Ion-dependent DNA Configuration in Bacteriophage Capsids

TL;DR

This paper presents a biophysical model linking ion types and concentrations to DNA configurations inside bacteriophage capsids, offering a computational approach that aligns well with experimental and molecular dynamics data.

Contribution

It introduces a new energy-based model and computational method to simulate DNA and ion distributions in large bacteriophage capsids, surpassing previous simulation limitations.

Findings

Model accurately predicts DNA configurations based on ion chemistry.

Simulation results agree with experimental data.

Method enables larger system simulations than prior approaches.

Abstract

Bacteriophages densely pack their long dsDNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy which combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is currently possible using the existing simulations, typically done at a molecular level. In particular, we are able to estimate bending and repulsion between DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and molecular dynamics simulations for small capsids.