PHYLOGENETIC ANALYSIS OF MEMBRANE TRAFFICKING PROTEINS - A FAMILY REUNION AND SECONDARY STRUCTURE PREDICTIONS

The realization that a highly conserved family of membrane proteins ar e localized to transport vesicles and selectively interact with protei ns anchored at appropriate target sites of membrane fusion inspired a simple and compelling explanation of how proteins might be trans ferre d and segregated within the cell, the ''SNARE hypothesis''. This model holds that vesicle and target membrane proteins (designated as v-SNAR E and t-SNARE proteins, respectively) wind around one another to form a three-stranded coiled coil structure, termed the prefusion complex. While the molecular topology of the prefusion complex has not been est ablished, the concept that phylogenetically diverse SNARE proteins may become interlocked in a stable coiled coil is particularly attractive , because such a tertiary fold would only be permitted between strictl y matched binding partners. For this reason, we have performed a phene tic analysis of all known SNARE sequences to assess the evolutionary a nd structural relatedness of these ancient protein families. Our phylo genetic analysis and consensus structure predictions revealed that syn taxin and SNAP-25 homologs are significantly related and constitute a superfamily of t-SNARE proteins that fall naturally into four major cl asses,vith distinct architectural motifs. The synaptobrevins sorted in to three different classes of v-SNARE proteins. Comparison of the cons ensus structure predictions within each lineage or class of SNARE prot eins strongly implied that coiled coil domains may not be required for fusion complex assembly in simple eukaryotic cells. It is our hypothe sis that SNARE proteins in the late secretory pathway of mammalian tel ls may have elaborated more complex secondary structures (coiled coils ), at about the time metazoan organisms diverged from yeast, that prov ide a sterically rigid foundation for positioning a conserved binding domain, the amphipathic alpha-helix.