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Oxygen Diffusion in Minihemoglobin from Cerebratulus lacteus - a Locally Enhanced Sampling Study SLAWOMIR ORLOWSKI, WIESLAW NOWAK Theoretical Molecular Biophysics Group Institute of Physics, N. Copernicus University 87-100 Torun, Poland Abstract Heme proteins serve as a source of oxygen in nervous tissue during anoxia. The functional routes of a dioxygen (O2) diffusion in a novel structure of a minihemoglobin (CerHb) molecule present in worm Cerebratulus lacteus are not known. In this paper, the results of 1 ns 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 O2. 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 O2. Full text: [pdf] |
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