Ion-dependent DNA configuration in bacteriophage capsids

Pei Liu, Javier Arsuaga, M. Carme Calderer, Dmitry Golovaty, Mariel Vazquez, Shawn Walker

Research output: Contribution to journalArticlepeer-review

Abstract

Bacteriophages densely pack their long double-stranded DNA 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 that 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 possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the 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 with molecular dynamics simulations for small capsids.

Original languageEnglish (US)
Pages (from-to)3292-3302
Number of pages11
JournalBiophysical journal
Volume120
Issue number16
DOIs
StatePublished - Aug 17 2021

Bibliographical note

Funding Information:
This work was partially supported by National Science Foundation grants DMS-1817156 (J.A. and M.V.), DMS-1816740 (M.C.C. and P.L.), DMS-1729538 (D.G.), and DMS-1555222 -CAREER (S.W.).

Publisher Copyright:
© 2021 Biophysical Society

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