Protein dimer interfaces : ligands, sidechains, hot spots and binding

Protein dimer interactions (homodimers and heterodimers) are common in molecular catalysis and regulation. Prediction of interaction sites or interaction partners from sequence is challenging. The significance of interface ligands, sidechain-sidechain prevalence at the interfaces, “hot spot” interface residues (high energy residues) and binding are discussed using structural data. A dataset of 62 identical homodimer pairs (one structure determined with interface ligands and the other without them) suggests that interfaces having ligands are less hydrophobic with small interface area compared to those without ligands and the effect of ligands occupying =7% interface area is negligible on dimer interactions. In addition, the analysis of homodimers, heterodimers and crystal-packing monomers shows preference for sidechain-sidechain interactions. “Hot spot” interface residues are compared with other interface residues using a dataset of alanine-mutated interface residues. It is found that “hot spot” residues have strong positive inter-atomic interactions and a simple effective “hot spot” prediction method is developed which has better accuracy than other ‘hot spot’ prediction methods. Some dimers form from unfolded monomers without intermediate (two-state (2S)) and others through the formation of stable intermediate (three-state (3S)). 25 ‘2S’ homodimers and 16 ‘3S’ homodimers are compared to estimate their structural differences. It is found that a combination of the properties (e.g. monomer length, subunit interface area, ratio of interface to interior hydrophobicity) can predominately distinguish 2S and 3S dimers.MASTER OF ENGINEERING (MPE