DNA Organization and Thermodynamics during Viral Packing

Abstract

An elastic DNA molecular mechanics model is used to compare DNA structures and packing thermodynamics in two bacteriophage systems, T7 and ϕ29. A discrete packing protocol allows for multiple molecular dynamics simulations of the entire packing event. In T7, the DNA is coaxially spooled around the cylindrical core protein, whereas the ϕ29 system, which lacks a core protein, organizes the DNA concentrically, but not coaxially. Two-dimensional projections of the packed structures from T7 simulations are consistent with cryo-electron micrographs of T7 phage DNA. The functional form of the force required to package the ϕ29 DNA is similar to forces determined experimentally, although the total free energy change is only 40% of the experimental value. Since electrostatics are not included in the simulations, this suggests that electrostatic repulsions are responsible for ∼60% of the free energy required for packaging. The entropic penalty from DNA confinement has not been computed in previous studies, but it is often assumed to make a negligible contribution to the total work done in packing the DNA. Conformational entropy can be measured in our approach, and it accounts for 70–80% of the total work done in packing the elastic model DNA in both phages. For ϕ29, this corresponds to an entropic penalty of ∼35% of the total work observed experimentally.