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Hybrid MD-PNP Simulations of the Alpha-Hemolysin Open Ion Currents

I. Cozmuta, J.T. O'Keeffe and V. Stolc
Eloret Corp, NASA Ames Research Center, US

Keywords: ionic current, alpha hemolysin, molecular dynamics, Poisson Nernst Planck theory, ion channel

Recent experimental studies have used the alpha hemolysin protein as a model system to decipher ionic signature patterns in the genetic code of nucleic acids. These studies show that single stranded nucleic acids polymers can be transported across an alpha hemolysin channel under the action of an applied electric field. The translocation of the nucleic acid polymers causes transient blockades in the ion current. However, the physical and chemical details of the interactions between polymer, channel and ionic solution that lead to the blockade events are not yet fully understood. The goal of the present work is to link atomistic and PNP simulations into a hybrid model to predict the alpha hemolysin open channel ion current. The model channel consists of a rigid, reduced atomistic representation of the pore with polar walls. In the MD simulations, the channel is inserted in a 1MKCl solution and an electric field was uniformly applied. All simulations were conducted using the Amber force field and the NAMD software NASA-ARC supercomputers. The diffusion coefficients of the ions inside the protein channel were calculated and input in the PNP model. The calculated value of 101pA is in good agreement with the experimental measured value of 120pA.

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