Modeling of the role of conformational dynamics in kinetics of the antigen-antibody interaction in heterogeneous phase.

A novel approach that may potentially be used to study biomolecular interactions including the simultaneous determination of structural and kinetic binding parameters is described in this Article for the first time. It allows a rigid distinction between the possible reaction mechanisms of biomolecular recognition, induced fit and conformational selection. The relative importance of the two pathways is determined not by comparing rate constants but the structural aspects of the interaction instead. So the exact location of antigen molecules with respect to the capture antibody is depicted experimentally, avoiding the use of X-ray crystallography. The proposed pattern is applied to study the anti-BSA Immunoglobulin G (IgG)-free Bovine Serum Albumin (BSA) interaction, in which IgG is anchored on a silicon chip sensing surface in an oriented manner. The exact location of the receptor with respect to the ligand was monitored during the binding process, thus drawing the full reaction scheme. IgG forms an asymmetric (FabBSA)2 complex with BSA molecules, even though it has two identical fragment antigen binding arms. This is thought to be due to steric hindrance caused by the binding of the first BSA molecule. Furthermore, the proposed model allows one to characterize reaction intermediates without the need of isolating them. These intermediates not characterized in situ so far are the keystone to understand how antibodies are able to identify antigens.