Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7

We investigated the relative free energies of hapten binding to the germ li ne and mature forms of the 48G7 antibody Fab fragments by applying a contin uum model to structures sampled from molecular dynamics simulations in expl icit solvent. Reasonable absolute sind very good relative free energies wer e obtained. As a result of nine somatic mutations that do not contact the h apten, the affinity-matured antibody binds the hapten >10(4) tighter than t he germ line antibody. Energetic analysis reveals that van der Waals intera ctions end nonpolar contributions to solvation are similar and drive the fo rmations of both the germ line and mature antibody-hapten complexes. Affini ty maturation of the 48G7 antibody therefore appears to occur through reorg anization of the combining site geometry in a manner that optimizes the bal ance of gaining favorable electrostatic interactions with the hapten and lo sing those with solvent during the binding process. As reflected by lower r ms fluctuations in the antibody-hapten complex, the mature complex undergoe s more restricted fluctuations than the germ line complex. The dramatically increased affinity of the 48G7 antibody over its germ line precursor is th us made possible by electrostatic optimization.