Dynamic behavior of fully solvated β2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist

Recently we predicted the 3D structure of the human β2-adrenergic receptor (β2AR) and of the binding site of several agonists and antagonists to β2AR. These predictions (MembStruk and HierDock) included no explicit water and only a few lipid molecules. Here we include explicit H₂O and an infinite lipid bilayer membrane in molecular dynamics (MD) simulations of three systems: apo-β2AR, epinephrine-bound β2AR, and butoxamine-bound β2AR (epinephrine is an endogenous agonist and butoxamine is a β2AR selective antagonist). The predicted structures for apo-β2AR and butoxamine-β2AR are stable in MD, but in epinephrine-β2AR, extracellular water trickles into the binding pocket to mediate hydrogen bonding between the catechol of epinephrine and Ser-204 on helix 5. The epinephrine-β2AR structure shows dynamic flexibility with small, piston-like movements of helices 3 and 6 and transient interhelical hydrogen bonding between Ser-165 on transmembrane 4 and Ser-207 on transmembrane 5. These couplings and motions may play a role in protein activation. The apo-β2AR shows less dynamic flexibility, whereas the antagonist-β2AR structure is quite rigid. This MD validation of the structure predictions for G protein-coupled receptors in explicit lipid and water suggests that these methods can be trusted for studying the mechanism of activation and the design of subtype-specific agonists and antagonists.