Modeling Inner Surface Electrostatics of the Capsid for DNA Packaging of phi29

The electrostatic properties of the bacteriophage capsid play a crucial role in the DNA packaging process, influencing genome conformation and stability within the confined environment. In this study, the inner surface electrostatics of the phi29 bacteriophage capsid were comprehensively mapped using structural data from cryo-electron microscopy (cryo-EM) and molecular dynamics simulations. A spatial grid-based approach was implemented to categorize the charge distribution of amino acids lining the capsid's interior. The findings indicate that the net charge of the inner surface is predominantly positive, with positively charged amino acids contributing significantly to the overall electrostatic landscape. This charge distribution has implications for the interactions between the capsid and the encapsidated DNA, which is negatively charged, potentially influencing the structural organization and packing efficiency of the genome. By integrating computational modeling and electrostatic analyses, this study provides novel insights into the role of capsid surface properties in bacteriophage DNA packaging dynamics. These findings highlight the necessity of incorporating realistic capsid surface electrostatics in future simulations to improve the accuracy of DNA confinement models and enhance the current understanding of viral assembly mechanisms.