GLIC in an open conformation shown from (A) the top and (B) the side in a POPC lipid bilayer. (C) Two opposing subunits highlighting the pore of the channel. Light colors represent the open …
Free-energy landscapes projected onto the first two tICA coordinates for (A) deprotonated wild-type, (B) protonated wild-type, (C) deprotonated I233T mutant, (D) protonated I233T mutant, (E) …
Simulations sample the initial transition pathway broadly. Simulation seeds, experimental structures and overall sampling projected onto principal component space for deprotonated wild-type (A), …
Assessment of convergence and sampling of the MSMs. The first 10 implied timescales representing the 10 slowest processes of the MSM for (A) deprotonated and (D) protonated system. The vertical …
Variational optimization of the slowest timescale enables selection of hyperparameters. Open probabilities for all two-state models as a function of the number of microstate clusters (A). The width …
Vector representation of the two tICA coordinates. The 20 largest eigenvector components of the two tICA coordinates projected onto the GLIC transmembrane domain. TIC 1 is overall more focused on …
(A) Two metastable states separated by the highest free energy barrier, with red representing closed-like states and blue open-like states. White dots indicate experimental structures, with labels …
Hydration of all 100 wild-type simulations, where each row represents one simulation with frames on the x-axis.The simulations have been grouped based on location of the starting seed in the …
Hydration of all 100 I233T simulations, where each row represents one simulation with frames on the x-axis. The simulations have been grouped based on location of the starting seed in the …
Hydration of all 100 H235Q simulations, where each row represents one simulation with frames on the x-axis. The simulations have been grouped based on location of the starting seed in the …
(A) Each free-energy landscape can be further clustered into models with four or five macrostates that – despite not being metastable– allow for more fine-grained structural analysis of the energy …
The left-most cartoons illustrate the definition of each variable, while data is presented as probability distributions with means and standard deviations plotted as bars. Colors represent the …
Probability distributions of a few variables proposed to be important in GLIC gating. The left-most cartoons illustrate the definition of each variable, while data is presented as four probability …
ECD spread and twist values show rapid adaption in response to pH. Time series of ECD spread and twist values for wild-type GLIC at protonated and deprotonated conditions. Initial simulation seeds …
M2 spread values projected onto the first two tICs. Line contours represent the macrostates in Figure 4.
9’ distances projected onto the first two tICs. Line contours represent the macrostates in Figure 4.
M2-M1(-) values projected onto the first two tICs. Line contours represent the macrostates in Figure 4.
Beta expansion values projected onto the first two tICs. Line contours represent the macrostates in Figure 4.
Line contours represent the macrostates in Figure 4.
Line contours represent the macrostates in Figure 4.
Line contours represent the macrostates in Figure 4.
Line contours represent the macrostates in Figure 4.
Line contours represent the macrostates in Figure 4.
Heatmaps show pairwise RMSDs between all subunits of the channel, measuring the conformational symmetry of the pentamer. The two top bars show pairwise RMSDs of the transmembrane (TMD) and …