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Boechi, L.; Mañez, P.A.; Javier Luque, F.; Marti, M.A.; Estrin, D.A. "Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case" (2010) Proteins: Structure, Function and Bioinformatics. 78(4):962-970
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Abstract:

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.

Registro:

Documento: Artículo
Título:Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case
Autor:Boechi, L.; Mañez, P.A.; Javier Luque, F.; Marti, M.A.; Estrin, D.A.
Filiación:Departamento de Química Inorgánica, Analítica y Quimica Fisica/Inquimae-Conicet, Universidad de Buenos Aires, Pabellón 2, Buenos Aires, C1428EHA, Argentina
Departament de Fisicoquímica and Institut de Biomcdicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avenida Diagonal 643, 08028, Barcelona, Spain
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires (C1428EHA), Argentina
Palabras clave:B. Subtilis; Ligand migration; Molecular dynamics; Truncated hemoglobin; carbon monoxide; oxygen; truncated hemoglobin; bacterial protein; article; Bacillus subtilis; controlled study; deoxygenation; ligand binding; molecular dynamics; oxygenation; priority journal; protein structure; simulation; Bacillus subtilis; chemistry; enzyme active site; kinetics; metabolism; protein secondary structure; Bacillus subtilis; Embryophyta; Protista; Bacillus subtilis; Bacterial Proteins; Carbon Monoxide; Catalytic Domain; Kinetics; Molecular Dynamics Simulation; Oxygen; Protein Structure, Secondary; Truncated Hemoglobins
Año:2010
Volumen:78
Número:4
Página de inicio:962
Página de fin:970
DOI: http://dx.doi.org/10.1002/prot.22620
Título revista:Proteins: Structure, Function and Bioinformatics
Título revista abreviado:Proteins Struct. Funct. Bioinformatics
ISSN:08873585
CAS:carbon monoxide, 630-08-0; oxygen, 7782-44-7; Bacterial Proteins; Carbon Monoxide, 630-08-0; Oxygen, 7782-44-7; Truncated Hemoglobins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v78_n4_p962_Boechi

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Citas:

---------- APA ----------
Boechi, L., Mañez, P.A., Javier Luque, F., Marti, M.A. & Estrin, D.A. (2010) . Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case. Proteins: Structure, Function and Bioinformatics, 78(4), 962-970.
http://dx.doi.org/10.1002/prot.22620
---------- CHICAGO ----------
Boechi, L., Mañez, P.A., Javier Luque, F., Marti, M.A., Estrin, D.A. "Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case" . Proteins: Structure, Function and Bioinformatics 78, no. 4 (2010) : 962-970.
http://dx.doi.org/10.1002/prot.22620
---------- MLA ----------
Boechi, L., Mañez, P.A., Javier Luque, F., Marti, M.A., Estrin, D.A. "Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case" . Proteins: Structure, Function and Bioinformatics, vol. 78, no. 4, 2010, pp. 962-970.
http://dx.doi.org/10.1002/prot.22620
---------- VANCOUVER ----------
Boechi, L., Mañez, P.A., Javier Luque, F., Marti, M.A., Estrin, D.A. Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case. Proteins Struct. Funct. Bioinformatics. 2010;78(4):962-970.
http://dx.doi.org/10.1002/prot.22620