Proteins with the HAEE tetrapeptide motif as potential targets for beta-amyloid

Introduction: Beta-amyloid (Aβ) is involved in numerous physiological and pathophysiological processes and is one of the key players in the pathogenesis of Alzheimer’s disease. Aβ interacts with the 35-HAEE-38 site of the α4 subunit of the α4β2 nicotinic acetylcholine receptor. The synthetic tetrapeptide HAEE effectively inhibits the aggregation of endogenous Aβ. HAEE specifically binds to the 11-EVHH-14 site of Aβ both in the absence and presence of zinc ions, leading to the formation of stable complexes. We hypothesized that the HAEE motif could represent a universal binding site for Aβ within the human proteome. Materials and Methods: To test this hypothesis, a large-scale search for all amino acid sequences containing the HAEE motif in the human (Homo sapiens) proteome was performed using our in-house PepString server (http://pepstring.eimb.ru/). The conservation of the identified sites was analyzed across jawed vertebrates using BLAST. Protein localization and structural features were determined based on data from UniProt, PDB, and AlphaFold. Results: We identified 85 proteins (including 200 isoforms) containing the HAEE motif. Of these, 26 proteins are membrane proteins, including receptors, ion channels, and transporters (e.g., CACNA1B, MRS2, SLC15A2), and 59 are intracellular proteins, mostly nuclear transcription factors (including 13 zinc finger proteins). Structural analysis revealed that the HAEE motif is often located within functionally important domains, such as cytoplasmic loops of transmembrane proteins or DNA-binding domains. Conclusion: Given that Aβ acts as an extracellular ligand and can also penetrate various intracellular compartments, all identified proteins with the HAEE motif are considered potential physiological and pathophysiological targets for Aβ. The most promising candidates are proteins whose HAEE sites are structurally similar to that in α4β2-nAChR and/or coordinate zinc ions. These findings enhance our understanding of the molecular mechanisms of Aβ function and open new avenues for the search of therapeutic targets in AD.