# Pore-Opening and Ion-Conduction Mechanism in Channelrhodopsins C1C2, ChR2, and iChloC by Computational Electrophysiology and Constant-pH Simulations

## TL;DR

This paper uses computational methods to study how different channelrhodopsins open and conduct ions, providing insights for optogenetics applications.

## Contribution

A new computational framework is introduced to determine open-state structures and ion conduction mechanisms in channelrhodopsins.

## Key findings

- Spontaneous ion permeation events were observed in cation-conducting and anion-conducting channelrhodopsins.
- Ion binding sites and hydration profiles were analyzed to understand ion selectivity.
- The framework enables rational engineering of ion selectivity and conductivity in ChRs.

## Abstract

Channelrhodopsins (ChRs) are photoreceptors that function
as light-gated
ion channels. Over the last two decades, they have become essential
tools in optogenetics, enabling precise manipulation of neurons, neural
circuits, and animal behavior through light. Although structural studies
have provided important mechanistic insights into channelrhodopsins,
a detailed understanding of their ion conduction mechanism and selectivity
was proven to be challenging due to difficulties in experimentally
resolving open-state structures. Here, we employed molecular dynamics
(MD)-based computational electrophysiology and constant-pH simulations
to obtain the fully open states of three different ChRs. A significant
number of spontaneous K+, Na+, and Ca2+ permeation events were observed in the cation-conducting C1C2 and
ChR2, as well as Cl– permeations in the anion-conducting
iChloC. Analyses of the ion binding sites and hydration profiles provided
key insights into ion selectivity. Our study presents a robust computational
framework for establishing the fully open-state structures of channelrhodopsins,
laying the groundwork for the rational engineering of ion selectivity
and conductivity.