Paper Citing NAMD - Abstract
Spijker, P.; Vaidehi, N.; Freddolino, P.L.; Hilbers, P.A.J.; Goddard, W.A.
Dynamic behavior of fully solvated beta 2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:4882-4887, MAR 28 2006
Recently we predicted the 3D structure of the human beta 2-adrenergic receptor (beta 2AR) and of the binding site of several agonists and antagonists to beta 2AR. 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 (MID) simulations of three systems: apo-beta 2AR, epinephrine-bound beta 2AR, and butoxamine-bound beta 2AR (epinephrine is an endogenous agonist, and butoxamine is a beta 2AR selective antagonist). The predicted structures for apo-beta 2AR and butoxamine-beta 2AR are stable in MD, but in epinephrine-beta 2AR, extracellular water trickles into the binding pocket to mediate hydrogen bonding between the catechol of epinephrine and Ser-204 on helix 5. The epinephrine-beta 2AR 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-beta 2AR shows less dynamic flexibility, whereas the antagonist-beta 2AR 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.
