Membrane protein simulations under asymmetric ionic concentrations

Important cellular processes, such as cell-cell recognition, signal transduction, and transport of electrical signals are controlled by membrane proteins. Membrane proteins act as gatekeepers of the cellular environment by allowing passage of ions, small molecules, or nascent proteins under specific environmental signals such as transmembrane voltage, changes in ionic concentration, or binding of a ligand. Molecular dynamics simulations of membrane proteins, performed in a lipid bilayer environment, mimic the cellular environment by representing the solvent, lipids, and the protein in full atomistic detail. These simulations employ periodic boundary conditions in three dimensions to avoid artifacts associated with the finite size of the system. Under these conditions, the membrane protein system is surrounded by ionic solutions on either side of the membrane whose properties cannot be changed independently. We have developed a computational method that allows simulations of membrane proteins under periodic boundary condition while controlling the two ionic solutions properties independently. In this method, an energy barrier is introduced between the two adjacent unit cells and separates the two ionic solutions. The height of the barrier affects the chemical potential of the ions on each side of the barrier, and thus allows for individual control over ionic properties. During the course of the simulation, the height of the barrier is adjusted dynamically to reach the proper ionic concentration on each side. This method has been implemented in the Tcl interface of the molecular dynamics program NAMD. We have applied this method to simulate the voltage-gated potassium channel Kv1.2 under physiological conditions, in which the extracellular solution is made of 10mM KCl and 100mM of NaCl solution, while the intracellular solution has an ionic concentration of 100mM KCl and 10mM NaCl. The simulations maintain a 1:10 and 10:1 ratio between ionic concentrations on each side. The simulations are performed under a voltage bias of 100mV and provide the first simulation of potassium channels under the exact physiological condition. The method has also been applied to simulate ionic currents passing through OmpF, an outer membrane porin, under membrane potentials. Here we were able to accurately calculate the reversal potential of the OmpF channel in a tenfold salt gradient of 0.1 intracellular to 1M extracellular KCl. Our results agree with experimental ion conductance measurements and reproduce key features of ion permeation and selectivity of the OmpF channel. Specifically, the I-V plots obtained under asymmetric ionic solutions revealed the natural asymmetry in the channel caused by increased conductance rates observed at positive potentials, as well as the inherent cation-selectivity of the OmpF pore. Therefore, we have developed a method that directly relates molecular dynamics simulations of ionic currents to electrophysiological measurements in ion channels.