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The Abs made by B lymphocytes on first encountering an antigen bind it with low intrinsic affinity, and, over time, the average affinity of the Abs made against that antigen gradually increases. These changes, known as affinity maturation, were found initially for serum antibodies that recognized small, chemically well-defined epitopes (e.g., 2,4-dinitrophenyl). That similar affinity increases occur in responses to protein antigens, which elicit most immune responses to infections or vaccination, has been generally assumed but difficult to prove (1) largely because of the complexity and multiplicity of epitopes (antigenic determinants) on even small, single-chain proteins (2). Though some protein epitopes are linear stretches of amino acids, they usually are configurational clusters of noncontiguous residues best delineated crystallographically in antibody–antigen complexes (3); and more often than not, the diverse antibodies elicited to a protein antigen bind to different epitopes on that protein (4), confounding efforts to convincingly demonstrate affinity maturation. There are at least five epitopes on the influenza virus hemagglutinin (HA) that binds the virions to host cells (5). By comparing the binding properties and structures of affinity matured Abs to one of the HA epitopes with those of their progenitor Abs, the elegant study by Schmidt et al. reported in PNAS (6) provides clear evidence for affinity maturation of Abs. The study is notable, moreover, for its focus on the human immune response to influenza virus vaccination with a conventional influenza seasonal vaccine (FLUZON flu shot). By bringing together diverse approaches (crystallography, molecular dynamics simulations, and kinetic studies), the authors shed intriguing light on how the affinity enhancement of affinity matured antibodies is achieved

Immunopaleontology reveals how affinity enhancement is achieved during affinity maturation of antibodies to influenza virus