immunoglobulin functional motions and their effects on the complementarity determining regions
Motions of the IgG structure are evaluated using normal mode analysis and a new time dependent form of the elastic network model, to detect hinges, the dominance of low frequency modes, and the most important internal motions. We also evaluate the protein crystal and its packing effects on the experimental temperature factors and disorder prediction. We find that the effects of the protein environment on the crystallographic temperature factors may be misleading 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 computationally evaluating the hinge motions and the spatial sampling of domains of 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.
igg normal mode elastic network model protein crystal internal distance hinge prediction immunoglobin