DETECTION OF LIKELY TRANSMEMBRANE BETA-STRAND REGIONS IN SEQUENCES OFMITOCHONDRIAL PORE PROTEINS USING THE GIBBS SAMPLER

The mitochondrial channel VDAC is presumed to fold as a beta-barrel al though the number and identity of transmembrane beta-strands in the pr otein are controversial. Previously, a novel multiple alignment algori thm called the Gibbs sampler was used to detect a residue-frequency mo tif 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 me mbrane protein sequences, with matches occurring in only two classes o f proteins: VDACs and the outer-membrane protein import pore (ISP42, M OM38). These results suggest a structural (and perhaps evolutionary) r elatedness between the bacterial and mitochondrial pore proteins; with the mitochondrial subsequences that match the bacterial motif corresp onding to transmembrane beta-strands as in the porins.