Paper Citing NAMD - Abstract
Newhouse, E. Irene; Newhouse, James S.; Alam, Maqsudul
Molecular dynamics study of hell's gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity
JOURNAL OF MOLECULAR MODELING, 19:2265-2271, JUN 2013
Hell's gate globin I (HGbI), a heme-containing protein from the extremophile Methylacidiphilum infernorum, has fast oxygen-binding/slow release characteristics due to its distal residues Gln and Tyr. The combination of Gln/Tyr distal iron coordination, adaptation to extreme environmental conditions, and lack of a D helix suggests that ligand migration in HGbI differs from other previously studied globins. Locally enhanced molecular dynamics trajectories of oxygen migration indicate a large internal cavity. This may increase the tendency of oxygen to exit from portals other than the most direct exit from the space near the heme. Oxygen may reside transiently in shallow surface depressions around the exits. Such surface trapping may enhance both oxygen uptake by increasing contact time between molecules, and decrease release by increasing the probability of oxygen reentry from the vicinity of the portal.
