Journal Article

FZJ-2015-03609

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Ion Permeation in the NanC Porin from Escherichia coli: Free Energy Calculations along Pathways Identified by Coarse-Grain Simulations

Dreyer, J.FZJ* ; Strodel, P.GRS* ; Ippoliti, E.FZJ* ; Finnerty, J.GRS* ; Eisenberg, B. ; Carloni, P. (Corresponding Author)FZJ*

2013
Soc. Washington, DC

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Please use a persistent id in citations: doi:10.1021/jp4081838

Abstract: 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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Contributing Institute(s):

1. GRS (GRS)
2. Computational Biomedicine (IAS-5)

Research Program(s):

1. 899 - ohne Topic (POF2-899) (POF2-899)

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Database coverage:
; Current Contents - Physical, Chemical and Earth Sciences ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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