화학공학소재연구정보센터
Journal of Physical Chemistry B, Vol.117, No.43, 13534-13542, 2013
Ion Permeation in the NanC Porin from Escherichia coli: Free Energy Calculations along Pathways Identified by Coarse-Grain Simulations
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(#) approximate to 4 kJ/mol and G(#) approximate to 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.