I on channels conduct charged species through otherwise imper-meable biological membranes. Their activity supports a number of physiological processes, and genetic mutations can disrupt their function dramatically. Among these channels, voltage gated cation channels (VGCCs) are ubiquitous transmembrane proteins involved in electrical signaling. In addition to their selectivity for ions, their function requires membrane-polarization-dependent gating. Triggered by changes in the transmembrane voltage, the activat-ion and deactivation of VGCCs proceed through a sensing mechanism that prompts motion of conserved positively charged (basic) residues within the S4 helix of a four-helix bundle, the voltage sensor domain (VSD). Decades of experimental investigations, using electrophysiology, molecular biology, pharmacology, and spectroscopy, have revealed details about the function of VGCCs. However, in 2005, the resolution of the crystal structure of the activated state of one member of the mammalian voltage gated potassium (Kv) channels family (the Kv1.2) enabled researchers to make significant progress in understanding the structureÀfunction relationship in these proteins on a molecular level. In this Account, we review the use of a complementary technique, molecular dynamics (MD) simulations, that has offered new insights on this timely issue. Starting from the "open-activated state" crystal structure, we have carried out large-scale all atom MD simulations of the Kv1.2 channel embedded in its lipidic environment and submitted to a hyperpolarizing (negative) transmembrane potential. We then used steered MD simulations to complete the full transition to the resting-closed state. Using these procedures, we have followed the operation of the VSDs and uncovered three intermediate states between their activated and deactivated conformations. Each conformational state is characterized by its network of salt bridges and by the occupation of the gating charge transfer center by a specific S4 basic residue. Overall, the global deactivation mechanism that we have uncovered agrees with proposed kinetic models and recent experimental results that point towards the presence of several intermediate states. The understanding of these conformations has allowed us to examine how mutations of the S4 basic residues analogous to those involved in genetic diseases affect the function of VGCCs. In agreement with electrophysiology experiments, mutations perturb the VSD structure and trigger the appearance of state-dependent "leak" currents. The simulation results unveil the key elementary molecular processes involved in these so-called "omega" currents. We generalize these observations to other members of the VGCC family, indicating which type of residues may generate such currents and which conditions might cause leaks that prevent proper function of the channel. Today, the understanding of the intermediate state conformations enables researchers to confidently tackle other key questions such as the mode of action of toxins or modulation of channel function by lipids.