Abstract
The atomic-level dopamine activation mechanism for transmitting extracellular ligand binding events through transmembrane helices to the cytoplasmic G protein remains unclear. In the present study, the complete dopamine D3 receptor (D3R), with a homology-modeled N-terminus, was constructed to dock different ligands to simulate conformational alterations in the receptor’s active and inactive forms during microsecond-timescale molecular dynamic simulations. In agonist-bound systems, the D3R N-terminus formed a “lid-like” structure and lay flat on the binding site opening, whereas in antagonist and inverse agonist-bound systems, the N-terminus exposed the binding cavity. Receptor activation was characterized using the different molecular switch residue distances, and G protein-binding site volumes. A continuous water pathway was observed only in the dopamine-Gαi-bound system. In the inactive D3Rs, water entry was hindered by the hydrophobic layers. Finally, a complete activation mechanism of D3R was proposed. Upon agonist binding, the “lid-like” conformation of the N-terminus induces a series of molecular switches to increase the volume of the D3R cytoplasmic binding part for G protein association. Meanwhile, water enters the transmembrane region inducing molecular switches to assist in opening the hydrophobic layers to form a continuous water channel, which is crucial for maintaining a fully active conformation for signal transduction.
Highlights
Considerable information regarding the association of the N-termini of GPCRs with chemokine receptors is available
To explore the role of the N-terminus in the activation mechanism of D3 receptor (D3R), the N-terminal region of D3R was homology modeled to combine with the resolved D3R structure to develop a new D3R with the N-terminus
Dopamine D3 receptor docked with various small compounds
Summary
Considerable information regarding the association of the N-termini of GPCRs with chemokine receptors is available. In previous studies aimed at clarifying the complete activation mechanism of β2AR15 and the M2 muscarinic receptor[16], the participation of the N-terminal domain was completely ignored. The connection between the activating conformational change of the receptor and the formation of the continuous water pathway remains ambiguous. In the cases of antagonist eticlopride-bound D3Rs and inverse agonist haloperidol-bound D3Rs, the drugs remained in the orthosteric binding site during the 1.5 μs simulation time, and the two hydrophobic layers blocked the water molecules passing through the receptor. Our simulations suggest that when an agonist binds to D3R, the N-terminal conformational change induces the TM molecular switches to form an internal water channel and increases the volume of the cytoplasmic side, which is suitable for G protein binding. The findings of this study elucidate how D3R assumes its active conformation, and could prove valuable in drug design for the treatment of CNS-related diseases
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