Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel

<div><p>The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (I_Ks) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel that lead to cardiotoxic effects.</p></div

The force profile of K⁺ ion pulled through the KCNQ1/KCNE1 protein complex.

<p>(a) The SMD force profile to show the different peaks formed by the barriers marked as BA1, BA2 and SF (selectivity filter), (b) Close up view of the BA1 barrier, (c) Close up view of the BA2 barrier. The potassium ion is shown in yellow sphere, the protein structure is shown in cartoon presentation and the residues are depicted by bonds.</p

The dimensions of the pore shown in surface representation.

<p>For the two model states: (a) KCNQ1 without KCNE1, (b) KCNQ1 in complex with KCNE1. *Colour code: Red is where the pore radius is too tight for a water molecule. Green where there is room for a single water molecule. Blue is where the radius is double the minimum for a single water molecule. (c) Pore radius plot of the KCNQ1 alone (red) and KCNQ1/KCNE1 complex (green) systems. There is a continuous constriction from the pore opening up to the selectivity filter in the KCNQ1/KCNE1 system as compared to the KCNQ1 pore which has a wide opening throughout the pore.</p

Clustering analysis of the KCNQ1/KCNE1 channel complex from the MD simulation based on the ligand binding site residues.

<p>(a) The clustering plot of DBI and SSR/SST parameters, (b) The 15 cluster representative conformations of the KCNQ1/KCNE1 complex protein. (c) The binding site residues of the Chromanol 293B and its derivatives shown in the structure of KCNQ1 (grey color cartoon) in complex with KCNE1 proteins (blue color cartoon). The binding cavity shown with bonds in licorice presentation, is located right below the selectivity filter (SF) of the channel. The residues with their names are shown in the close-up of the binding site.</p

Force profiles for the pulling of a potassium ion through the ligand-bound KCNQ1/KCNE1 complex during the SMD simulations.

<p>The force profiles and the ion permeation processes of a strong channel blocker, or Ligand #2 (a-b), and a weak blocker, or Ligand #9 (c-d) are shown.</p

Superimposition of the KCNQ1 alone (yellow) and KCNQ1/KCNE1 complex (purple).

<p>(a) rear view of the channel, (b) zoomed view to show the shift in the S6 helices.</p

The SMD force profile of K⁺ ion pulled through the KCNQ1 protein alone.

<p>(a) The force profile for the potassium ion pulled through eh KCNQ1 channel pore, showing the high peak corresponding to the selectivity filter (SF) of the protein. (b) The zoomed-in peaks of the force profile corresponding to the energy barriers marked as B1, B2, B3 and B4. (c) Snapshots from the SMD showing the location of the ion at the different binding sites (B1, B2, B3 and B4) in the selectivity filter with respect to the force profiles. The potassium ion is shown in yellow, the S5, S6 and P-loop of two subunits are shown in cartoon. The KCNQ1 VSD and the other two subunits are not shown for clarity.</p

The 2D structures of the Chromanol 293B and its derivatives employed in the molecular docking calculations.

<p>The 2D structures of the compounds and their respective ChEMBL identification numbers are provided.</p

Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel - Fig 8

<p><b>(a) A 2D scatter plot of the compounds’ docking score vs. pIC</b>_<b>50</b><b>.</b> The linear line shows the positive correlation between the two variables (r_pearson = 0.7). <b>(b) The binding mode of ligands (#2, #4, #8 and #9) within the binding pocket of the channel.</b></p

The starting systems for SMD simulation.

<p>(a) RMSD plots of classical MD simulation for KCNQ1 and KCNQ1/KCNE1 Systems, (b) structure of KCNQ1 protein alone, (c) structure of KCNQ1/KCNE1 protein complex.</p