Molecular recognition via face center representation of a molecular surface

While docking methodologies are now frequently being developed, a careful examination of the molecular surface representation, which necessarily is employed by them, is largely overlooked. There are two important aspects here that need to be addressed: how the surface representation quantifies surface complementarity, and whether a minimal representation is employed. Although complementarity is an accepted concept regarding molecular recognition, its quantification for computation is not trivial, and requires verification. A minimal representation is important because docking searches a conformational space whose extent and/ or dimensionality grows quickly with the size of surface representation, making it especially costly with big molecules, imperfect interfaces, and changes of conformation that occur in binding. It is essential for a docking methodology to establish that it employs an accurate, concise molecular surface representation.

Here we employ the face center representation of molecular surface, developed by Lin et al.,¹ to investigate the complementarity of molecular interface. We study a wide variety of complexes: protein/small ligand, oligomeric chain-chain interfaces, proteinase/protein inhibitors, antibody/antigen, NMR structures, and complexes built from unbound, separately solved structures. The complementarity is examined at different levels of reduction, and hence roughness, of the surface representation, from one that describes subatomic details to a very sparse one that captures only the prominent features on the surface. Our simulation of molecular recognition indicates that in all cases, quality interface complementarity is obtained. We show that the representation is powerful in monitoring the complementarity either in its entirety, or in selected subsets that maintain a fraction of the face centers, and is capable of supporting molecular docking at high fidelity and efficiency. Furthermore, we also demonstrate that the presence of explicit hydrogens in molecular structures may not benefit docking, and that the different classes of protein complexes and may hold slightly different degrees of interface complementarity.