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

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

PROTEINS: STRUCTURE, FUNCTION AND GENETICS

WILEY-LISS, DIV JOHN WILEY & SONS INC

Año: 2010 vol. 68 p. 962 - 970

0887-3585

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 displaytypically an inner tunnel/cavity system for ligand migration and/or storage.The microorganism B. subtilis contains a peculiar trHb, which does not show an evidenttunnel/cavity system connecting the protein active site with the solvent, and exhibits anyway a veryhigh oxygen association rate. Moreover, resonant Raman results of CO bound protein, showed thata complex hydrogen bond network exists in the distal cavity, making it difficult to assignunambiguously the residues involved in the stabilization of the bound ligand.In order to understand these experimental results with atomistic detail, we performedclassical molecular dynamics simulations of the oxy, carboxy and deoxy protein. The free energyprofiles for ligand migration suggest that there is a key residue, GlnE11, that presents an alternateconformation 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 resultsfor the CO and O2 bound protein show also that GlnE11 is directly involved in the stabilization ofthe 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 alsoprovide additional insight into the general behaviour of trHbs.