Locating dynamic contributions to allostery via determining rates of vibrational energy transfer

Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relation between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β2-adrenergic receptor (β2AR), a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist bound active state. From structures sampled during molecular dynamics (MD) simulations we find the active state to have on average a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after transition between states thereby provides information about dynamic contributions to activation and allostery.