Density-functional theory study of gramicidin A ion channel geometry and electronic properties

TL;DR

This study uses density functional theory to analyze the geometry and electronic properties of the ion channel gramicidin A, revealing how side chains influence its structure but not its electrostatic potential, and demonstrating the feasibility of linear scaling DFT for large biomolecular systems.

Contribution

It provides the first DFT-based analysis of gramicidin A's geometry and electronic properties, highlighting the impact of side chains and validating linear scaling DFT methods for large biomolecules.

Findings

Side chains affect the ground state geometry.

Electrostatic potential of the pore is independent of side chains.

Linear scaling DFT can model large biomolecular systems efficiently.

Abstract

Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A, whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground-state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gramicidin A in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10,000 to 100,000 atoms and beyond, and will be an important new tool for biomolecular simulations.