Computational Modeling and Characterization of the Human Tri-Heteromeric GABAA Receptor

Abstract: -aminobutyric acid receptors of type A (GABAARs) are the majorinhibitory neurotransmitter receptors in the human brain, andare modulated by a vast range of exogenous molecules, such assedatives and anesthetics. In the last year, the first cryo-electronmicroscopy (cryo-EM) images of the closed and desensitized statesof the GABAAR were released, enabling fruitful research throughsimulations of these complex proteins. This report investigatesthe characteristics of the two structures. Specifically, pore hydration,radius, and hydrophobicity is compared, and a major focuslies in the general anesthetic (GA) binding pockets in the transmembranedomain, as well as the ligands propofol, etomidate,and pentobarbital. Furthermore, different models for the missingstructure of the intracellular domain (ICD) are compared. Thestructures were simulated for 1 μs using GROMACS. Using multiplesequence alignment as the basis of different models with theheptapeptid SQPARAA in the place of the ICD, resulted in stablestructures with a backbone RMSD close to 2 Å after 1 μs. Thepores are shown to exhibit significant differences between the twostates, with heavier constriction at the 9’ site of the closed state,but also suspected faulty expansion of the pore near the top in thedesensitized state after equilibration. Two of the pockets in thedesensitized state further deviates from expectation, by being tooconstricted. The other pockets were large enough to bind ligandsin the desensitized state, but not in the closed state, as expected.The binding analysis of the GAs suggests that etomidate bindswith the phenyl ring pointing towards the ICD, and that pentobarbitalbinds with the head group pointing towards the pore. Italso suggests that the GAs can bind to every GA pocket, but thatmodulatory activity is dependent on consistently low binding energies,which varies between the ligands for the different pockets.