Abstract
Protein-protein interactions (PPI) are pivotal to the numerous processes in the cell. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the of forces interactions. The interaction interface of obligatory protein-protein complexes differs from that of the transient interactions. We have created a large database of protein-protein interactions containing over100 thousand interfaces. The structural redundancy was eliminated to obtain a non-redundant database of over 2,265 interaction interfaces. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the offorces interactions. The residue interaction propensity and all of the rest of the parametric scores converged to a statistical indistinguishable common sub-range and followed the similar distribution trends for all three classes of sequence-based classifications PPInS. This indicates that the principles of molecular recognition are dependent on the preciseness of the fit in the interaction interfaces. Thus, it reinforces the importance of geometrical and electrostatic complementarity as the main determinants for PPIs.
Highlights
The cellular milieu where proteins perform their function is crowded
This indicates that the principles of molecular recognition are dependent on the preciseness of the fit in the interaction interfaces
If the interacting protein chains were similar homologous up to 49%, the corresponding Protein-protein interaction interface (PPII) was marked under low sequence similarity (LSS) class; the PPIIs with protein chains sharing 50-89% sequence similarity were grouped under moderate sequence similarity (MSS) class; and the PPIIs with protein chains sharing 90-100% sequence similarity were grouped under high sequence similarity (HSS) class
Summary
The cellular milieu where proteins perform their function is crowded. the spatial and temporal preciseness of interactions is rarely violated. Protein– protein interactions (PPIs) form the very basis for all biological processes, such as signal transduction, material /energy transport, metabolic reactions, regulation of gene expression, cellular growth and proliferation[3,4,5,6] These interactions form the fundamentals of the intracellular / intercellular communications [7]. In protein-protein complexes, the interaction of two or more proteins is very specific and is usually characterized by only a small subset of their surfaces [12,13,14,15] Those sites which own the proper binding features participate in the formation of PPCs [16,17,18,19,20] (Supplementary Figure 1).Such understanding may augment the development of computational tools for PPI sites prediction [9], and drug discovery [20,21,22]. All three classes of NRDB dataset were examined for six important parameters of: residue interface propensity, hydrophobic content, solvation energy, compactness of interacting residue’s neighborhood, planarity, and depth index
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