Predicting molecular interactions and inducible complementarity: Fragment docking of fab‐peptide complexes

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Abstract
Antibody‐antigen interactions are representative of a broad class of receptor‐ligand interactions involving both specificity and potential inducible complementarity. To test possible mechanisms of antigenantibody recognition and specificity computationally, we have used a Metropolis Monte Carlo algorithm to dock fragments of the epitope Glu‐Val‐Val‐Pro‐His‐Lys‐Lys to the X‐ray structures of both the free and the complexed Fab of the antibody B13I2 (raised against the C‐helix of myohemerythri). The fragments Pro‐His and Val‐Pro‐His, which contain residues experimentally identified as important for binding, docked correctly to both structures, but all tetrapeptide and larger fragments docked correctly only to the complexed Fab, even when torsional flexibility was added to the ligand. However, only tetrapeptide and larger fragments showed significantly more favorable energies when docked to the complexed Fab coordinates than when docked to either the free Fab or a non‐specific site remote from the combining site. Comparison of the free and complexed B13I2 structures revealed that atoms within 5 Å of Val‐Pro‐His showed little movement upon peptide binding, but atoms within 5 Å of the other four epitope residues showed greater movements. These results computationally distinguish recognition and binding processes with practical implications for drug design strategies. Overall, this new fragment docking approach establishes distinct roles for the “lock‐and‐key” (recognition) and the “handshake” (binding) paradigms in antibody‐antigen interaction, suggests an incremental approach to incorporating flexibility in computational docking, and identifies critical regions within receptor binding sites for ligand recognition.