MAJOR ANTIGEN-INDUCED DOMAIN REARRANGEMENTS IN AN ANTIBODY

Background: Recent structural results have shown that antibodies use a n induced fit mechanism to recognize and bind their antigens. Here we present the crystallographically determined structure of an Fab direct ed against an HN-1 peptide (Fab 50.1) in the unliganded state and comp are it with the peptide-bound structure. We perform a detailed analysi s of the components that contribute to enhanced antigen binding and re cognition. Results: Induced fit of Fab 50.1 to its peptide antigen inv olves a substantial rearrangement of the third complementarity determi ning region loop of the heavy chain (H3), as well as a large rotation of the variable heavy (V-H) chain relative to the variable light (V-L) chain. Analysis of other Fab structures suggests that the extent of t he surface area buried at the V-L-V-H interface correlates with the ab ility to alter antibody quaternary structure by reorientation of the V -L-V-H domains. Conclusion: Fab 50.1 exhibits the largest conformation al changes yet observed in a single antibody. These can be attributed to the flexibility of the variable region. Comparisons of new data wit h previous examples lend to the general conclusion that a small V-L-V- H interface, due in part to a short H3 loop, permits substantial alter ations to the antigen-binding pocket. This has major implications for the prediction, engineering and design of antibody-combining sites.