Communication Maps: Exploring Energy Transport through Proteins and Water

Abstract

Frequency-resolved communication maps provide a coarse-grained, global mapping of energy transport channels in a protein as a function of frequency of modes that carry energy. We illustrate the approach with a study of the homodimeric hemoglobin of Scapharca inaequivalvis, which exhibits cooperativity during ligand binding. We compare energy transport between the two hemes of the unliganded and oxygenated protein, which is mediated by water as well as residues forming a hydrogen-bonding network at the interface between the globules, and lies along the pathway for allosteric transitions observed in time-resolved X-ray studies. Non-equilibrium molecular simulations on energy transport from the heme corroborate the energy transport pathways identified by the communication maps.