Paper Citing NAMD - Abstract
Pietra, Francesco
On the Egress of Carbon Monoxide from Myoglobin
CHEMISTRY & BIODIVERSITY, 8:1410-1421, AUG 2011
The pathways of escape of carbon monoxide (CO) from sperm whale myoglobin were investigated by means of a biased form of all-atoms molecular dynamics (RAMD), whereby a weak, randomly oriented force is applied to the center of mass of CO. The force only persists if the direction taken by CO continues for a given period of time, otherwise a new direction is randomly chosen. A statistically significant number of RAMD runs gave distinct responses according to the level of approximations used for the model. Thus, with rigid bonds to all H-atoms, several portals for CO egress toward the solvent, besides the main H64 gate, were identified, like in recently published unbiased massive MD, six orders of magnitude acceleration of CO escape in RAMD notwithstanding. In contrast, by removing the approximation of rigid bonds in the model, only one of these extra portals was identified, besides the H64 portal. Sticking to this all-free-bonds model, Perutz's early suggestion that the H64 imidazole must rotate 'out' toward the solvent in order that CO can cross the H64 gate was directly implemented. RAMD Simulations with this model led to CO egress from the H64 gate only, reconciling theory with experiments.
