Identifying the nature of the interface in protein-protein complexes

Abstract

The role of molecular recognition is critical to the proper self-assembly of biological macromolecules and their function. Shape complementarity of the mutual recognition interfaces is one of the important factors that guide this interaction. The lock-and-key mechanism involving enzyme-substrate is a classical hallmark of shape complementarities at work in biochemical reaction. Recognition principles between macromolecular entities, however, has been difficult formulate. Sensitive surface complementarity recognition algorithms are computationally prohibitive, while accuracy of the heuristic methods is limited by the choice of proper biochemical information. This is a major drawback in understanding macromolecular recognition which entails critical assessment of biochemical information involving large interacting interfaces. Here we data mine on a number of biochemical parameters to highlight their individual merits and demerits and propose specific properties suitable for designing heuristic algorithms. The work is expected to find utility within bioinformatics algorithms seeking docking macromolecules and designing of protein complex interfaces.