Fig. 4.

Computational analysis of the relative ion selectivity of the I. tartaricus and E. hirae c-rings. (A) Calculated values of the free energy of H⁺/Na⁺ selectivity (ΔG_sel) for the I. tartaricus and E. hirae c-rings (gray bars), compared with that previously reported for S. platensis (29). Note that all calculated values are shifted uniformly, so that the value for E. hirae matches the experimental measurement (47) and serves as the reference for this comparative analysis. The experimental and calculated values of the difference in the free energy of selectivity (ΔΔG_sel) between the I. tartaricus the E. hirae c-rings are indicated. Two alternative models of the I. tartaricus H⁺-bound state (a and b) were considered (Results). (B) Breakdown of the calculated value of the difference in the ion selectivity (ΔΔG) between the I. tartaricus the E. hirae c-rings [“total (FEP)” and “total (TI)”] into local and nonlocal contributions (SI Materials and Methods). The local contributions (“binding site”) comprise all of the ion–protein and protein–protein interactions within an ion-binding site, i.e., involving Q32, V63, E65, S66, T67, Y70, and a structural water molecule in I. tartaricus (Fig. 5A), and L61, T64, Q65, Y68, Q110, and E139 in E. hirae (Fig. 5A). Nonlocal contributions (“rest”) include all interactions between the binding site (as defined above) and the rest of the system (e.g., other regions in the protein, other binding sites, the lipid membrane, etc.).