Dynamical regulation of ligand migration by a gate-opening molecular switch in truncated hemoglobin-N from Mycobacterium tuberculosis

Truncated hemoglobin-N is believed to constitute a defense mechanism of Mycobacterium tuberculosis against NO produced by macrophages, which is converted to the harmless nitrate anion. This process is catalyzed very efficiently, as the enzyme activity is limited by ligand diffusion. By using extended molecular dynamics simulations we explore the mechanism that regulates ligand diffusion and, particularly, the role played by residues that assist binding of O2 to the heme group. Our data strongly support the hypothesis that the access of NO to the heme cavity is dynamically regulated by the TyrB10-GlnE11 pair, which acts as a molecular switch that controls opening of the ligand diffusion tunnel. Binding of O2 to the heme group triggers local conformational changes in the TyrB10-GlnE11 pair, which favor opening of the PheE15 gate residue through global changes in the essential motions of the protein skeleton. The complex pattern of conformational changes triggered upon O2 binding is drastically altered in the GlnE11-->Ala and TyrB10-->Phe mutants, which justifies the poor enzymatic activity observed experimentally for the TyrB10-->Phe form. The results support a molecular mechanism evolved to ensure access of NO to the heme cavity in the oxygenated form of the protein, which should warrant survival of the microorganism under stress conditions.