1. A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions 
Andrés Córdoba, Daniel M. Hinckley, Joshua Lequieu, Juan J. de Pablo 
Biophysical Journal 
Volume 112, Issue 7, Pages (April 2017)
DOI: /j.bpj
Copyright © 2017 Biophysical Society Terms and Conditions

2. Figure 1
Viral capsid model and snapshots of packing simulations. (A) Model for the spherical capsid shell (Rcapsid = 12.5 nm) to which the dsDNA is packaged. A motor protein applies a constant force (either 75 or 150 pN) to the DNA segment inside the yellow cylinder (Lmotor = 1.7 nm). There is a 5-nm padding around the capsid. The red tube of diameter Dtube = 2.8 nm is used to constrain the DNA when outside of the capsid. (B)–(F) Representative snapshots of the viral DNA encapsidation simulations with the 3SPN.2C model with explicit ions. (Blue spheres) Na+ ions; (red spheres) Mg2+ ions; (cyan spheres) Cl− ions; (magenta spheres) Sp3+. (First row) 320 bp packaged. (Second row) 1020 bp packaged. (Third row) 3020 bp packaged. (B) System with high spermidine3+ content; (C) system with low spermidine3+ content; (D) system with lowest spermidine3+ content; (E) system with no spermidine3+ but with Mg2+; (F) system with Na+ and Cl− only. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions

3. Figure 2
(A) Number of basepairs (or DNA length) packaged as a function of time for different ionic environments. (Inset) Fraction of DNA inside the capsid that is hybridized as a function of DNA length packaged. (B) Average DNA packing velocity versus number of basepairs packaged inside the viral capsid. Error bars are standard errors of the mean. (Inset) Cumulative probability distributions for the packing velocities. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions

4. Figure 3
Bonded energy of DNA during the packing process for different ionic environments considered here. (A) The mean bonded energy (bond + bend + dihedral) per basepair, as well as the maximum values of this energy, for a given number of basepairs encapsidated. (B) Distribution of bend angles in the helical axis of DNA at the point when packing stalls for different ionic environments. Error bars are standard errors of the mean. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions

5. Figure 4
Basepairing and electrostatic energies of DNA during the packing process for different ionic environments considered here. (A) The figure shows the average basepairing energy per basepair, as well as the maximum (most attractive) and minimum (most repulsive) values of this energy. (B) Net electrostatic energy of the DNA per basepair as a function of the length of DNA packaged inside the capsid. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions

6. Figure 5
(A) Average interhelical spacing for the dsDNA inside the capsid as a function of the number of basepairs encapsidated (Eq. 3), for different concentrations of spermidine considered here. (B) Toroidal order parameter for the dsDNA inside the capsid as a function of the number of basepairs encapsidated. This order parameter approaches unity for a perfect stack of hoops, whereas a group of random coils gives a value of 0.5. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions

7. Figure 6
(A) Pressure inside the capsid as a function of the number of basepairs (or DNA length) encapsidated for different ionic environments in the simulation box. A significant increase in internal pressure during the latter stages of packing is due to the crowded environment within the capsid, and indicative of high forces necessary to fully package the viral genome. (B) Average von Mises stress in the capsid as a function of basepairs encapsidated (or DNA contour length) for different ionic environments in the simulation box. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions

8. Figure 7
(A) Relative radial distance between the packaged DNA phosphate sites and cations (Spe3+, Mg2+, and Na+) as a function of packing time (see Eq. 7). Lower values of this relative squared separation indicate higher cation localization while larger values indicate a smaller degree of cation localization relative to the packaged DNA phosphate sites. (B)–(F) Radial probability distributions for the ions and DNA in the simulation box at the time when packing stalls. (B) System with the highest content of spermidine; (C) system with low content of spermidine; (D) system with the lowest content of spermidine; (E) system with no spermidine; (F) system with only salt. To see this figure in color, go online.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2017 Biophysical Society Terms and Conditions