Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein

The effects of ligand binding on an oxygen sensor protein, FixLH, were investigated by molecular dynamics simulation. To illustrate the network of residue interactions in the deoxy, oxy, and carbomonoxy states of FixLH, we employed the energy exchange network (EEN) model in which residue interactions were evaluated in terms of local transport coefficients of energy flow. As a result, the difference map of EEN between the deoxy and oxy (deoxy and carbomonooxy) states clearly demonstrated the allosteric transition, although the structural changes by ligand binding are small. It is known that the FixLH forms a homodimer in solution, although neither O₂ nor CO binding exhibits cooperativity. Therefore, we conjectured that the primary event after ligand binding occurs essentially at the monomer level, and it is subsequently followed by quaternary structural changes. The difference EEN maps showed that two regions, (A) the junction between the coiled-coil linker and the sensor domain and (B) the potential dimer interface, experienced considerable change of the energy-transport coefficients, indicating that these two regions play important roles in quaternary structural changes and signal transduction in response to ligand binding.