Ligand binding by antibody IgE lb4: Assessment of binding site preferencesusing microcalorimetry, docking, and free energy simulations

Antibody IgE Lb4 interacts favorably with a large number of different compo unds. To improve the current understanding of the structural basis of this vast cross-reactivity, the binding of three dinitrophenyl (DNP) amino acids (DNP-alanine, DNP-glycine, and DNP-serine) is investigated in detail by me ans of docking and molecular dynamics free energy simulations. Experimental binding energies obtained by isothermal titration microcalorimetry are use d to judge the results of the computational studies. For all three ligands, the docking procedure proposes two plausible subsites within the binding r egion formed by the antibody CDR loops. By subsequent molecular dynamics si mulations and calculations of relative free energies of binding, one of the se subsites, a tyrosine-surrounded pocket, is revealed as the preferred poi nt of complexation, For this subsite, results consistent with experimental observations are obtained; DNP-glycine is found to bind better than DNP-ser ine, and this, in turn, is found to bind better than DNP-alanine. the sugge sted binding mode makes it possible to explain both the moderate binding af finity and the differences in binding energy among the three ligands.