobins (trHbs) are heme proteins present in bacteria, unicellular eukaryotes, and higher plants. Their tertiary structure consists in a 2-over-2 helical sandwich, which display typically an inner tunnel/cavity system for ligand migration and/or storage. The microorganism Bacillus subtilis contains a peculiar trHb, which does not show an evident tunnel/cavity system connecting the protein active site with the solvent, and exhibits anyway a very high oxygen association rate. Moreover, resonant Raman results of CO bound protein, showed that a complex hydrogen bond network exists in the distal cavity, making it difficult to assign unambiguously the residues involved in the stabilization of the bound ligand. To understand these experimental results with atomistic detail, we performed classical molecular dynamics simulations of the oxy, carboxy, and deoxy proteins. The free energy profiles for ligand migration suggest that there is a key residue, GlnE11, that presents an alternate conformation, in which a wide ligand migration tunnel is formed, consistently with the kinetic data. This tunnel is topologically related to the one found in group I trHbs. On the other hand, the results for the CO and O 2 bound protein show that GlnE11 is directly involved in the stabilization of the cordinated ligand, playing a similar role as TyrB10 and TrpG8 in other trHbs. Our results not only reconcile the structural data with the kinetic information, but also provide additional insight into the general behaviour of trHbs. © 2009 Wiley-Liss, Inc.  |l eng 
593 |a Departamento de Química Inorgánica, Analítica y Quimica Fisica/Inquimae-Conicet, Universidad de Buenos Aires, Pabellón 2, Buenos Aires, C1428EHA, Argentina 
593 |a Departament de Fisicoquímica and Institut de Biomcdicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avenida Diagonal 643, 08028, Barcelona, Spain 
593 |a Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires (C1428EHA), Argentina 
690 1 0 |a B. SUBTILIS 
690 1 0 |a LIGAND MIGRATION 
690 1 0 |a MOLECULAR DYNAMICS 
690 1 0 |a TRUNCATED HEMOGLOBIN 
690 1 0 |a CARBON MONOXIDE 
690 1 0 |a OXYGEN 
690 1 0 |a TRUNCATED HEMOGLOBIN 
690 1 0 |a BACTERIAL PROTEIN 
690 1 0 |a ARTICLE 
690 1 0 |a BACILLUS SUBTILIS 
690 1 0 |a CONTROLLED STUDY 
690 1 0 |a DEOXYGENATION 
690 1 0 |a LIGAND BINDING 
690 1 0 |a MOLECULAR DYNAMICS 
690 1 0 |a OXYGENATION 
690 1 0 |a PRIORITY JOURNAL 
690 1 0 |a PROTEIN STRUCTURE 
690 1 0 |a SIMULATION 
690 1 0 |a BACILLUS SUBTILIS 
690 1 0 |a CHEMISTRY 
690 1 0 |a ENZYME ACTIVE SITE 
690 1 0 |a KINETICS 
690 1 0 |a METABOLISM 
690 1 0 |a PROTEIN SECONDARY STRUCTURE 
690 1 0 |a BACILLUS SUBTILIS 
690 1 0 |a EMBRYOPHYTA 
690 1 0 |a PROTISTA 
690 1 0 |a BACILLUS SUBTILIS 
690 1 0 |a BACTERIAL PROTEINS 
690 1 0 |a CARBON MONOXIDE 
690 1 0 |a CATALYTIC DOMAIN 
690 1 0 |a KINETICS 
690 1 0 |a MOLECULAR DYNAMICS SIMULATION 
690 1 0 |a OXYGEN 
690 1 0 |a PROTEIN STRUCTURE, SECONDARY 
690 1 0 |a TRUNCATED HEMOGLOBINS 
700 1 |a Mañez, P.A. 
700 1 |a Javier Luque, F. 
700 1 |a Marti, M.A. 
700 1 |a Estrin, D.A. 
773 0 |d 2010  |g v. 78  |h pp. 962-970  |k n. 4  |p Proteins Struct. Funct. Bioinformatics  |x 08873585  |t Proteins: Structure, Function and Bioinformatics 
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856 4 0 |u https://doi.org/10.1002/prot.22620  |y DOI 
856 4 0 |u https://hdl.handle.net/20.500.12110/paper_08873585_v78_n4_p962_Boechi  |y Handle 
856 4 0 |u https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v78_n4_p962_Boechi  |y Registro en la Biblioteca Digital 
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962 |a info:eu-repo/semantics/article  |a info:ar-repo/semantics/artículo  |b info:eu-repo/semantics/publishedVersion 
999 |c 68905 

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