Mapping heme-ligand tunnels in group I truncated(2/2) hemoglobins

Protein matrix cavities and extended tunnels can effectively channel substrates and products to and from active sites in enzymes. Substrate and product channeling can enhance catalytic efficiency by reducing the intramolecular diffusion times to and from reaction centers. Moreover, protected transfer between sites may prevent the release of reactive intermediates, thus promoting efficiency or regulation in a series of interconnected reactions. This overview concerns the characterization of matrix tunnels in 2/2 hemoglobins, the recently described family of small hemoproteins (found in bacteria, plants, and unicellular eukaryotes) that form a separate cluster within the hemoglobin superfamily. Crystallographic investigations have shown that the 2/2 hemoglobin fold (a 2-on-2 alpha-helical sandwich) hosts a protein matrix tunnel system offering a potential path for ligand diffusion to and from the heme distal site. The tunnel topology is conserved in 2/2 hemoglobin group I, although with modulation of its size and/or structure. This article describes the methods that were adopted to characterize such matrix tunnels through analysis of the crystal structures and through binding of small apolar ligands to crystalline 2/2 hemoglobins. The methods are generally applicable and, in the case of 2/2 hemoglobins, underline the potential role of the tunnel system in supporting ligand diffusion to and from the heme, as well as ligand storage within the protein matrix.