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Ion conductance in bulk and nanopores

Ion conductance in bulk and nanopores. Catalin Chimerel, Liviu Movileanu, Mathias Winterhalter Soroosh Pezeshki, U. Kleinekathöfer. Bulk - Nanopore. Electrolyte: Solvent Ions. Cl(-). Salt is not fully dissociate in the solvent!. Ion Pairing Increases with the increase in

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Ion conductance in bulk and nanopores

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  1. Ion conductance in bulk and nanopores Catalin Chimerel, Liviu Movileanu, Mathias Winterhalter Soroosh Pezeshki, U. Kleinekathöfer

  2. Bulk - Nanopore • Electrolyte: • Solvent • Ions Cl(-) Salt is not fully dissociate in the solvent! • Ion Pairing • Increases with the increase in salt concentration • Decreases with the increase in temperature Reference: V.N. Alexeev, Qualitative Analysis, MIR, Moscow (1971) K(+) Cl(-) • Question: • Is the ion pairing influencing conductance through nanopores?

  3. Investigation of conductance Experimental Method (BLM) • M. Montal and P. Mueller • PNAS, Vol. 69, No. 12, 1972 Temperature No. Carriers Molecular Dynamics • Aleksij Aksimentiev and Klaus Schulten • Biophysical Journal, Vol. 88, 2005

  4. Nanopore OmpF • Geometry: asymmetric hourglass • Trimer – each monomer has an elliptical cross-section ~4nm in diameter and a constriction zone of ~1nm2; • Constriction zone: 4 positive residues and a L3 loop with overall negative charge • Conductance, Ionic Selectivity, Gating.

  5. Experimental Specific Recordings 50mV 100mV Figure 1. Representative single channel traces obtained at different temperatures for wt OmpF in 1M KCl, 10mM phosphate buffer at pH 7.5. (A). 50mV (B). 100mV • OmpF conductance increases with temperature • Gating is enhanced by the increase in temperature

  6. Temperature dependence of OmpF conductance Ohmic Model Figure 2. Temperature dependence of OmpF conductance compared with the temperature dependence of an bulk-like Pore (KCl – pH 7.5 – 50mV) - experiment With: κ – cylinder conductance σ – electrolyte conductivity A – virtual pore area l - Virtual pore length

  7. Temperature dependence of OmpF conductance • Low salts concentration OmpF and the Ohmic Model behave similarly • Rate of increase of conductance with temperature at high salt concentrations (>0.5M) is faster for the OmpF than for the Ohmic Model • discrepancy accentuated by the increase in salt concentration Figure 2. Temperature dependence of OmpF conductance compared with the temperature dependence of an bulk-like Pore - experiment

  8. Comparison: Experiment – Molecular D. Figure 2. Temperature dependence of OmpF conductance compared with the temperature dependence of an bulk-like Pore - experiment Figure 3. Temperature dependence of OmpF conductance compared with the temperature dependence of an bulk-like Pore – molecular dynamics • Molecular dynamics simulations are qualitatively agreeing with the experiment

  9. Ion paring Figure 4. Temperature dependence ion pairing per number of ions in bulk and OmpF • Ion pairing is stronger in the pore compared to the bulk

  10. Average pairing time Figure 5. Temperature dependence of average pairing time for bulk and OmpF • Pairing average time is longer in the pore then in the bulk • Pairing average time is decreasing with the increase in temperature

  11. Question: Why the increase in conductance with temperature is faster for OmpF than for the Ohmic Model? Premises: Ion pairing is more present in the pore compared to the bulk (Ohmic Model) Average pairing time is decreasing with the increase in temperature Suggested mechanism: Increase in temperature releases supplemental carriers in the OmpF as compared to the Ohmic Model

  12. Outlooks Figure 6.Experimental conductance of the nanopore as a function of salt concentration at 23°C. • Looking for: • comparison with MD – ion pairing

  13. Conclusions • Temperature dependence of a nanopore (OmpF) conductance was for the first time investigated in both Molecular Dynamics and experiment. • Experimental results show a linear dependence of OmpF conductance on temperature. • Classical Molecular Dynamics simulation is qualitatively reproducing the experimental results for ionic conductance. • Bulk and pore in low salts (0.1M) behave similarly showing the same type of energetic barriers • High salt concentrations conductance measurements are possibly influenced by ion pairing.

  14. Acknowledgements Syracuse University • Liviu Movileanu and Group Jacobs University • Mathias Winterhalter and Group • Ulrich Kleinekathöfer and Group

  15. Simulation setup • atoms move according to classical mechanics • interaction between atoms is defined by molecular dynamics force fields (CHARMM27) • 112035 atoms including 57570 atoms belonging to water (TIP3P) • trimer from protein 2OMF inserted into POPE membrane • electric field applied in z-direction • no bond constraints, time step of 1 fs (SHAKE for water changes ionic current by about 20 % ) • electrostatics calculated using partial mesh Ewald (PME) • using the NAMD2 parallel program on 30 CPUs - about 1 day per ns on a Opteron cluster

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