Diversity of protein-protein interactions

Abstract

In this review, we discuss the structural and functional diversity of protein-protein interactions (PPIs) based primarily on protein families for which three-dimensional structural data are available. PPIs play diverse roles in biology and differ based on the composition, affinity and whether the association is permanent or transient. In vivo, the protomer's localization, concentration and local environment can affect the interaction between protomers and are vital to control the composition and oligomeric state of protein complexes. Since a change in quaternary state is often coupled with biological function or activity, transient PPIs are important biological regulators. Structural characteristics of different types of PPIs are discussed and related to their physiological function, specificity and evolution.

Fig. 1. Examples of different types of protein–protein interactions as described in the text: (A) obligate homodimer, P22 Arc repressor; (B) obligate heterodimer, human cathepsin D that consists of a non-homologous light (red) and heavy (green) chain; (C) non-obligate homodimer, sperm lysin; (D) non-obligate heterodimer, RhoA (green) and RhoGAP (red) signalling complex; (E) non-obligate permanent heterodimer, thrombin (red) and rodniin inhibitor (green); (F) non-obligate transient heterotrimer, bovine G protein, i.e. the interaction between Gα (green) and Gβγ (red, orange) is transient.

Fig. 2. Illustration of (A) the control of protein oligomerization and (B) the relation between different types of protein–protein interactions (PPIs), their binding affinity and the localization of their protomers. The triggers that control the transient oligomerization are given in red in (B). *Large conformational changes are usually associated with these transient PPIs.

Fig. 3. Contact area and polarity of the interfaces of various non- obligate and obligate complexes. Obligate complexes with a small and hydrophobic interface include coiled-coil proteins. The ellipse denotes the contact area–polarity space of weak transient interactions.

Fig. 4. (A) Illustration of multispecific oligomerization between two families of homologous proteins (A1–A3 and B1–B3). The lines between the proteins denote interactions with differing affinities. Protein contacts are exchanged between homologous members of a family (e.g. A1–B1 and A1–B2), depending on protomer co-localization and concentration, and their mutual affinities. Examples are given for multispecific oligomerization within one protein family (i.e. where A∼B): (B) Bacillus stearothermophilus HU homodimer and Escherichia coli IHF heterodimer (the α and β chain are depicted in red and orange, respectively), including the target DNA; (C) mouse NFκB P50–P50 homodimer and P50–P65 heterodimer (the P50 and P65 protomers are depicted in red and orange, respectively) of the dimerization and DNA-binding domain, including the bound operator DNA.

Fig. 5. (A) Illustration of homologous monospecific oligomerization between one family (A1–A3) and three different ligands (C, D and E). Each member of the family has a specific binding partner. An example is given for the SH3-substrate heterodimers: (B) p53bp2, including the ankyrin repeat (orange) and the SH3 domain (red), with p53 (green), and (C) Fyn kinase SH3 domain (red) with HIV-1 Nef (green).