Unraveling the molecular basis for ligand binding in truncated hemoglobins: the B. subtilis case

L. BOECHI , P. ARROYO MAÑEZ , J. F. LUQUE , M. A. MARTI, D. A. ESTRIN

Génova - Italia

Congreso; VII European Biophysics Congress (EBSA); 2009

<!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } --> Truncated hemoglobins (trHbs) are heme proteins present in bacteria, unicellular eukaryotes, and higher plants. Three phylogenetic groups (N, O, and P) have been identified in trHbs. The crystal structure of truncated hemoglobin O of B.subtilis, does not show an evident tunnel/cavity system connecting the protein active site with the solvent, a fact that cannot be easily rationalized considering the very high oxygen association rate. Moreover, resonant Raman results of the 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 stabi- lization of the bound ligand. For these reasons we performed classical molecular dynamics simulations of the oxy, carboxy and deoxy protein, and computed the free energy profiles associated with ligand migration to the active site. Our re- sults suggest that there is a key residue, GlnE11, that may present an alternate conformation in which a wide ligand mi- gration tunnel is formed, consistently with the kinetic data. The results for the CO and O2 bound protein show also that GlnE11 is directly involved in the stabilization of the coor- dinated 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 about the general behaviour of trHbs.