A Global and Local Structure-Based Method for Predicting Binary Protein-Protein Interaction Partners: Proof of Principle and Feasibility

We report a novel 3D structure-based method of predicting protein-protein (PP) interaction (PPI) partners. The method involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the PP complex, with one tetrahedron on each protomer*. H-bonds and VDW interactions at the interface of the two interacting protein molecules in the complex are first determined, and then interacting tetrahedral motifs one from each protomer – representing backbone or side chain centroids of the interacting amino acids, are built from them. The method requires that the protein protomers be transformed first into double-centroid reduced representation (DCRR; Reyes, V.M. & Sheth, V.N., 2011; Reyes, V.M., 2015a). The method is applied to a collection of 801 functionally unannotated protein structures in the Protein Data Bank (PDB), which were screened for pairs of tetrahedral motifs characteristic of nine binary complexes, namely: (1.) RAP-Gmppnp c-RAF1 Ras-binding domain; (2.) RHOA protein kinase PKN/PRK1 effector domain; (3.) RAC RHOGD1; (4.) RAC P67PHOX; (5.) kinase-associated phosphatase (KAP) phospho-CDK2; (6.) Ig Fc – protein A fragment B; (7.) Ig light chain dimers; (8.) beta-catenin HTCF-4; and (9.) IL-2 homodimers. Our search procedure found 33, 297, 62, 63, 120, 0, 108, 16 and 504 putative complexes, respectively. After considering the degree of interfacial overlap between the two protomers in the binary complex, these numbers were significantly trimmed down to 4, 2, 1, 8, 3, 0, 1, 1, and 1, respectively. Negative and positive control experiments indicate that the screening process has better than acceptable specificity and sensitivity. The results were further validated by applying the “Cutting Plane” and ‘Tangent Sphere” methods (Reyes, V.M., 2015b) for the quantitative determination of interface burial, which is indicative of inter-protomer overlap (IPO) in the binary complex; which we, in turn, assume to be a conserved property of any specific family of binary complexes. One advantage of our method is its simplicity, speed and scalability, as well as its protein docking nature -i.e., once the partner interface 3D SMs are identified, they can be used to computationally dock the two protomers together to form the putative binary complex -a property that we shall describe briefly in this work. ______________________________ *We shall use the term “protomer” to refer to each of the two monomer molecules making up the binary protein complex.