Constant Domain of Fab Fragment Affects Antigen Binding of Antibodies: Molecular Dynamics Study

Abstract

The fragment antigen binding (Fab) is a region on an antibody that binds to antigens. It is composed of one constant and one variable domain (Fv), which contain the heavy (H) and the light (L) chains. Antibodies bind antigens via contacts with amino acids in complementarity-determining regions (CDRs) in Fv domain. It may seem to be plausible that there is no difference of the binding structure and affinity between Fv and Fab format if the both format have same CDRs. Recently, however, numerous studies have compared the binding affinity of the single chain Fv (scFv) and Fab variants of the same antibody and have found that the changing the format to a Fab resulted in equal or higher binding affinity. However, the affects of the structural format on the antibody binding affinity remains poorly understood. In order to investigate the difference of physical properties between Fab and Fv fragments, from a structural and thermodynamical point of view, we have carried out 1 μs molecular dynamics (MD) simulations for each format. We have used the antibodies of epiregulin (EPR) as a simulation model, which is a member of the epidermal growth factor (EGF) family and a factor affecting pancreatic cancer, exhibiting high biological activities.We have found that constant region of Fab fragment of the antibody play an important role in the Fv domain stability, which reduce a fluctuation between H chain and L chain, and reduce the surface area of basic and hydrophobic amino acid exposed to solvent. And also find that binding free energy of Fab fragments and EPR is lower than that of Fv fragments. This indicates that the presence of the constant region of Fab fragment affects the binding structure of EPR and antibody.