Protein–Protein‐Binding Interfaces

Abstract

Proteins accomplish vital functions in many cellular processes through their interactions with other molecules. They can act as structural building blocks or catalysts; they may store and transport different molecules; or they may take part in various signaling pathways and are responsible for phase separation in cells. These are only some of the vast number of actions they may take an important role in. These actions can be accomplished via interactions with other proteins, DNA, RNA, etc. Proteins interact through their binding interfaces on their surfaces. Therefore, understanding the structural and functional properties of the protein-binding interfaces is key to explaining mechanisms of action for proteins. A comprehensive understanding of protein–protein interfaces may enable better characterization of disease-related signaling pathways and efficient drug design. In this chapter, we focus on protein–protein interfaces. We define protein–protein interfaces, explain the computational methods to identify them, and discuss their physicochemical properties. We also introduce some of the current databases and tools that can be used for the identification and analysis of protein–protein interfaces.