Viral genome packaging and ejection are exceptionally efficient and elegant mechanisms that govern the viral life cycle. Through a coarse-grained representation of the ϕ29 bacteriophage, a paradigm for biological mechanisms, we study the intertwined effect of cationic concentration and motor packaging forces on the dynamics of packaging and ejection. Viruses rely on cations in solution, particularly the multivalent polyamines, to screen the repulsive interactions caused by the negatively charged DNA phosphate backbone. The resulting attractive electrostatic DNA-DNA interactions can be approximated by a Debye-Hückel interaction, avoiding the explicit inclusion of ions. Unlike previous computational models that overlook DNA outside the capsid for the sake of computational efficiency, we monitor the evolution of the entire genome's conformation both inside and outside of the viral shell. This allows us to replicate the formation of DNA condensates outside the capsid, including experimentally observed toroids, rod-like, and asymmetrical globular conformations. We show that a combination of low packaging forces and high cationic concentration favors condensed DNA states outside the capsid that are difficult to unravel and can result in the premature stalling of DNA packaging. Stalling of DNA packaging has been observed experimentally, but it was postulated that the cause of stalling was a non-equilibrium jamming transition inside the capsid, even at very low filling fractions of the capsid. Our proposal provides an alternate explanation for the origin of stalling. The bending and electrostatic energy evolution as a function of packaged genome length point to the DNA reaching an equilibrium state by the end of packaging, inconsistent with a non-equilibrium jamming transition. Our results show that higher cationic concentrations lead to more compact but less ordered structures outside the capsid which require higher motor packaging forces. Accordingly, higher cationic concentrations lead to smaller interhelical spacing in fully packaged DNA. In accordance with previous findings, we find no correlation between the cationic concentration and the toroidal order of fully packaged DNA configurations. We further provide evidence that promotes the folded toroid model of packaged DNA. An analysis of waiting times distribution reveals possible DNA slipping patterns during the packaging of the last DNA bases. Our ejection simulation results are in accordance with previous theoretical models that predict a fast pressure-driven initial ejection stage followed by a diffusive ejection phase. We provide evidence that more ordered packaged structures may lead to slower initial ejection rates but higher efficiency overall. Our findings offer insight into the combined effect of DNA confinement and condensation, and, most importantly, an alternate mechanism to explain stalled packaging. By furthering our understanding of the interplay between DNA, cations, and motor packaging forces, our findings can aid the optimization of antiviral drugs, induce or block viral mechanisms, and be implemented in the design of controlled viral drug delivery systems.
"},{"label":"Degree","value":["Bachelor of Arts with Departmental Honors"]},{"label":"Author-supplied Keywords","value":["Viral life cycle","Molecular dynamics","Md","Bacteriophage","Translocation","Viral ejection","Viral DNA","Viral packaging","Virus","Simulations"]},{"label":"Administrative Note","value":"Drupal Node ID: 24225