Abstract

The structures of mitochondrial transporters and uncoupling proteins are threefold pseudosymmetrical, but their substrates and coupling ions are not. Thus, deviations from symmetry are to be expected in the substrate and ion-binding sites in the central aqueous cavity. By analysing the threefold pseudosymmetrical repeats from which their sequences are made, conserved asymmetric residues were found to cluster in a region of the central cavity identified previously as the substrate binding site. In contrast, conserved symmetrical residues required for the transport mechanism were found at the water-membrane interfaces. Three PX[DE]XX[RK] motifs form a salt bridge network on the matrix side of the cavity, when the substrate binding site is open to the mitochondrial intermembrane space. Three [FY][DE]XX[RK] motifs are present on the cytoplasmic side of the cavity and they could form a salt bridge network when the substrate binding site is accessible from the mitochondrial matrix. It is proposed that the opening and closing of the carrier could be coupled to the disruption and formation of the two salt bridge networks induced by substrate binding. The interaction energies of the networks allow members of the transporter family to be classified as strict exchangers or uniporters.