The E2 domains of APP and APLP1 share a conserved mode of dimerization.

Amyloid precursor protein (APP) has generated great interest in both medical and basic research. Mutations in APP are known to cause familial Alzheimer’s disease (for a recent review, see ref. 1), yet the physiological function of the precursor protein remains elusive. In mammals APP has two homologs, APLP1 and APLP2 (2, 3). Knocking out all three genes is lethal to the animal (4). APP and the two APLPs are type-I membrane proteins (5), and are found both inside the cell and on the cell surface. Proteolysis by secretases releases various fragments of the protein from the membrane. These include amyloid β-peptide, widely believed to play an important role in Alzheimer’s disease (6), a number of different ectodomain fragmenets that have been shown to have various biological activities (e.g., see ref. 7–9), and a small intracellular domain that is thought to function in transcriptive regulation (e.g., see ref. 10–12). The oligomeric structure of APP is potentially important because this may affect its proteolytic processing (13), or play a role in the transmembrane signaling mechanism that the protein is involved in (14). Biochemical and cell biological studies have shown that APP can form dimers in the cell (14–18), but many questions remain controversial. For example, which domain of the membrane protein is responsible for dimerization (16, 19, 20)? Is dimerization obligatory, or induced by ligand binding (e.g., heparan sulfate proteoglycans; ref. 20, 21)? The matter is further complicated by the possibilities that APP may heterodimerize with the APLPs, and that dimerization can occur not only in cis, but also in trans between molecules from different cells (16, 18). The ectodomains of APP and APLPs have two conserved regions called E1 and E2 (Fig. 1A), both of which have been proposed to contribute to dimerization. A recently solved crystal structure of E1 reveals an interesting dimeric arrangement of the protein where the dimeric contact is mediated exclusively through the N-terminal portion of the molecule, a substructure called the growth-factor-like-domain (GFLD) (20). In an earlier study, however, the isolated GFLD crystallized as monomers (22). The crystal structures of E2 (19, 23), and the NMR structure of a fragment of it (24), have also been solved. The crystal structure shows that E2 forms an antiparallel dimer (19). Nevertheless, the hypothesis that E2 may function as the dimerization domain of the full-length molecule was recently challenged by the observation that the E2 domain of the C. elegans homolog APL-1 has been crystallized as monomers (25). To help clarify the oligomeric structure of E2, here we report two new crystal structures of E2, one from APP and the other from APLP1, and show that they share the same mode of antiparallel dimerization. We also show for the first time that heparin binding induces E2 dimerization. Since the APP family of proteins travels to cell surface, and can be secreted into the extracellular matrix, the possibility that heparan sulfate proteoglycans might modulate their oligomerization states has important biological implications. Figure 1 The E2 domains of APP and APLP1 have similar dimeric structures. (A) The domain structure of APP. The residue numbers shown above the diagram are according to the common APP isoform-751. (B) The structure of the E2 domain of APP in crystal form “B”. ...