Identification and Analysis of Binding Site Residues in Protein-Protein Complexes

We have developed an energy based approach for identifying the binding sites and important residues for binding in protein-protein complexes. We found that the residues and residuepairs with charged and aromatic side chains are important for binding. These residues influence to form cation-¤Ç, electrostatic and aromatic interactions. Our observation has been verified with the experimental binding specificity of protein-protein complexes and found good agreement with experiments. The analysis on surrounding hydrophobicity reveals that the binding residues are less hydrophobic than non-binding sites, which suggests that the hydrophobic core are important for folding and stability whereas the surface seeking residues play a critical role in binding. Further, the propensity of residues in the binding sites of receptors and ligands, number of medium and long-range contacts, and influence of neighboring residues will be discussed.

• M. Michael Gromiha
• Kiyonobu Yokota
• Kazuhiko Fukui

• Protein-protein interactions
• energy based approach;binding sites
• propensity
• long-range contacts
• hydrophobicity

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