Paper Citing NAMD - Abstract
Daigle, Richard; Rousseau, Julie-Anne; Guertin, Michel; Laguee, Patrick
Theoretical Investigations of Nitric Oxide Channeling in Mycobacterium tuberculosis Truncated Hemoglobin N
BIOPHYSICAL JOURNAL, 97:2967-2977, DEC 2 2009
Mycobacterium tuberculosis group I truncated hemoglobin trHbN catalyzes the oxidation of nitric oxide (center dot NO) to nitrate with a second-order rate constant k approximate to 745 mu M(-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 center dot 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 center dot NO molecules. Successful center dot NO diffusion from the bulk solvent to the distal heme pocket was observed in all simulations performed. The simulations revealed that center dot NO interacts with trHbN at specific surface sites, composed of hydrophobic residues located at tunnel entrances. The entry and the internal diffusion of center dot NO inside trHbN were performed using the Long, Short, and EH tunnels reported earlier. The Short tunnel was preferentially used by center dot 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 center dot NO molecules, thereby accelerating center dot NO capture and entry. The importance of hydrophobicity of entrances for center dot 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 center dot NO diffusion pathways inside trHbN matrix was calculated, and center dot 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 center dot 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 center dot 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.
