Unraveling the molecular basis for ligand binding in truncated hemoglobins: the trHbO Bacillus subtilis case.
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. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
Boechi
Leonardo
L
Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina. lboechi@qi.fcen.uba.ar
Mañez
Pau Arroyo
PA
Luque
F Javier
FJ
Marti
Marcelo A
MA
Estrin
Dario A
DA
D001412:Bacillus subtilis / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002248:Carbon Monoxide / Q000378:metabolism; D020134:Catalytic Domain; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010100:Oxygen / Q000378:metabolism; D017433:Protein Structure, Secondary; D054793:Truncated Hemoglobins / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; D054793:Truncated Hemoglobins; D002248:Carbon Monoxide; D010100:Oxygen