Paper Citing NAMD - Abstract
Pietra, Francesco
On CO Egress from, and Re-Uptake by, the Enzyme MauG, as a Mimic of the Acquisition of Oxidizing Agents by the pre-MADH_MauG System. A Molecular Mechanics Approach
CHEMISTRY & BIODIVERSITY, 9:1425-1435, AUG 2012
In this work, by applying a non-deterministic, randomly-oriented minimal force to the dissociated CO ligand of the MauG-CO system, the molecular-dynamics (MD) behavior of this system could be quickly unraveled. It turned out that CO has no marked directional egress from the high-spin c-heme iron distal pocket. Rather, CO is able to exploit all interstices created during the protein fluctuations. Nonetheless, no steady route toward the surrounding solvent was ever observed: CO jumped first into other binding pockets before being able to escape the protein. In a few cases, on hitting the surrounding H2O molecules, CO was observed to reverse direction, re-entering the protein. A contention that conformational inversion of the P107 ring provides a gate to the iron ion is not supported by the present simulations.
