Paper Citing NAMD - Abstract
Orlowski, Slawomir; Nowak, Wieslaw
Oxygen diffusion in minihemoglobin from Cerebratulus lacteus: a locally enhanced sampling study
THEORETICAL CHEMISTRY ACCOUNTS, 117:253-258, FEB 2007
Heme proteins serve as a source of oxygen in nervous tissue during anoxia. The functional routes of a dioxygen (O-2) diffusion in a novel structure of a minihemoglobin (CerHb) molecule present in worm Cerebratulus lacteus are not known. In this paper, the results of 1ns molecular dynamics simulations of this process are presented. The locally enhanced sampling method (LES) and CHARMM force field were used for simulations of CerHb with 1-15 copies of O-2. It was found, that several alternative routes are possible. The dominant path consists of two steps. Firstly, ligands move from the heme pocket to a different cavity through the barrier defined by the residues Phe10 and Tyr48. Secondly, ligands leave the protein passing through the more complex barrier situated between the E/F loop and the H helix. We note that the number of paths observed depends on a number of LES copies of (O-2).
