Characterization of Protein–Protein Interfaces, Considering Surface-Roughness and Local Shape

Abstract This chapter attempts to provide an account of works that have attempted to characterize protein–protein interaction interfaces, with fractal dimension. However, such characterization of interfaces is not solely dependent upon interface roughness. Without involving the biophysical factors, we will concentrate only on geometric characterization of these interfaces. To be specific, we will attempt to talk about a possible algorithm to quantify the changes in two parameters describing any protein–protein interaction interface; namely, the curvature of shape of protein–protein interaction interface and the surface roughness of it. One can connect these two parameters through a novel methodology, ‘extended unit iterated shuffle transformation’. Results show that although the interface patch for enzyme-inhibitor interaction is flatter and smoother than the non-interfacial surface patches, absolute magnitudes of shape curvatures and surface roughness of bound interfaces are greater than what they were in unbound states of concerned entities. Trends observed on antigen–antibody interfaces are found to be somewhat contradictory to the trends observed in case of enzyme-inhibitor interfaces. Antigen–antibody interfaces, like the enzyme-inhibitor interfaces, are found to be flatter and smoother than the non-interfacial surface patches. However, unlike the enzyme-inhibitor interfaces, absolute magnitudes of shape curvatures and surface roughness of bound antigen–antibody interfaces are observed to be less than what they were in unbound states of concerned entities. Algorithm proposed in the present work could quantify the effects due to changes in two extremely important interfacial parameters, through a unified scheme.