We have described a common TM packing motif in membrane proteins, the glycine zipper. The importance of the motif in membrane protein structure is implied by its statistically significant overrepresentation in TM helices, its unusual conservation in membrane protein families, and its clear influence on helix packing seen in proteins of known structure. Thus, glycine zippers likely play a significant structural role in the many membrane proteins where they are found.
The glycine zipper involves a row of small residues on one face of a helix. The preference for small residues in TM helix packing interactions is well known (4, 5), but the confluence of three small residues spaced by four appears to have special significance. In particular, TM glycines in a glycine zipper motif are much more strongly conserved than random TM glycines. Moreover, the GXXXG pattern by itself is not necessarily significant unless it is associated with additional sequence constraints (34, 35) as are found in the glycine zipper.
The most favorable glycine zippers have at least two glycines, and glycine occupies the central position. The source of the glycine preference may be manifold. One possibility is the minimal entropy cost required to bury a small residue (36). The exposure of backbone atoms could also facilitate weakly polar interactions such as the CH···O hydrogen bonds found in the glycophorin A dimer (37, 38). In addition, small residues can allow closer approach of the helices, perhaps maximizing packing interactions (37-39).
The finding of glycine zipper motifs in A
and PrP, which are associated with Alzheimer's and prion diseases, suggests the possibility of a common pathological role for the motif. Although there are many similarities in these diseases, to our knowledge, no other obvious protein sequence or structural connections have been identified. A hallmark of both Alzheimer's disease and spongiform encephalopathies is the formation of fibrillar deposits in the brain (40). Although these fibrillar aggregates can be an obvious symptom of the diseases, their presence is not well correlated with disease progression, and there is growing evidence that smaller, prefibrillar aggregates are significantly more cytotoxic than mature fibrils (41-44). Both toxic A peptides and PrP peptides (residues 106-126) have been found to form ion channels, suggesting a channel hypothesis of pathogenesis in which a loss of ion hemeostasis ultimately leads to neuronal cell death (30-33). Moreover, pore-like structures have been observed by electron and atomic force microscopy (28, 33). In view of this hypothesis, it is an interesting coincidence that both A and PrP contain glycine zipper motifs, which are so common in channel proteins. It is also notable that diseases involving the extended glycine zipper proteins we identified (VacA, Rickettsia surface protein, A, and PrP) all induce extensive vacuolation in the affected cells. Thus, despite the complete lack of any other apparent relationship among these proteins, the associated diseases show a remarkable histological similarity, suggesting that glycine zipper motifs may impart a common vacuolating channel function to all of these proteins. The many commonalities between Alzheimer's disease and the spongiform encephalopathies, and the absence of any other apparent sequence relationships, suggest that the involvement of the glycine zippers in disease etiology deserves further scrutiny.
The findings that all glycine zipper motifs in known structures are directly involved in helix interactions and that nearly 80% pack in a right-handed orientation make strong structural predictions. In particular, an important subset of glycine zipper TM helices create right-handed homooligomers that can line membrane pores. Thus, the presence of a glycine zipper motif presents simple and testable structural models for proteins that are often beyond the reach of current structure determination methods. For example, the A pores, fusion pores, and TJ channels exist only transiently, impeding high-resolution structure determination. Thus, the identification of glycine zipper motifs can provide a critical structural foundation for the design of structure-based, hypothesis-driven experiments in the thousands of membrane proteins where they are found.
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