Interaction analyses between a arginine residue and the surrounding residues on protein-protein interfaces

Abstract

It is widely known that the structural/physico-chemical complementarities in each protein surface is very important in protein-protein interaction (PPI) interface, since the stability of the complex is affected by the complementarity. And, a decrease in the existence ratio of charged amino acid residues and an increase in that of non-polar residues on the PPI interface have been reported compared with on the surface of protein. However, it has been also reported that there is no difference in the existence ratio of Arg between protein surface and PPI interface. So, we analyzed the complementarities focusing on Arg at PPI interface using 143 PDB data and we picked up the charged amino acid residue’s pairs and the surrounding residues existing within 5Å in a PPI interface to generate the model structures for our calculations. Then, to analyze the inter-residue interactions between charged amino acid residue’s pair and the surrounding residues, we have performed ab initio molecular orbital calculations and density functional calculations.