Frequency-resolved communication maps provide a coarse-grained picture of energy transport in nanoscale systems. We calculate communication maps for homodimeric hemoglobin from Scapharca inaequivalvis and sample them to elucidate energy transfer pathways between the binding sites and other parts of the protein with focus on the role of the cluster of water molecules at the interface between the globules. We complement analysis of communication maps with molecular simulations of energy flow. Both approaches reveal that excess energy in one heme flows mainly to regions of the interface where early hydrogen bond rearrangements occur in the allosteric transition. In particular, energy is carried disproportionately by the water molecules, consistent with the larger thermal conductivity of water compared to proteins.

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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.