Variation of Energy Transfer Rates across Protein-Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin.

Abstract

Molecular dynamics simulations of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) have been carried out to examine relations between rates of vibrational energy transfer across nonbonded contacts and equilibrium structural fluctuations, with emphasis on protein-water contacts. The scaling of rates of energy transfer with equilibrium fluctuations of the contact length is found to hold up well for contacts between residues and hemes at the interface and the cluster of 17 interface water molecules in the unliganded state of HbI, as well as for the liganded state, for which the cluster contains on average 11 water molecules. In both states, the rate of energy transfer is also found to satisfy a diffusion relation. Within each globule, the scaling for polar contacts is similar to that found in an earlier analysis of myoglobin. Entropy associated with dynamics of polar contacts within each globule and with contacts between the hemes and water cluster is found to increase upon ligation. Energy exchange networks (EENs) for liganded and unliganded states obtained from the simulations are also presented and discussed. Energy transport networks through which nonbonded contacts transport energy in HbI, referred to as nonbonded networks (NBNs), are determined from the EENs and compared for the two states.