Epitopes of Protein Binders Are Related to the Structural Flexibility of a Target Protein Surface

Protein binders including antibodies
are known not to bind to random
sites of target proteins, and their functional effectiveness mainly
depends on the binding region, called the epitope. For the development
of protein binders with desired functions, it is thus critical to
understand which surface region protein binders prefer (or do not
prefer) to bind. The current methods for epitope prediction focus
on static indicators such as structural geometry or amino acid propensity,
whereas protein binding events are in fact a consequence of dynamic
interactions. Here, we demonstrate that the preference for a binding
site by protein binders is strongly related to the structural flexibility
of a target protein surface. Molecular dynamics simulations on unbound
forms of antigen structures revealed that the antigen surface in direct
contact with antibodies is less flexible than the rest of the surface.
This tendency was shown to be similar in other non-antibody protein
binders such as affibody, DARPin, monobody, and repebody. We also
found that the relatedness of epitopes to the structural flexibility
of a target protein surface is dependent on the secondary structure
elements of paratopes. Monobody and repebody, whose binding sites
are composed of β-strands, distinctively prefer to bind to a
relatively more rigid region of a target protein. These observations
enabled us to develop a simple epitope prediction method which shows
a comparable performance to the commonly used ones.