Title: Free Energy Difference Calculations on Thermodynamic Model of Beta 2 Adrenergic Receptor Activation
Abstract: We have developed a thermodynamic model that describes the full agonist activation of the β1 and β2 adrenergic receptors. The activation mechanism of Rhodopsin is well understood, for other class A GPCRs the process is not as well resolved. Rhodopsin combines conformational change with proton uptake by two internal proton switches to achieve a stable active conformation. There is evidence to suggest that the β1 and β2 adrenergic receptors use a similar process. It has been demonstrated that the β2 adrenergic receptor activity increases at acidic pH, the result of Asp134 protonation. Molecular dynamics simulations revealed that deprotonation of Asp79 results in disruption of the ionic lock. Our hypothesis is that a proton transfer from Asp79 to an unknown proton acceptor facilitates the transition from inactive to the intermediate state in our model. This is followed by a conformational change that results in the protonation of Asp134, a transition that stabilizes active state. We tested our hypothesis by performing free energy difference (ΔΔG) calculations from a set of Molecular Dynamics simulations of the β1 and β2 receptors with these Aspartic acid residues occupying different ionization states. These calculations test whether transitions in ionization states of these residues provide favorable energy for activation.