Molecular Dynamics and Continuum Electrostatics Studies of Inactivation in the HERG Potassium Channel

Abstract

Fast inactivation of the HERG potassium channel plays a critical role in normal cardiac function. Malfunction of these channels due to either genetic mutations or blockade by drugs leads to cardiac arrhythmias. An unusually long S5-P linker in the outer mouth of HERG is implicated in the fast inactivation mechanism. To examine the role of the S5-P linker in this inactivation mechanism, we study the permeation properties of the open and inactive states of a recent homology model of HERG. This model was constructed using the KcsA potassium channel as a template and contains specific conformations of the S5-P linker in the open and inactive states. We perform molecular dynamics simulations on the HERG model, followed by free energy, structural, and continuum electrostatics calculations. Our free energy calculations lead to selectivity results of the model channel (K + over Na + ) that are different in some respects from those of other potassium channels but consistent with experimental observations. Our structural results show that, in the inactive state, the S5-P linkers move closer to the channel axis, possibly causing a steric hindrance to permeating K + ions. Our electrostatics calculations reveal, in the inactive state, an electrostatic potential energy barrier of approximately 14 kT at the extracellular pore entrance, again sufficient to stop K + ion permeation through the pore. These results suggest that a steric and/or electrostatic plug mechanism contributes to inactivation in the HERG homology model.

Modeling hERG and its Interactions with Drugs: Recent Advances in Light of Current Potassium Channel Simulations

“…However, the recent papers illustrated in the second part of this review account for studies accurately addressing critical basic issues, and witness the progresses made in building hERG models [62,63] and the first attempts to simulate channel functions. [61] The simulation of the docking of drugs at the inner cavity is certainly the most frequently addressed aspect when dealing with hERG modeling. However, instead of leading closer to a definitive solution (one might expect to find "the" binding mode of single blockers), it seems that more accurate studies have brought to light new problems to be tackled.…”

“…[61] Further work could be done, even considering the limitations imposed by the need of using a homology model as the starting structure. For instance, simulations of the gating mechanism may be feasible, in the line of analogous works carried out on other potassium channels, and, in this context, a reappraisal of the lipid models used to simulate the membrane environment might also be appropriate.…”

“…At this point, it is worth mentioning the first relevant example of a simulation study regarding the functioning of hERG recently reported by Kutteh et al [61] In this work, the authors, using the model including the S5-P linker developed by Robert Guy, [63] first examined the K + selectivity of the channel as a means to check the reliability of the model, and then investigated the mechanism of the hERG inactivation (a process involving the "closure" of the channel at the outer mouth, while keeping the intracellular gate open [15,70] ). To determine the selectivity between Na + and K + ions at the selectivity filter, the FEP [76] method was employed, whereby the relative free energies of binding of the ions to the pore were estimated.…”

“…Among the former, it has to be noted that in some papers published in 2007, the use of MD simulations to equilibrate the structures and investigate the stability of the models was reported. [61,63,64,68] The use of MD in the hERG modeling protocols developed by Tseng et al [63] and Yi et al [68] was already illustrated, and it can be considered as inherent to the construction of the protein complex as an assembly of different domains. The actual MD simulations extended to the whole system possibly including the membrane and the water environment come next, and (hopefully) result in the overall stabilization of the system that allows one to obtain a final model in a putative low-energy state.…”

Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies

“…In particular, Ö sterberg and Å qvist, 32 Farid et al 33 and Stansfeld et al 34 investigated the docking of drugs to the inner pore of hERG by using carefully built models of the channel and molecular dynamics simulations as well. On another side, the work by Tseng et al 35 was aimed at modeling the outer part of the channel including the 43-residues S5-Ph linker, while Kutteh et al 36 using the same model studied the electrostatic contributions to the inactivation mechanism. In the present work, we took into consideration some aspects of hERG modeling that still deserve attention, e.g., the molecular dynamics of the pore region and the ligand docking, the latter also in the light of the dynamic fluctuations of the pore volume.…”