Molecular dynamics simulations of dihydro‐β‐erythroidine bound to the human α4β2 nicotinic acetylcholine receptor

Abstract

Background and Purpose: The heteromeric α4β2 nicotinic acetylcholine receptor (nAChR) is abundant in the human brain and is associated with a range of CNS disorders. This nAChR subtype has been recently crystallised in a conformation that was proposed to represent a desensitised state. Here, we investigated the conformational transition mechanism of this nAChR from a desensitised to a closed/resting state.Experimental Approach: The competitive antagonist dihydro-β-erythroidine (DHβE) was modelled by replacement of the agonist nicotine in the α4β2 nAChR experimental structure. DHβE is used both in vitro and in vivo for its ability to block α4β2 nAChRs. This system was studied by three molecular dynamics simulations with a combined simulation time of 2.6 μs. Electrophysiological studies of mutated receptors were performed to validate the simulation results. Key Results: The relative positions of the extracellular and transmembrane domains in the models are distinct from those of the desensitised state structure and are compatible with experimental structures of Cys-loop receptors captured in a closed/resting state.Conclusions and Implications: Our model suggests that the side chains of α4 L257 (9′) and α4 L264 (16′) are the main constrictions in the transmembrane pore. The involvement of position 9′ in channel gating is well established, but position 16′ was only previously identified as a gate for the bacterial channels, ELIC and GLIC. L257 but not L264 was found to influence the slow component of desensitisation.The structure of the antagonist-bound state proposed here should be valuable for the development of therapeutic or insecticide compounds.

Antagonistic Mechanism of α-Conotoxin BuIA toward the Human α3β2 Nicotinic Acetylcholine Receptor

“…The crystal structure of AChBP in complex with an antagonist α-conotoxin GIC (PDB: 5CO5) exhibited a C-loop opening distance of 18.4 Å, which is comparable to our model. In our α3β2 nAChR/BuIA model, the C-loop that correlates with the agonist or antagonist activity of the ligand displayed an open conformation. Besides its stabilization effects on the C-loop, BuIA also has stabilization effects on A, B, D, E, and F loops and thus on the whole ECD.…”

“…The C-loop is one of the most important components of the orthosteric ligand-binding site, and it can allow binding of various ligands through mediation of its conformation. , The C-loop is in a relatively closed conformation when it binds with an agonist, whereas it is in a larger open conformation when it binds with an antagonist. , Previously, we measured the C-loop opening distance for crystal structures of AChBP bound with agonists and antagonists . The C-loop opening distances are under 10 Å when AChBP binds with agonists, while they are above 13 Å when AChBP binds with antagonists. , In the α3β2 nAChR-BuIA complex model, the C-loop opening distance is comparably stable during the MD simulation.…”

“…It was reported that there is a strong energy coupling between these two linkers . We measured the C α distance between V46 (at the center of the β1-β2 linker) and P264 (at the center of the TM2-TM3 linker), which was named “activation distance” . The activation distance can be used to characterize different states, 6–8 Å in the closed/resting state and 4–5 Å in the open/desensitized state .…”

A Computational Analysis of the Factors Governing the Dynamics of α7 nAChR and Its Homologs

“…In summary, our results suggest that a single MD simulation with AChBP and a7-AChBP is sufficient to sample protein dynamics over 500 ns, whereas a single MD simulation with a7 ECD is not enough based on the RMSD and RMSF profile differences observed among the replica simulations. An inconsistency of results from independent MD simulations has been reported in a recent study focusing on the recently crystallized a4b2 nAChR (ECD-TMD), showing that these inconsistencies are not confined to homology models (45).…”

Simulations of Promising Indolizidine—α6-β2 Nicotinic Acetylcholine Receptor Complexes

“…An example of this has been seen in how coupling MD with docking was useful in identifying and confirming binding modes of propidium at the peripheral anionic site of the acetylcholinesterase enzyme. In the specific context of nicotinic receptors, MD simulations of dihydro-beta-erythrodione bound to 4 2 receptor revealed structural changes that eventually lead to the closure of the ion pore in the transmembrane domain [ 27 ]. In our study, results from the MD simulations of the top docked candidates give further support of those analogs as high-affinity binders as exhibited by low RMSD and low predicted binding free energies towards 6 2 nAChR compared to the 4 2 subtype.…”