Generation of a dataset for studying ligand effect on homodimer interface.

Protein dimer interfaces (homodimer - same polypeptide and heterodimer - different polypeptide) display geometric and chemical properties that give the non-covalent assembly its stability and specificity. Therefore, it is important to understand the molecular principles of dimer interaction. Several studies on homodimer interaction are available. However, a study on the effect of ligands (i.e. non-peptide compounds) on subunit interactions is not available. Hence, we generated a dataset of 62 identical homodimer pairs (one structure determined with an interface ligand and the other without an interface ligand) and analyzed the effect of interface ligands on dimer interface. The analysis suggests that homodimer interfaces having ligands are less hydrophobic with small interface area compared to those without ligands. We also found that ligands occupying = 7% interface area have negligible effect on dimer interaction.