Design of conformation-specific antibodies against unfolded and misfolded proteins

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1159943/ Tessier A grand, unmet challenge in the protein engineering community is to design antibodies that bind to target antigens with high affinity and specificity. The goal of this proposal is elucidate general principles for designing antibodies against unfolded and misfolded (aggregated) proteins. Importantly, there are no previously reported antibodies specific for diverse unfolded proteins, few reported conformation-specific antibodies against misfolded proteins that recognize linear sequence epitopes, and no reported strategies for designing antibodies against either protein conformation. This proposal is based on two recent discoveries from the PIs laboratory. First, they have discovered that a tyrosine-rich motif within a single antigen-binding loop mediates antibody binding to unfolded proteins (but not to folded proteins). Second, they have discovered that amyloidogenic motifs from the amyloid beta peptide grafted into a single antibody loop mediate conformation-specific antibody recognition of aggregated forms of amyloid beta (but not monomeric amyloid beta).Intellectual Merit: Based on these discoveries, the PI aims to test the following two hypotheses related to the design of conformation-specific antibodies: i) antibodies displaying aromatic peptide motifs (including aromatic residues other than tyrosine) bind selectively to unfolded proteins, and such binding is mediated via pi-stacking interactions involving solvent-exposed aromatic residues within unfolded proteins (which are solvent-shielded within folded proteins); and ii) antibodies displaying amyloid motifs from diverse proteins selectively recognize amyloid fibrils (but not monomers) containing the cognate motifs, and such antibody recognition is mediated via homotypic interactions between amyloid motifs.Broader Impacts: The work has broad implications for designing antibodies against diverse biomolecules (including several disease-linked proteins), as well as for understanding and manipulating biomolecular recognition. The investigator is committed to strong outreach to underrepresented minorities and other disadvantaged peoples through two efforts: i) a 4th grade science outreach program in an elementary school with a significant fraction of reduced-cost lunch (~80%) and African American (~40%) students focused on molecules using animated cartoons and hands-on activities to interest these students in science at an early age; and ii) a 12th grade outreach program to diverse students from rural towns in New York's Capital District lacking advanced science courses that involves these students in the process of discovery and development of a therapeutic antibody to encourage them to pursue biomolecular aspects of science and engineering during their undergraduate and graduate education.