Engineering a circularly permuted GFP scaffold for peptide presentation

The use of peptides as in vivo and in vitro ligand binding agents is hampered by the high flexibility, low stability and lack of intrinsic detection signal of peptide aptamers. Recent attempts to overcome these limitations included the integration of the binding peptide into a stable protein scaffold. In this paper, we present the optimization and testing of a circularly permuted variant of the green fluorescent protein (GFP). We examined the ability of the optimized scaffold to accept peptide insertions at three different regions. The three regions chosen are localized in close spatial proximity to each other and support different conformations of the inserted peptides. In all the three regions peptides with a biased, but still comprehensive, amino acid repertoire could be presented without disturbing the function of the optimized GFP-scaffold.