Figure 7.
The pulling of hNa+ ion out of the central cavity of the hNav1.5 model in the final snapshot (or snap1) through pathway 1. The 3D representation (A) describes that the hNa+ ion (shown as a yellow vdW sphere) was trapped near the DEKA motif at the central cavity of the ion channel exiting through the S6 helices (shown as blue ribbons) of the domains DII and DIII (pathway 1). The ion, under the influence of external force, passes through a number of hydrophobic residues (shown as sticks and listed in the figure) and is finally released by the conformational changes of F934 (within the circle) and the disruption of H-bonds between N1463 and L938 residues (shown as broken lines in black). The positions of the ion surrounded by water molecules at different timescales (3, 42, 63, and 78 ps) during the SMD simulation are shown as vdW spheres in yellow and the positions of the ions along each step until the release are shown as smaller CPK spheres in red. The corresponding force profile for the pulling of the ion and the numbers of water molecules surrounding the ions throughout this trajectory are shown (B), respectively, of the image on the right.
Abbreviations: CPK, Corey-Pauling-Koltun; SMD, steered molecular dynamics; vdW, van derWaals.