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The Role of Long-Range Forces in Porin Channel Conduction

The Role of Long-Range Forces in Porin Channel Conduction. D. Marreiro, M. Saraniti Electrical and Computer Engineering Department, Illinois Institute of technology, Chicago IL 60612. S. Aboud Electrical and Computer Engineering Department,

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The Role of Long-Range Forces in Porin Channel Conduction

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  1. The Role of Long-Range Forces in Porin Channel Conduction D. Marreiro, M. Saraniti Electrical and Computer Engineering Department, Illinois Institute of technology, Chicago IL 60612 S. Aboud Electrical and Computer Engineering Department, Worcester Polytechnic Institute, Worcester MA 01760 R. Eisenberg Molecular Biophysics Department Rush University, Chicago IL 60616

  2. Introduction Motivation: Examine the influence of a fully self-consistent force field scheme on conduction in ion channels. • Particle-Based Simulation Tool • Brownian Dynamics • Force-Field Scheme • Computational Domain/Results • Electrolyte/Lipid System • OmpF Porin Channel • Conclusion/Future Work

  3. initialization calculate charge field equation particle dynamics NO end simulation time ? YES calculate averages end Particle-Based Brownian Dynamics Simulation Langevin Equation Gaussian white noise Friction coefficient 3rd order integration scheme: 20 fs timestep

  4. Poisson P3M Force Field Scheme TSC Interaction between cation and anion in a 0.5 M KCl solution.

  5. Electrolyte Solution Boundary Conditions Dirichlet: Neumann: Thermodynamic Properties Radial distribution function RDF

  6. GLU117 ASP113 TYR40 ARG42 TYR106 ARG82 TYR102 ARG132 OmpF Porin Channel Atomic structure: 2OMF.pdb, S. W. Cowen et al. Nature 358 (1992). Charge distribution: GROMACS pH=7; total charge: -30e

  7. Lipid Membrane/Channel System e=80 e=80 e=80 e=2 e=2 e=80 e=80 e=2 e=80

  8. Potential Energy Profile I: P3M vs PP 11 nm 10 nm 9 nm P3M PP VA=0.0 V cation (K+)

  9. Potential Energy Profile II: cation vs anion 11 nm 10 nm 9 nm cation (K+) anion (Cl-) VA=0.0 V P3M

  10. Potential Energy Profile III: cation in pore 11 nm 10 nm 9 nm no cation cation in pore I P3M VA=0.0 V anion (Cl+)

  11. cation in pore 1 cation in pore 1 Minimum potential energy pathway pore 2 pore 3

  12. Channel flux correlation VA=1.0 V 100 mM KCl correlation coefficient • Ion-ion pairing within a single pore is observed in BD/MD simulations (W. Im et al. J. Mol. Biol. v322 2002).

  13. Channel Flexibility -1e GLU ARG +1e ASP -1e • Bending • Rotation

  14. Conclusion For the specific charge distribution and dielectric constants: • The long-range interactions are apparent at zero bias. • The presence of ions in one pore can change the electrostatic profile seen by charges in the other pores. • The number of positive and negative charges in the 3 pores shows evidence of correlation. • Different charge distribution scheme: e.g. CHARM • Different dielectric constants • Current-voltage characteristics • Flexible channel structure Future Work

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