Ion channels

Abstract:

The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 [c36] fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in chloride-pumping rhodopsin. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and can yield results comparable with more accurate and computationally demanding methods.

Abstract:

Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 Cl⁻ channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. Here, we implement the fully polarizable forcefield AMOEBA in MD simulations on different conformations of hBest1. This forcefield models multipole moments up to the quadrupole; therefore, it captures induced dipole and anion-π interactions. We show that key biophysical properties of the channel can only be simulated when electronic polarization is included in the molecular models and that Cl⁻ permeation through the neck of the pore is achieved through hydrophobic solvation concomitant with partial ion dehydration. Furthermore, we demonstrate how such polarizable simulations can help determine the identity of ion-like densities within high-resolution cryo-EM structures and that neglecting polarization places Cl⁻ at positions that do not correspond with their experimentally resolved location. Overall, our results demonstrate the importance of including electronic polarization in realistic and physically accurate models of biological systems, especially channels and pores that selectively permeate anions.

Statement of Significance

Ion channels are nanoscale protein pores that enable the selective passage of charged ions across cell membranes. Understanding the underlying mechanisms for selective anion permeation through such pores remains a challenge. To simulate their behavior efficiently in silico , fixed charge models are typically employed. However, this approach is insufficient for the study of anions. Here, we use simulations with explicit treatment of electrostatics to investigate the interactions of chloride ions in the human bestrophin 1 channel. We find that electronic polarization tunes the state of the channel and affects the interactions of chloride ions thereby revealing a mechanism for permeation. Furthermore, these simulations can be used to resolve experimental ambiguity in ion-like densities from cryo-EM structures.