Comparative Study of State-Dependent Cholesterol Binding Sites in Adenosine A_2A and A₁ Receptors Using Coarse-Grained Molecular Dynamics Simulations in Biologically Relevant Membranes

Abstract

In this study we used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and A1 adenosine receptor (A1R). Three different membranes were used, of which a plasma mimetic membrane best matched cholesterol binding sites previously detected in X-ray structures and computationally for the inactive state of A2AR. Here, cholesterol binds stably between TM5 and TM6 in the intracellular leaf and between the extracellular part of TM6 and TM7. The stability of the identified binding sites to A1R with CG MD simulations were further investigated using potential of mean force calculations combined with umbrella sampling. Cholesterol binding to certain cavities in active or inactive state can stabilize a conformation of active or inactive state respectively and is important to identify these cavities. For the active state the cholesterol binding sites have much longer residence times compared to the inactive state for both A2AR and A1R. We observed for the active A1R two cholesterol binding sites in the extracellular membrane leaf in a cavity between TM2/TM3 and along TM3 in the intracellular leaf. We found a partially overlapped binding area between TM6 and TM7 in the extracellular membrane leaf for active state and inactive A1R state which can be antagonized by cholesterol molecules although the site has a much longer residence time for active A1R. For the active A2AR we predicted a high residence time cholesterol position between TM1 and TM7 in the middle region of TMD which is different from the binding sites calculated in active or inactive A1R and for the inactive A2AR. For the inactive A2AR cholesterol binds to the same extracellular area between TM6 and TM7 as in the inactive A1R. The differences in stable, long residence time cholesterol binding sites between active and inactive states of A1R and for A2AR can be important for functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators which can bind through lipid pathways.

Photochemical affinity switches to resolve ligand dissociation from a G protein-coupled receptor by time-resolved serial crystallography

“…6C). Cholesterol is another allosteric regulator of A 2A R activity with statedependent binding sites 57,58,59 . Interestingly, illumination of StilSwitch3 causes a loss of cholesterol from the antagonist bound A 2A R binding sites, whereas, for StilSwitch2 we observe less negative difference density over the cholesterol molecules (Extended Data Fig.…”