 In oxidative phosphorylation , the passage of electrons from NADH and FADH2 through the electron transport chain powers the pumping of protons out of the mitochondrial matrix and into the intermembrane space . This creates a proton motive force that is the net effect of a pH gradient and an electric potential gradient across the inner mitochondrial membrane . Flow of protons down this potential gradient – that is , from the intermembrane space to the matrix – provides the driving force for ATP synthesis by ATP synthase . This enzyme contains a rotor subunit that physically rotates relative to the static portions of the protein during ATP synthesis . 
