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Bringing Oxygen into an Enzyme (Aug 2007)
Copper amine oxidase

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made with VMD

Because oxygen gas is very reactive, it is frequently employed by the cell as a reagent by proteins called enzymes, which build the organic compounds that the cell needs. One such enzyme belongs to the copper amine oxidase family. These proteins transform amine-containing compounds into molecules needed by the cell, by reacting the compounds with oxygen. Researchers have long been interested in finding out how the various reagents reach the buried copper active site before the final oxidation reaction can occur. While copper amine oxidases exhibit an obvious channel for capturing the amine compounds to be modified, it had been unclear until now how oxygen molecules make their way through the enzyme. With the help of computer simulations using NAMD, researchers have identified in a recent publication, the routes taken by oxygen inside various copper amine oxidases from different species. In order to accomplish this, they analyzed simulations of the motions of four copper amine oxidases, using the VMD analysis and visualization software, which can predict the probability of finding oxygen molecules anywhere inside the simulated proteins. This analysis found numerous oxygen conduction routes inside each copper amine oxidase, i.e., oxygen can enter the protein through many routes, as it would in a sponge. More information on finding O2 migration pathways in proteins can be found here.