Berlin 2005 – scientific programme

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AKB: Biologische Physik

AKB 90: Protein Folding and Molecular Dynamics

AKB 90.6: Talk

Wednesday, March 9, 2005, 15:15–15:30, TU H2013

Identification of Oxygen Channels in Proteins by Molecular Dynamics — •Jan Saam, Christopher Ozdoba und Hermann-Georg Holzhütter — Institut für Biochemie, Charité, Monbijoustr 2. 10117 Berlin

Cells contain a variety of enzymes that use molecular oxygen in the reactions they catalyze. In most cases the influence of oxygen-protein interaction on the reaction is unknown. We employed molecular dynamics simulations to determine the oxygen pathway from the solvent phase to the active site and to study the oxygen adsorption at the inner surface of two different oxygenases.

Our results show that in each enzyme there exists an oxygen channel different from the substrate entrance leading through the protein matrix to the catalytic site. The channels cannot be seen in the crystal structure but open their different segments temporarily yet allowing oxygen molecules to diffuse to the active center. With its high probability density for oxygen the interior end of the tunnel represents the ideal point for the stereo- and position specific insertion of dioxygen into the substrate. Subsequently these results could be confirmed by mutation experiments.