Compositional Analysis of Phage Φ29’s Capsid and its Effect on DNA Packaging

A fundamental step in a bacteriophage’s life cycle is the packaging of DNA inside a protective protein capsid. For tailed, double-stranded DNA phages such as Φ29, this is achieved with the help of a molecular motor which helps thread the genome inside the empty capsid. The negatively charged DNA has to overcome large forces due to electrostatic repulsions and it's packaged under great amounts of pressure inside the capsid. Computational methods have been developed to model this process, but little has been said about the effects of the capsid-DNA interaction on the packaged DNA conformation. Chemically, the capsid is composed of many amino acids that interact with the genome via a combination of short and long range forces: Van der Waals and electrostatic. The goal of this project is to not only analyze and quantify the atomic details of the inner surface of the capsid but also run simulations to see their contributions to how the DNA is packaged.