Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field.

Jigneshkumar Dahyabhai Prajapati, Crystal Mele, Mehmet Alphan Aksoyoglu, Mathias Winterhalter, Ulrich Kleinekathöfer

Journal of chemical information and modeling 2020 Jun 22

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In the past two decades, molecular dynamics simulations have become the method of choice for elucidating the transport mechanisms of ions through various membrane channels. Often, these simulations heavily rely on classical nonpolarizable force fields (FFs), which lack electronic polarizability in the treatment of the electrostatics. The recent advancements in the Drude polarizable FF lead to a complete set of parameters for water, ions, protein, and lipids, allowing for a more realistic modeling of membrane proteins. However, the quality of these Drude FFs remains untested for such systems. Here, we examine the quality of this FF set in two ways, i.e., (i) in simple ionic aqueous solution simulations and (ii) in more complex membrane channel simulations. First, the aqueous solutions of KCl, NaCl, MgCl2, and CaCl2 salts are simulated using the polarizable Drude and the nonpolarizable CHARMM36 FFs. The bulk conductivity has been estimated for both FF sets using applied-field simulations for several concentrations and temperatures in the case of all investigated salts and compared to experimental findings. An excellent improvement in the ability of the Drude FF to reproduce the experimental bulk conductivities for KCl, NaCl, and MgCl2 solutions can be observed but not in the case of CaCl2. Moreover, the outer membrane channel OmpC from the bacterium Escherichia coli has been employed to examine the ability of the polarizable and nonpolarizable FFs to reproduce ion transport-related quantities known from experiment. Unbiased and applied-field simulations have been performed in the presence of KCl using both FF sets. Unlike for the bulk systems of aqueous salt solutions, it has been found that the Drude FF is not accurate in modeling KCl transport properties across the OmpC porin.

Citation

Jigneshkumar Dahyabhai Prajapati, Crystal Mele, Mehmet Alphan Aksoyoglu, Mathias Winterhalter, Ulrich Kleinekathöfer. Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field. Journal of chemical information and modeling. 2020 Jun 22;60(6):3188-3203