Detection of likely transmembrane beta-strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler

The mitochondrial channel VDAC is presumed to fold as a beta-barrel although the number and identity of transmembrane beta-strands in the protein are controversial. Previously, a novel multiple alignment algorithm called the Gibbs sampler was used to detect a residue-frequency motif in sequences of bacterial outer-membrane proteins that corresponds to transmembrane beta-strands in bacterial porins of known structure (Neuwald et al., 1995, Protein Science, 4, 1618. In the present study, this bacterial motif has been used to screen sets of mitochondrial membrane protein sequences, with matches occurring in only two classes of proteins: VDACs and the outer-membrane protein import pore (ISP42, MOM38). These results suggest a structural (and perhaps evolutionary) relatedness between the bacterial and mitochondrial pore proteins; with the mitochondrial subsequences that match the bacterial motif corresponding to transmembrane beta-strands as in the porins.