Figure 6
From: De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide
Proposed binding interactions between EEf15.4 and DYKD. The same coloring scheme and antibody orientation was used as in Fig. 5. The EEf15.4 antibody is shown (A) with the designed peptide interaction and (B) without the peptide. The DYKD residues of the peptide fit into a deep cavity formed by the interface of the heavy and light chain CDRs. The remaining FLAG peptide residues extend over the light chain CDRs but are not predicted to form any interactions. (C) Specific binding activity of scFv phage with single amino acid substitutions in CDR residues predicted to be involved in ligand binding. All specific binding values were calculated as the ligand binding signal divided by the anti-c-myc binding signal at a single phage concentration in the linear dose-response regime. These values were then normalized to the specific binding of the unmodified, wild-type EEf15.4 scFv phage (15.4 WT).
