Immunome Research
Open Access

Abstract

Immunoglobulin Structure Exhibits Control over CDR Motion

Michael T. Zimmermann, Aris Skliros, Andrzej Kloczkowski, and Robert L. Jernigan

Motions of the IgG structure are evaluated using normal mode analysis of an elastic network model to de-tect hinges, the dominance of low frequency modes, and the most important internal motions. One ques-tion we seek to answer is whether or not IgG hinge motions facilitate antigen binding. We also evaluate the protein crystal and packing effects on the experimental temperature factors and disorder predictions. We find that the effects of the protein environment on the crystallographic temperature factors may be mislead-ing for evaluating specific functional motions of IgG. The extent of motion of the antigen binding domains is computed to show their large spatial sampling. We conclude that the IgG structure is specifically designed to facilitate large excursions of the antigen binding domains. Normal modes are shown as capable of com-putationally evaluating the hinge motions and the spatial sampling by the structure. The antigen binding loops and the major hinge appear to behave similarly to the rest of the structure when we consider the dominance of the low frequency modes and the extent of internal motion. The full IgG structure has a lower spectral dimension than individual Fab domains, pointing to more efficient information transfer through the antibody than through each domain. This supports the claim that the IgG structure is specifically con-structed to facilitate antigen binding by coupling motion of the antigen binding loops with the large scale hinge motions.