Structural mechanism for affinity maturation of an anti-lysozyme antibody

Abstract

In the immune response against a typical T cell-dependent protein antigen, the affinity maturation process is fast and is associated with the early class switch from IgM to IgG. As such, a comprehension of the molecular basis of affinity maturation could be of great importance in biomedical and biotechnological applications. Affinity maturation of anti-protein antibodies has been reported to be the result of small structural changes, mostly confined to the periphery of the antigen-combining site. However, little is understood about how these small structural changes account for the increase in the affinity toward the antigen. Herein, we present the three-dimensional structure of the Fab fragment from BALB͞c mouse mAb F10.6.6 in complex with the antigen lysozyme. This antibody was obtained from a long-term exposure to the antigen. mAb F10.6.6, and the previously described antibody D44.1, are the result of identical or nearly identical somatic recombination events. However, different mutations in the framework and variable regions result in an Ϸ10 3 higher affinity for the F10.6.6 antibody. The comparison of the three-dimensional structures of these Fablysozyme complexes reveals that the affinity maturation produces a fine tuning of the complementarity of the antigen-combining site toward the epitope, explaining at the molecular level how the immune system is able to increase the affinity of an anti-protein antibody to subnanomolar levels.

Chemical Basis for the Affinity Maturation of a Camel Single Domain Antibody

“…Comparison of the antibody complexes to the free structures of HyHEL63 crystallized in different space groups, showed minor conformational differences. Furthermore, no correlation was found between the amount of buried surface area or number of contacts and the observed affinity difference, albeit that such a correlation has been observed in the comparison of the structures of the antibodies D.44.1 and the more matured F10.6.6 in complex with HEWL (31). However, one should note that all these antibodies were already considerably matured and therefore might not represent early events in the maturation pathway.…”

First molecular and biochemical analysis ofin vivoaffinity maturation in an ectothermic vertebrate

“…In some instances, the more flexible ''induced fit'' binding observed for germ-line clones was ''fixed'' in mutationmatured clones to give a ''lock-and-key'' mode of binding and, consequently, a higher binding affinity and specificity (7,8). Other groups have shown that improvements in shape-complementarity with antigen are responsible for increasing affinity and specificity (9,10). Much less research has focused on affinity maturation in ectothermic vertebrates.…”

A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv)

“…Indeed, in silico design of mutations based on co-crystal structural analyses have shown that such new contacts can significantly enhance binding affinity in protein-protein (24) and protein-hapten interactions (25). In contrast, post hoc structural analyses of mutations generated naturally during B-cell development (26) or by Darwinian display-based evolution (27), have shown that considerable changes in binding energy can be achieved not by adding significant new contacts with antigen, but rather by "fine tuning" or "rigidification" of the antibody-antigen interface (28).…”