PMC

Bottleneck Analysis for AMPA and NMDA receptor LBDs.
(A) Residues defining the bottleneck to the glutamate binding site of GluA2. Access tunnels are shown in blue.
(B, C) Average bottleneck distance at each (ξ₁, ξ₂) overlaid with the corresponding PMF contours for (B) apo and (C) glutamate-bound GluA2 LBDs. Dashed boxes in upper right corners approximately demarcate open conformations (average bottleneck distance ≥ 12 Å).
(D) Residues defining the bottleneck to the glycine binding site of GluN1. Access tunnels are shown in purple.
(E, F) Average bottleneck distance at each (ξ₁, ξ₂) overlaid with the corresponding PMF contours for (E) apo and (F) glycine-bound GluN1 LBDs. Dashed boxes in upper right corners approximately demarcate open conformations (average bottleneck distance ≥ 10 Å).
(G) Residues defining the bottleneck to the glutamate binding site of GluN2A. Access tunnels are shown in blue.
(H, I) Average bottleneck distance at each (ξ₁, ξ₂) overlaid with the corresponding PMF contours for (H) apo and (I) glutamate-bound GluN2A LBDs. Dashed boxes in upper right corners approximately demarcate open conformations (average bottleneck distance ≥ 12 Å).
(J) Residues defining the bottleneck to the glutamate binding site of GluN3A. Access tunnels are shown in black.
(K, L) Average bottleneck distance at each (ξ₁, ξ₂) overlaid with the corresponding PMF contours for (K) apo and (L) glycine-bound GluN3A LBDs. Dashed boxes in upper right corners approximately demarcate open conformations (average bottleneck distance ≥ 10 Å).

(A) The bottleneck 1 represents the most frequent bottleneck of the p1 tunnel and is mostly formed by Ala145, Phe149, Ala172 and Cys176. Comparison of snapshots with an open (red) and closed (blue) p1 tunnels suggested that the gating is mediated by: (i) movement of the N-terminal part of the cap domain carrying Ala145 and Phe149; (ii) movement of the α5-helix with Cys176 and Ala172; and (iii) conformational change of the bottleneck residues Phe149 and Cys176. The bottleneck radius in the selected snapshots with an open and closed tunnel was 2.3 Å and 0.9 Å, respectively. (B) The bottleneck 2 of the p1 tunnel is mostly formed by Thr148, Ala172 and Lys175. Comparison of snapshots with an open (red) and closed (green) p1 tunnel suggested that gating is mediated by: (i) movement of the N-terminal part of the cap domain carrying Thr148; (ii) movement of the α5-helix carrying Ala172; and (iii) the conformational change of the bottleneck residues Thr148 and Lys175. The bottleneck radius in the selected snapshot with an open and closed tunnel was 2.3 Å and 0.9 Å, respectively.

Test for changing sex-bias applied to bottleneck simulations with a proportion of females of p₁ outside the bottleneck and p₂ during the bottleneck. (A) Off-diagonal entries are power: values greater than 0.85 are in blue, values between 0.85 and 0.10 are in light yellow, and values less than 0.10 are in orange. Entries on the diagonal are false positive rates and are in gray. (B, C) Data was simulated with a female bias outside the bottleneck (p₁ = 0.8) and a varying proportion of females during the bottleneck, p₂. Our method produces separate estimates for p₁ and p₂ (, in blue), while the the π-based estimator produces one estimate (p_π, in red). Bias of estimators of the proportion of females (B) outside the bottleneck, , and (C) during the bottleneck, , is shown for both methods. The π-based estimator is biased when p₁ and p₂ differ (here, when p₂ is not 0.8), whereas our estimator is unbiased.

A: original Bottleneck module. B:depthwise convolution. C: improved Bottleneck module.