Figure S4.
Panel A shows a molecular surface representation of a protein with colored subunits embedded within a gray membrane region. Black arrows indicate the distance along the ion conduction pore and the distance from the center of the ion conduction pore. Panel B shows a heat map of the potential of mean force for sodium ion translocation in kilocalories per mole. The x-axis represents the distance from the center of the ion conduction pore in angstroms, ranging from 0 to 40 angstroms, and the y-axis represents the distance along the ion conduction pore in angstroms, ranging from minus 60 angstroms to 70 angstroms. The extracellular region, intracellular region, and the extracellular domain to transmembrane domain interface are indicated with dashed horizontal lines, and a black curve labeled channel radius is overlaid on the heat map. Panel C shows a heat map of the upper bound of error for the sampling window in kilocalories per mole. The x-axis represents the distance from the center of the ion conduction pore in angstroms, ranging from 0 to 40 angstroms, and the y-axis represents the distance along the ion conduction pore in angstroms, ranging from minus 60 angstroms to 70 angstroms. Numbered sampling windows 1 through 21 are displayed across the plot, with the extracellular region, intracellular region, extracellular domain to transmembrane domain interface, and the channel radius curve also indicated.
Error associated with ABF calculation. (A and B) A snapshot describing the axes used (i.e., distance along ion conduction pore and distance from center of ion conduction pore in calculating the free energy surface) is shown in A along with the resultant free energy surface for Na+ ion translocation (B), as shown in Fig. 4. (C) A calculation for the upper bound of error for each sampling window is shown in C according to the equation in the Materials and methods section. The numbers in each window in C correspond to the same windows in Fig. S5.