Molecular dynamics simulations on apo ADP/ATP carrier shed new lights on the featured motif of the mitochondrial carriers.

The ADP/ATP carrier (AAC) is a transporter responsible for the equal molar exchange of cytosolic ADP and ATP synthesized within mitochondrial matrix across the mitochondrial membrane. Its primary structure consists of three homologous repeats, and each repeat contains a conserved motif that is shared by all members of the mitochondrial carrier family (MCF). Although these MCF motif residues cluster together in the crystal structure of AAC, detailed analyses on the interactions among the motif residues are still limited. In the present study, all-atom molecular dynamics (MD) simulations of up to 10 μs have been carried out on AAC, and interactions and structural dynamics of the MCF motif residues have been specifically investigated. Our simulations have revealed: i) a very asymmetrical electrostatic network at the bottom of the pocket of apo AAC, ii) the asymmetrical interactions between the Pro kink region and the [YWF][KR] G motif in three repeats, iii) the role of the conserved Arg residues in stabilizing the C-ends of the odd-numbered helices, iv) the structural change of the [YWF][KR] G motif and its potential involvement in substrate translocation process. Our results highlight the asymmetry of the MCF residues in the three repeats, which might contribute to the ability of the carriers to transport the asymmetrical substrates. Our observations provide microscopic basis for further research on the translocation mechanism of mitochondrial carriers. • An asymmetrical electrostatic network forms at the bottom of the pocket of apo AAC. • Pro kink-[YWF][RK]G interactions, between the first and the second part of MCF sequence motif, are asymmetrical in the three AAC repeats. • The three capping Arg residues are important in stabilizing the odd-numbered helices. • Structural change of the [YWF][RK]G portion of second part of AAC sequence motif is observed. [ABSTRACT FROM AUTHOR]