Soft regions of protein surface are potent for stable dimer formation

By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins' quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids' affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. AbbreviationsAABaverage affinity for bindingANManisotropic network modelAPCaffinity propagation clusteringASAaccessible surface areaCCDinter residues distanceCSCcomplex stability codeDMdistance matrixΔG_dissPISA-computed dissociation free energyGNMGaussian normal mode analysisNMAnormal mode analysisPBPprotein binding patchPISAproteins, interfaces, structures and assembliesrASArelative accessible area in respect to unfolded state of residuesRMrecurrence matrixrPrelative protrusionRPrecurrence plotRQArecurrence quantitative analysisSEMstandard error of meanCommunicated by Ramaswamy H. Sarma.