Nitric oxide dynamics in truncated hemoglobin : docking sites, migration pathways, and vibrational spectroscopy from molecular dynamics simulations

Atomistic simulations of nitric oxide (NO) dynamics and migration in the trHbN of Mycobacterium tuberculosis are reported. From extensive molecular dynamics simulations (48 ns in total), the structural and energetic properties of the ligand docking sites in the protein have been characterized and a connectivity network between the ligand docking sites has been built. Several novel migration and exit pathways are found and are analyzed in detail. The interplay between a hydrogen-bonding network involving residues Tyr(33) and Gln(58) and the bound O(2) ligand is discussed and the role of Phe(62) residue in ligand migration is examined. It is found that Phe(62) is directly involved in controlling ligand migration. This is reminiscent of His(64) in myoglobin, which also plays a central role in CO migration pathways. Finally, infrared spectra of the NO molecule in different ligand docking sites of the protein are calculated. The pocket-specific spectra are typically blue-shifted by 5-10 cm(-1), which should be detectable in future spectroscopic experiments.