The modular architecture of protein–protein binding interfaces

Abstract

Protein-protein interactions are essential for life. Yet, our understanding of the general principles governing binding is not complete. In the present study, we show that the interface between proteins is built in a modular fashion; each module is comprised of a number of closely interacting residues, with few interactions between the modules. The boundaries between modules are defined by clustering the contact map of the interface. We show that mutations in one module do not affect residues located in a neighboring module. As a result, the structural and energetic consequences of the deletion of entire modules are surprisingly small. To the contrary, within their module, mutations cause complex energetic and structural consequences. Experimentally, this phenomenon is shown on the interaction between TEM1-␤-lactamase and ␤-lactamase inhibitor protein (BLIP) by using multiple-mutant analysis and x-ray crystallography. Replacing an entire module of five interface residues with Ala created a large cavity in the interface, with no effect on the detailed structure of the remaining interface. The modular architecture of binding sites, which resembles human engineering design, greatly simplifies the design of new protein interactions and provides a feasible view of how these interactions evolved.cluster analysis ͉ binding energy ͉ protein-protein interaction ͉ structure T he evolution of protein-protein binding sites is a result of optimization with three boundary conditions: the definition of the complex structure, optimization of the binding affinity for a given task, and the generation of specificity. Thermodynamic, kinetic, and structural studies of protein-protein interactions have taught us much of how proteins interact rapidly, tightly, and in a specific manner. These results have been translated into the development of in silico tools to calculate binding free energies, to weigh the energetic consequence of mutations, and for protein design (1-4). However, from the modest degree of success of the aforementioned methods, it is clear that our understanding of protein-protein interactions is still lacking (5).The most popular approach for studying the energetic contribution of an amino acid to the free energy of binding (or stability) of proteins is to introduce a mutation and then measure the subsequent change in free energy (6). However, accurate interpretation of the results of such experiments is limited by the fact that the properties of a protein are a function of the entire system, and not necessarily the sum of its parts (7). As a result, the energetic impact of any given residue on binding is not a simple additive quantity (8). A more elaborate approach to study the contributions of amino acids to binding and stability involves the use of double and higher-order mutant cycles, where interactions between amino acids are treated within their native contexts (7, 9). Such cycles reveal whether the contributions from a pair of residues are additive, or whether the effects of mutations are coupled (10, 11).Cha...

Energetic determinants of protein binding specificity: Insights into protein interaction networks

“…These findings show that the modular distribution of hot spots in binding sites relates to binding specificity. Thus, despite the complexity of mechanisms by which binding sites modulate binding affinity and specificity for biological function, consistent with experimental data [25], it appears that the modular distribution of hot spots plays a major role in achieving this goal. This binding site architecture might have been designed by evolution to generate a wide range of binding affinities and specificities.…”

“…Alanine scanning analysis has revealed that some binding hot spots are conserved within protein families [19], whereas others are specific to each family member [20][21][22]. Experiments have emphasized the modular design of binding sites, with energetic cooperative contribution of single residues within the module; and additive between modules [23][24][25]. Computational protein design methods have also been used to elucidate the tradeoff between stability and specificity for the optimization of biological function [8,26].…”

New insight into long‐range nonadditivity within protein double‐mutant cycles

“…A hypothesis that is very similar to the one analyzed here has been first proposed by Reichmann et al (27) to quantify the nonadditivity of changes in binding energies between protein-protein interfaces. In Ref.…”

“…In Ref. (27), this hypothesis was confirmed experimentally on the example of the interaction between TEM1-β-lactamase and β-lactamase inhibitor protein.…”

Interaction of C1q with IgG1, C-reactive Protein and Pentraxin 3: Mutational Studies Using Recombinant Globular Head Modules of Human C1q A, B, and C Chains

“…Reichmann et al (40) have recently suggested that protein-protein binding sites have a modular architecture made up of clusters of residues with both strong intracluster connections and weak intercluster connections. The deletion of a whole cluster of residues has no impact on the structure of the interface, whereas single mutations within a given cluster may lead to the structural rearrangement of their cluster.…”