State transitions of coupled G_i-protein: Insights into internal water channel dynamics within dopamine receptor D3 from in silico submolecular analyses

Dopamine is a crucial neurotransmitter in the central nervous system (CNS) that facilitates communication among neurons. Activation of dopamine receptors in the CNS regulates key functions such as movement, cognition, and emotion. Disruption of these receptors can result in severe neurological diseases. Although recent research has elucidated the structure of D3R in complex with G_i-protein, revealing the binding and activation mechanisms, the precise conformational changes induced by G-protein activation and GDP/GTP exchange remain unclear. In this study, atomic-level long-term molecular dynamics (MD) simulations were employed to investigate the dynamics of D3R in complex with different states of G_i-protein and β-arrestin. Our simulations revealed distinct molecular switches within D3R and fluctuations in the distance between Ras and helical domains of G-protein across different G-protein-D3R states. Notably, the D3R-GTP-G_i state exhibited increased activity compared with the D3R-empty-G_i state. Additionally, analyses of potential of mean force (PMF) and free energy landscapes for various systems revealed the formation of a continuous water channel exclusively in the D3R-G_i-GTP state. Furthermore, allosteric communication pathways were proposed for active D3R bound to G_i-protein. This study offers insights into the activation mechanism when G_i-protein interacts with active D3R, potentially aiding in developing selective drugs targeting the dopaminergic system.