Protease-Antiprotease Interactions: An Overview of the Process from an “In Silico” Perspective

Abstract

Most if not all of the cellular processes involve protein-protein interactions (PPIs). The detailed information of the amino acid residues involved in PPIs may, therefore, be used in many important aspects like drug development, elucidation of molecular pathways, generation of protein mimetic, understanding of disease mechanisms, and development of docking methodologies to build structural models of protein complexes. Among the different physiological PPIs, protease-antiprotease interactions play a significant role. An imbalance between proteases and antiproteases is involved in many pathogenic reactions. This special class of PPI, therefore, needs a thorough scrutiny. There are different PPIs determining experimental tools. However, these tools are time-consuming and expensive. In response to these difficulties, a number of bioinformatic software tool have been developed. The algorithms are meant for prediction of three-dimensional structures of proteins as well as protein complexes. The structure prediction methods involve homology modeling, threading, and ab initio modeling. These methods have nearly 75%–80% overall accuracies. The other method is molecular docking which is meant to generate the three-dimensional conformations of protein complexes. The docking methods can broadly be classified as rigid body docking and flexible docking. In this chapter, the different aspects of experimental and computational modeling and docking strategies will be discussed. The basic terminologies will be revisited. This chapter is aimed at providing a firsthand knowledge on protein interaction methods using protease-antiprotease interactions as an example.