Probing Mechanisms through which Drugs Affect Voltage-Sensitive Gating

Abstract

Voltage-dependent potassium channels are crucial for electrical excitability and cellular signaling; however, the molecular machinery that the channel employs, to relay the state of the voltage sensor to the pore, is not well understood. To gain insight into this voltage-transduction pathway, interacting networks need to be reliably mapped. Here we present a methodology to estimate the strength of site specific interactions called the Generalized Interaction-energy Analysis (or GIA). Our approach involves combining thermodynamic cycle analysis with information from the gating charge verses voltage curves of putative interactors. This methodology was benchmarked against well established kinetic models of Shaker potassium channels and BK channels using Monte Carlo like sampling. Our simulations show that GIA can provide free energy estimates in a selfconsistent manner that will be useful to identify site-specific interactors that contribute to gating transitions. Implementing this approach on the Shaker potassium channel, we identify a cluster of highly conserved residues, located in the intracellular side of the channel pore, by the gate, that are energetically coupled.Specifically, it appears that tyrosine 485, on the S6 helix, is critical for maintaining the flexibility of an important hinge in the electromechanical coupling pathway.