Abstract: The transport of various metabolites across the mitochondrial membranes is essential for eukaryotic metabolism. Specific transport through the inner mitochondrial membrane is achieved by nuclear encoded carriers which form a large transport family, the mitochondrial carrier family. The structure of the ADP/ATP carrier in complex with its inhibitor carboxyatractyloside (CATR) has been recently solved by X-ray crystallography providing for the first time an insight into one conformation of the protein. In order to shed light on the possible conformation sampled by the protein and on the effect of CATR on constraining a definite configuration we have carried out two 10 ns molecular dynamics simulation of the protein embedded in a lipid bilayer of palmitoyl-oleoyl-phosphatidyl-choline (POPC) with and without its co-crystallized inhibitor CATR.