Structural, functional, and physiological properties of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during the course of affinity maturation.

Structural and functional analyses of antibodies in the affinity maturation pathway can help us understand the molecular mechanisms of protein recognition. Using one of the haptens, (4-hydroxy-3-nitrophenyl)acetyl (NP), various monoclonal antibodies have been obtained, either at the early or late stage of immunization. The variable regions of monoclonal antibodies and their site-directed mutants can also be obtained as single-chain Fv (scFv) antibodies. The change in antigen-binding affinity and avidity of matured-type antibodies from germline-type antibodies could be evaluated based on binding kinetics and thermodynamics, proposing the antigen recognition mode. Crystal structures of a germline-type antibody, N1G9, and a matured-type antibody, C6, in complex with NP were determined, revealing different antigen-binding mode at atomic resolution. Notably, the Tyr to Gly mutation at the 95th residue of the heavy chain is critical for changing the configuration of complementarity determining region 3, which is involved in antigen binding. Furthermore, thermal stability analyses of scFv antibodies have revealed trade-off between antigen-binding affinity and thermal stability in the antigen-unbound state. To increase affinity, the stability of the variable region may be decreased, possibly due to protein architecture. The high stability of germline-type antibodies and the low stability of matured-type antibodies, which increase upon antigen binding, can be explained by the stability of antibodies required at the respective stages of immunization.