Paper Citing NAMD - Abstract
Pietra, Francesco
On the Pathways for CO Egress from Carboxy Human Cytoglobin. A Molecular-Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 10:86-95, JAN 2013
This work discloses two bona fide gates through which the CO ligand can leave the distal cavity of carboxy human cytoglobin, reaching the solvent. The investigation was based on molecular dynamics, aided by a minimal randomly-oriented force applied to the ligand. The shortest pathway progresses toward the main gate, H81-R84, in the open state, with the H81 imidazole moiety turned toward the solvent. A longer pathway develops toward the diametrically opposed W31-W151 gate. In between, CO may be entrapped into binding cavities, either along the path toward the gates, or in a cul-de-sac, from which CO may even be incapable to escape. This behavior contrasts with carboxy myoglobin, where the corresponding H64 gate, when opened, is the sole used by CO to get to the solvent. These observations, which could hold also for other small ligands of biological interest, such as O-2, NO, and NO3-, provide an answer to a neglected aspect of the mysterious six-coordinated globins.
