(704c) Toward Design of Antibody Binding Loops That Mediate Conformation- and Sequence-Specific Recognition of Amyloid-Forming Polypeptides

Antibodies with conformational and sequence specificity for protein aggregates linked to disorders such as Alzheimer’s and Parkinson’s disease are valuable for a wide range of applications. We are investigating to what extent such antibodies can be designed by mimicking the natural process of protein aggregation. Our approach is to graft peptide segments that mediate amyloid formation into the complementarity-determining regions (CDRs) of single- and multidomain antibodies. Here we have investigated the impact of inserting polar mutations at the edges of a large hydrophobic Aβ peptide segment in CDR3 on the solubility and binding of the corresponding domain antibodies. We find that antibody expression and solubility are strongly enhanced by introducing multiple negatively charged or asparagine residues in CDR3, while other polar mutations are less effective. Moreover, Aβ domain antibodies with negatively charged CDR mutations show significant preference for recognizing Aβ fibrils relative to Aβ monomers, while the same domain antibodies with other polar CDR mutations recognize both Aβ conformers. We observe similar behavior for a domain antibody grafted with a large hydrophobic peptide segment from islet amyloid polypeptide (IAPP) that contains negatively charged mutations in CDR3. These findings highlight the sensitivity of antibody binding and solubility to residues at the edges of CDRs, and provide guidelines for designing other grafted antibody fragments with hydrophobic binding loops.