Extended Data Fig. 2: Electrostatic properties of empty and packaged capsids.
From: The structure and physical properties of a packaged bacteriophage particle
a, Ion exchange rate during equilibration of the empty (left), “slow” (center) and “slow with twist” (right) packaged capsids. Ion exchange data were collected every 10 ns. The lines shown were obtained from the data using a Savitzky-Golay filter with a 110 ns window. b, Radial profiles of the electrostatic potential averaged over 50 ns (empty; left) or 100 ns (slow and slow with twist; center and right) windows. The electrostatic potential was computed using VMD PMEpot plugin91. c, Image depicting the final result of an algorithm used to select the interior and exterior of the capsid, see Methods for details. d, Total charge inside the protein capsid in the units of proton charge. Traces are shown with (solid lines) and without (dotted lines) inclusion of the protein capsid in the analysis. Water molecules were neglected in the analysis. e, Charge inside a spherical volume centered at the center of the capsid as a function of the sphere’s radius. Data were averaged over the last 100 ns of each simulation. For reference, the density of Cα atoms is shown (blue histogram; right axis). f, Electrostatic dipole moment of an asymmetric subunit projected along the radial axis. At each frame, the moment was averaged over all sixty copies of the asymmetric subunit. For reference, the blue line shows the average dipole moment of the residues resolved in the X-ray structure. g, Theoretical model used to estimate the electrostatic potential across the capsid (see Methods). h, Average potential difference between solvent occupied regions inside and outside the capsid as computed using PMEpot (circles) and from a fit using the theoretical model (dashed lines). In contrast to analysis shown in Fig. 3i, j, the PMEpot averaging was restricted to the solvent region within the capsid. That was done by blurring the mass density of DNA nucleobases via convolution with a 1 nm wide gaussian kernel and then selecting regions where the blurred density was less than 0.05 Da Å−3. The fit was performed by minimizing the MSD between predicted and measured data points, yielding the following values for the parameters of the model: qextra, empty = 248.4 e, qextra, slow = 404.9 e, and εpro = 6.53.
