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Figure 2. Free energy simulations with PDB:4NTW.(A) MD simulation system for PDB:4NTW (gray) embedded in a lipid bilayer (cyan) in NaCl solution (water, red and white sticks; Na+ and Cl-, orange and yellow balls). (B) Snapshots from simulation (left) and single ion-free energy profiles (right) for Na+ or K+ permeating the chick ASIC1 pore. See Figure 2—figure supplement 1 for convergence analysis. Insets show hydrated Na+ in the GAS belt (left) and two Na+ ions or K+ ions at the level of E18’ and D21’ (lower). (C) Distribution of ion occupancies in sites formed by E18’ and D21’ in 4NTW. Single ion occupancy is favored for Na+ and K+, but double ion occupancy occurs more frequently for Na+ (left graph). For the doubly occupied site (right graph), binding to E18’ dominates (‘1 carboxylate’), but with increased probability of tight binding to both E18’ and D21’ (‘2 carboxylates’) for Na+. Insets: representative double Na+ ion complexes.DOI:
http://dx.doi.org/10.7554/eLife.24630.004Figure 2—figure supplement 1. Convergence of Free Energy Calculations. (A) Convergence of Umbrella Sampling free energy profiles for PDBs 4NTW (left graphs) and 2QTS (right graphs). Convergence to within 1 kcal/mol was achieved within 6 ns for Na+ and 3 ns for K+.(4NTW), and 6 ns for Na+ and 7 ns for K+ (2QTS). Convergence of lateral sampling of ions was observed in the channel (not shown). (B) FEP binding free energy difference △△G for Na+→K+ (with results for K+→Na+ negated) for the site formed by E18’/D21’ occupied by a single ion in 4NTW (left) and 2QTS (right). Results for transformations Na+Na+→ Na+K+ are shown in (C), while transformations Na+ K+ → K+ K+ are shown in (D). Mean values from independent transformations are shown above each panel, with values for complete transformation Na+Na+→ K+K+ being the sum of individual transformations Na+Na+→K+Na+ and Na+K+→K+K+: 3.0 ± 0.4 for 4NTW and 5.9 ± 0.6 for 4NTW. 2QTS displays higher selectivity due to increased involvement of carboxylates in the narrower pore. Results for the 4NTW GAS site (E; left), reveal near-zero preference for Na+, with bulk values on the right, in agreement with experiment (18.2 kcal/mol). (Friedman and Krishnan, 1973a).DOI:
http://dx.doi.org/10.7554/eLife.24630.005 Image published in: Lynagh T et al. (2017) © 2017, Lynagh et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View |