Ion Permeation in the NanC Porin from Escherichia coli: Free Energy Calculations along Pathways Identified by Coarse-Grain Simulations
2013
Using the X-ray structure of a recently discovered bacterial protein, the N-acetylneuraminic acid-inducible channel (NanC), we investigate computationally K⁺ and Cl– ions’ permeation. We identify ion permeation pathways that are likely to be populated using coarse-grain Monte Carlo simulations. Next, we use these pathways as reaction coordinates for umbrella sampling-based free energy simulations. We find distinct tubelike pathways connecting specific binding sites for K⁺ and, more pronounced, for Cl– ions. Both ions permeate the porin preserving almost all of their first hydration shell. The calculated free energy barriers are G# ≈ 4 kJ/mol and G# ≈ 8 kJ/mol for Cl– and K⁺, respectively. Within the approximations associated with these values, discussed in detail in this work, we suggest that the porin is slightly selective for Cl– versus K⁺. Our suggestion is consistent with the experimentally observed weak Cl– over K⁺ selectivity. A rationale for the latter is suggested by a comparison with previous calculations on strongly anion selective porins.
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