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

TitleUnraveling the molecular basis for ligand binding in truncated hemoglobins: the trHbO Bacillus subtilis case
Publication TypeJournal Article
Year of Publication2010
AuthorsBoechi, L, Manez PA, Luque FJ, Marti MA, Estrin DA
Pagination962 - 970
Date Published2010/03//
KeywordsBacillus subtilis/metabolism; Bacterial Proteins/chemistry/metabolism; Carbon Monoxide/metabolism; Catalytic Domain; Kinetics; Molecular Dynamics Simulation; Oxygen/metabolism; Protein Structure, Secondary; Truncated Hemoglobins/chemistry/metabolism
AbstractTruncated 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.