8 - Protein–Protein Systems

Summary

A discussion on the relevance of protein–protein interactions (PPIs) in biochemistry and biophysics is presented, with the definitions of the proteome, interactome, and the classification of the PPIs. In particular, the essential role played by the Protein Data Bank (PDB) for the study of the PPIs is highlighted, as well as the use of classical molecular dynamics to improve the quality of PDB data and to test novel ligand geometries to improve drug efficiency. Focusing directly on the theoretical description of PPIs using physics, a detailed assessment of the dielectric function of proteins is carried out, with the definition of homogeneous and inhomogeneous dielectric constants and the description of the hydration layer of a solvated protein. Three strategies for the description of the inhomogeneous dielectric constant of proteins are shown, and a fragmentation procedure using density function theory (DFT) to obtain detailed energetic profiles of PPIs is depicted.