Theoretical investigations of nitric oxide channeling in Mycobacterium tuberculosis truncated hemoglobin N.
Mycobacterium tuberculosis group I truncated hemoglobin trHbN catalyzes the oxidation of nitric oxide (NO) to nitrate with a second-order rate constant k approximately 745 microM(-1) s(-1) at 23 degrees C (nitric oxide dioxygenase reaction). It was proposed that this high efficiency is associated with the presence of hydrophobic tunnels inside trHbN structure that allow substrate diffusion to the distal heme pocket. In this work, we investigated the mechanisms of NO diffusion within trHbN tunnels in the context of the nitric oxide dioxygenase reaction using two independent approaches. Molecular dynamics simulations of trHbN were performed in the presence of explicit NO molecules. Successful NO diffusion from the bulk solvent to the distal heme pocket was observed in all simulations performed. The simulations revealed that NO interacts with trHbN at specific surface sites, composed of hydrophobic residues located at tunnel entrances. The entry and the internal diffusion of NO inside trHbN were performed using the Long, Short, and EH tunnels reported earlier. The Short tunnel was preferentially used by NO to reach the distal heme pocket. This preference is ascribed to its hydrophobic funnel-shape entrance, covering a large area extending far from the tunnel entrance. This funnel-shape entrance triggers the frequent formation of solvent-excluded cavities capable of hosting up to three NO molecules, thereby accelerating NO capture and entry. The importance of hydrophobicity of entrances for NO capture is highlighted by a comparison with a polar mutant for which residues at entrances were mutated with polar residues. A complete map of NO diffusion pathways inside trHbN matrix was calculated, and NO molecules were found to diffuse from Xe cavity to Xe cavity. This scheme was in perfect agreement with the three-dimensional free-energy distribution calculated using implicit ligand sampling. The trajectories showed that NO significantly alters the dynamics of the key amino acids of Phe(62)(E15), a residue proposed to act as a gate controlling ligand traffic inside the Long tunnel, and also of Ile(119)(H11), at the entrance of the Short tunnel. It is noteworthy that NO diffusion inside trHbN tunnels is much faster than that reported previously for myoglobin. The results presented in this work shed light on the diffusion mechanism of apolar gaseous substrates inside protein matrix.
Daigle
Richard
R
Department of Biochemistry, Laval University, Québec City, Québec, Canada.
Rousseau
Julie-Anne
JA
Guertin
Michel
M
Lagüe
Patrick
P
D000818:Animals; D004058:Diffusion; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009169:Mycobacterium tuberculosis; D009569:Nitric Oxide / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D054793:Truncated Hemoglobins / Q000737:chemistry* / Q000378:metabolism*
D008024:Ligands; D012997:Solvents; D054793:Truncated Hemoglobins; D009569:Nitric Oxide; D006418:Heme