Protons (Yellow) go from the high concentration side (below) to the side with lower concentration. They do that by binding to the transmembrane portion of the ATP-Synthase. However, the place where the Protons enter and where they leave are in different locations. Therefore, the transmembrane portion of the ATP-Synthase has to rotate to bring the protons from one side to the other. The rotating motion of parts of the protein causes the non-rotating subunits to deform in specific places. This deformation catalyzes the reaction of ADP (green) + inorganic phosphate to ATP (red).
