A Gly-Zipper Motif Mediates Homodimerization of the Transmembrane Domain of the Mitochondrial Kinase ADCK3

Interactions
between α-helices within the hydrophobic environment
of lipid bilayers are integral to the folding and function of transmembrane
proteins; however, the major forces that mediate these interactions
remain debated, and our ability to predict these interactions is still
largely untested. We recently demonstrated that the frequent transmembrane
association motif GASright, the GxxxG-containing fold of
the glycophorin A dimer, is optimal for the formation of extended
networks of Cα–H hydrogen bonds, supporting the hypothesis
that these bonds are major contributors to association. We also found
that optimization of Cα–H hydrogen bonding and interhelical
packing is sufficient to computationally predict the structure of
known GASright dimers at near atomic level. Here, we demonstrate
that this computational method can be used to characterize the structure
of a protein not previously known to dimerize, by predicting and validating
the transmembrane dimer of ADCK3, a mitochondrial kinase. ADCK3 is
involved in the biosynthesis of the redox active lipid, ubiquinone,
and human ADCK3 mutations cause a cerebellar ataxia associated with
ubiquinone deficiency, but the biochemical functions of ADCK3 remain
largely undefined. Our experimental analyses show that the transmembrane
helix of ADCK3 oligomerizes, with an interface based on an extended
Gly-zipper motif, as predicted by our models. The data provide strong
evidence for the hypothesis that optimization of Cα–H
hydrogen bonding is an important factor in the association of transmembrane
helices. This work also provides a structural foundation for investigating
the role of transmembrane association in regulating the biological
activity of ADCK3.