Ion Permeation in the NanC Porin from Escherichia coli: Free Energy Calculations along Pathways Identified by Coarse-Grain Simulations
| Autor: | Bob Eisenberg, Paolo Carloni, Jens Dreyer, Paul Strodel, Justin J. Finnerty, Emiliano Ippoliti |
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| Rok vydání: | 2013 |
| Předmět: |
Ions
Work (thermodynamics) Chemistry Escherichia coli Proteins Monte Carlo method Porins Molecular Dynamics Simulation Permeation Surfaces Coatings and Films Ion Crystallography Solvation shell Porin Escherichia coli Materials Chemistry Thermodynamics Physical and Theoretical Chemistry Umbrella sampling Selectivity Monte Carlo Method Bacterial Outer Membrane Proteins |
| Zdroj: | The Journal of Physical Chemistry B. 117:13534-13542 |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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