Figure S4.
Contact analysis for AA LIN simulations. The LIN molecules that had a total interaction time in the upper quartile (UQ) were selected for the analysis and referred to in the text as the “LIN UQ binders.” The focus on LIN UQ binders enables direct elucidation of the long-term interactions and exclusion of random and short-lived interactions. There were in total 17 LIN UQ binders in each system. The total interaction time and longest lifetime measurements reported are averaged across the four channel subunits. We also tracked the “constant binder” LIN molecules for each specific site during the entire 5-µs simulation. There were in total two and three LIN constant binders in the LIN site I and LIN site II systems, respectively. (A) Left top: Histogram of total interaction time of each residue in KCNQ1 for LIN UQ binders in the LIN site I system. The gray highlighted boxes in the background indicate the position of the transmembrane helices. Left bottom: Heat maps of total interaction times in the 3-D structure of the channel shown both from top and side views. Right: Same as in A and B but for longest lifetime of each residue. The unit for the color scale is in microseconds. The longest interaction time and the longest lifetime for the LIN site I system reinforces the previously identified site I. High-contact and stable-contact residues were situated primarily on S4 and S5, but also on S3. (B) Same as A but for LIN UQ binders in the LIN site II system. The LIN site II simulations reveal the same interaction site II as before. The high-contact and stable-contact residues were located in S5, the pore helix and S6 of the pore domain, and S1 of the voltage-sensing domain. (C) 3-D contour map of the occupancy of a LIN constant binder at interaction site Iβ for AA simulations shown from side view (left) and top view (right). LIN is also observed on the S3 portion of site I, with density of a LIN constant binder concentrated between S3 and S4. This mode of binding will be referred to as site Iβ. Similar to site Iα, the density of the LIN head group is more well defined at the top of S4, as opposed to the tail density that is scattered between S3 and S4. Threshold values are set at 10% (blue) and 30% (pink) of the total time. Potassium ions in the permeation pathway are indicated as green spheres.

Contact analysis for AA LIN simulations. The LIN molecules that had a total interaction time in the upper quartile (UQ) were selected for the analysis and referred to in the text as the “LIN UQ binders.” The focus on LIN UQ binders enables direct elucidation of the long-term interactions and exclusion of random and short-lived interactions. There were in total 17 LIN UQ binders in each system. The total interaction time and longest lifetime measurements reported are averaged across the four channel subunits. We also tracked the “constant binder” LIN molecules for each specific site during the entire 5-µs simulation. There were in total two and three LIN constant binders in the LIN site I and LIN site II systems, respectively. (A) Left top: Histogram of total interaction time of each residue in KCNQ1 for LIN UQ binders in the LIN site I system. The gray highlighted boxes in the background indicate the position of the transmembrane helices. Left bottom: Heat maps of total interaction times in the 3-D structure of the channel shown both from top and side views. Right: Same as in A and B but for longest lifetime of each residue. The unit for the color scale is in microseconds. The longest interaction time and the longest lifetime for the LIN site I system reinforces the previously identified site I. High-contact and stable-contact residues were situated primarily on S4 and S5, but also on S3. (B) Same as A but for LIN UQ binders in the LIN site II system. The LIN site II simulations reveal the same interaction site II as before. The high-contact and stable-contact residues were located in S5, the pore helix and S6 of the pore domain, and S1 of the voltage-sensing domain. (C) 3-D contour map of the occupancy of a LIN constant binder at interaction site Iβ for AA simulations shown from side view (left) and top view (right). LIN is also observed on the S3 portion of site I, with density of a LIN constant binder concentrated between S3 and S4. This mode of binding will be referred to as site Iβ. Similar to site Iα, the density of the LIN head group is more well defined at the top of S4, as opposed to the tail density that is scattered between S3 and S4. Threshold values are set at 10% (blue) and 30% (pink) of the total time. Potassium ions in the permeation pathway are indicated as green spheres.

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