Mechanistic aspects of the binding of acid–base ligands to ferric heme proteins

The kinetics of ligand binding to ferric heme proteins is relevant in a variety of biochemical processes. With a few exceptions, ferric heme proteins at physiological pH typically show the sixth (distal) coordination position of the heme iron occupied by a water molecule. This contrasts with ferrous heme proteins, where this position is usually vacant in the absence of external ligands. In this review, we shed light on mechanistic aspects of this process, by discussing our recent results of binding of hydrogen sulfide and hydrosulfide (H2S/HS–) and disulfane and hydrodisulfid (HSSH/HSS–) to ferric microperoxidase 11 (MP11FeIII) and metmyoglobin (MbFeIII), as well as binding of peroxynitrous acid/peroxynitrite (ONOOH/ONOO–) to ferric M. tuberculosis nitrobindin (NbFeIII). Stopped flow experimental results of ligand binding rates as a function of pH can be analyzed with a mechanistic proposal consisting of ligand migration and ligand binding steps. Ligand migration to the active site was studied by using steered classical molecular dynamics simulations. The process of ligand binding substitution of the coordinated water molecule has been studied using hybrid quantum–classical (QM-MM) tools. Our results suggest that water molecule release is the critical event of the process in most of the cases, consistently with previous proposals. However, the scenario is complex, since water release depends subtly on the heme environment and may be also assisted by the acid–base behavior of the incoming ligands. Ligand migration may also play a key role in cases in which the active site entrance is hindered.