Immunoglobulin cross-reactivity examined by library screening, crystallography and docking studies

Antibodies are extremely diverse with respect to their specificities and af finities for target molecules. Despite rigorous selection, some antibodies are cross-reactive whereby they recognize their natural antigens along with other molecules. In this review, we discuss our efforts toward understandi ng the cross-reactivity of selected immunoglobulins. Investigations that ar e discussed employed screens of combinatorial peptide libraries, crystallog raphy of ligand-protein complexes, and computer-based peptide docking simul ations. In the first example, two different antibodies (NC6.8 and NC10.14) bound the same trisubstituted guanidine (NC174) with similar affinities, bu t utilized predominantly dissimilar binding strategies. However, there was one common binding strategy, in which the cyanophenyl portion of NC174 was inserted end-on into the binding crevices of the NC6.8 and NC 10.14 antibod ies. In the second example, scanning of peptide libraries and X-ray crystal lography were used to design and test synthetic peptides for binding to the Mcg L chain dimer. Again, end-on insertion was favored for all peptides la rger than dipeptides in the voluminous Mcg binding cavity. Finally, automat ed docking was used for rapid predictions of complexes for the Fv molecule from a broadly cross-reactive human IgM (Mez) and nearly two thousand pepti des. Certain amino acids, including the aromatic residues Trp and Phe, func tioned as anchoring groups in automated docking. Anchoring groups acted in most of the peptides that were otherwise accommodated by a variety of bindi ng strategies in the docked complexes. We suggest that anchoring of at leas t a portion of a ligand in a binding site is a common mechanism for antibod y recognition.