Structure, Dynamics, and Ligand Recognition of Human-Specific CHRFAM7A (Dupα7) Nicotinic Receptor Linked to Neuropsychiatric Disorders

Abstract

Cholinergic α7 nicotinic receptors encoded by the CHRNA7 gene are ligand-gated ion channels directly related to memory and immunomodulation. Exons 5-7 in CHRNA7 can be duplicated and fused to exons A-E of FAR7a, resulting in a hybrid gene known as CHRFAM7A, unique to humans. Its product, denoted herein as Dupα7, is a truncated subunit where the N-terminal 146 residues of the ligand binding domain of the α7 receptor have been replaced by 27 residues from FAM7. Dupα7 negatively affects the functioning of α7 receptors associated with neurological disorders, including Alzheimer's diseases and schizophrenia. However, the stoichiometry for the α7 nicotinic receptor containing dupα7 monomers remains unknown. In this work, we developed computational models of all possible combinations of wild-type α7 and dupα7 pentamers and evaluated their stability via atomistic molecular dynamics and coarse-grain simulations. We assessed the effect of dupα7 subunits on the Ca²⁺ conductance using free energy calculations. We showed that receptors comprising of four or more dupα7 subunits are not stable enough to constitute a functional ion channel. We also showed that models with dupα7/α7 interfaces are more stable and are less detrimental for the ion conductance in comparison to dupα7/dupα7 interfaces. Based on these models, we used protein-protein docking to evaluate how such interfaces would interact with an antagonist, α-bungarotoxin, and amyloid Aβ₄₂. Our findings show that the optimal stoichiometry of dupα7/α7 functional pentamers should be no more than three dupα7 monomers, in favour of a dupα7/α7 interface in comparison to a homodimer dupα7/dupα7 interface. We also showed that receptors bearing dupα7 subunits are less sensitive to Aβ₄₂ effects, which may shed light on the translational gap reported for strategies focused on nicotinic receptors in 'Alzheimer's disease research.

Keywords: CHRFAM7A; CHRNA7; coarse grain simulation; molecular dynamics; umbrella simulations; α7 nicotinic receptors.

Figure 1

The extracellular EC domain conformation of α7 subunit (residues 1–180). (A) and Dupα7 subunit (B). The structures are coloured by gradient, from blue (N-terminus) to red (C-terminus).

Figure 2

(A) Root-mean-square deviation (RMSD) results of eight complete transmembrane models during 1 μs CG MD simulation. (B) Total potential energy vs. time results of eight complete transmembrane models during 1 μs MD simulation. The black line shows the data for α7 WT model, red-A-Dup, green-AB-Dup, blue-AC-Dup, yellow-ABC-Dup, brown-ACD-Dup, grey-4-Dup, and purple-5-Dup. The schematic arrangements of all models are shown in the methods section.

Figure 3

(A) Root-mean-square deviation (RMSD) results of eight EC domain models during 100 ns MD simulation. (B) Root-mean-square deviation (RMSD) of eight full-length receptor models during 100 ns MD simulation. (C) Total potential energy vs. time of eight EC domain during 100 ns MD simulation. (D) Total potential energy vs. time of eight complete transmembrane structure during 100 ns MD simulation. The canonical a7 (WT) model is shown in black, A-Dupα7-red, AB-Dupα7-green, AC-Dupα7-green, ABC-Dupα7-yellow, ACD-Dupα7-brown, 4-Dupα7-grey, and 5-Dupα7-purple. The schematic arrangements of all models are shown in methods section.

Figure 4

(A) The total number of hydrogen bonds vs. time of the eight EC domain combinations. (B) The total number of hydrogen bonds vs. time of eight fully models during 100 ns MD simulation. The black line shows α7 WT model; red-A-Dupα7, green-AB-Dupα7, blue-AC-Dupα7, yellow-ABC-Dupα7, brown-ACD-Dupα7, grey-4-Dupα7, and purple-5-Dupα7. The schematic arrangements of all models are shown in the methods section.

Figure 5

(A) Principal component analysis, showing the 2D projection of eight different models of the extracellular (EC) domain. (B) Principal component 2D projection of eight different fully models during 100 ns of the atomistic MD simulation. The data for α7 WT model is coloured black; A-Dupα7-red, AB-Dupα7-green, AC-Dupα-blue, ABC-Dupα7-yellow, ACD-Dupα7-brown, 4-Dupα7-grey, 5-Dupα7-purple. The schematic arrangements of all models are shown in the methods section.

Figure 6

(A) Left panel: The extracellular view of the three conformations of the α7 model EC domain. Right panel: the Loop C motion. The representative configurations sampled around 15 ns, 50 ns and 85 ns are coloured yellow, orange and red, respectively. (B) The extracellular view of the three conformations of the AB-Dupα7 model EC domain. The representative configurations for the starting conformation’s state (around 15 ns) are coloured yellow and cyan; the representative configurations for the state sampled around 50 ns are coloured orange and cornflower blue; the representative configurations for state sampled around 85 ns are coloured red and blue. The dashed lines represent the interfacial loops, which are the areas with the highest fluctuation; the arrows within the dashed circles represent the low-amplitude motions within the loop C for both WT and Dupα7.

Figure 7

Potential of mean force (PMF) calculated for the position of the Ca²⁺ moving through the pentamer axis. The black line shows the PMF obtained for the canonical α7 (WT) receptor, A-Dupα7-red, AB-Dupα7-green, AC-Dupα7-blue, ABC-Dupα7-yellow, ACD-Dupα7-brown, 4-Dupα7-grey, and 5-Dupα7-purple. The schematic arrangements of all models are shown in Figure 8B.

Figure 8

(A) Sequence alignment of α7/dupα7 extracellular (EC) domains (residues 1–180), performed by ClustalW, green are the residues with high similarity and in red the conserved residues. (B) Schematic representation of all eight different model arrangements dupα7-α7 pentamer, considered in this study: the canonical (WT) α7 subunits are coloured blue; dupα7 subunits are coloured red.