Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective

Background: A protein binding hot spot is a small cluster of residues tightly packed at the center of the interface between two interacting proteins. Though a hot spot constitutes a small fraction of the interface, it is vital to the stability of protein complexes. Recently, there are a series of hypotheses proposed to characterize binding hot spots, including the pioneering O-ring theory, the insightful `coupling' and `hot region' principle, and our `double water exclusion' (DWE) hypothesis. As the perspective changes from the O-ring theory to the DWE hypothesis, we examine the physicochemical properties of the binding hot spots under the new hypothesis and compare with those under the O-ring theory. Results: The requirements for a cluster of residues to form a hot spot under the DWE hypothesis can be mathematically satisfied by a biclique subgraph if a vertex is used to represent a residue, an edge to indicate a close distance between two residues, and a bipartite gra...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Qian Liu, Jinyan Li
• Keywords: BMCBI 2010, Hot Spots, O-ring Theory, Proteins