Extended Data Fig. 10: Multi-resolution model of DNA–DNA and DNA–protein interactions.
From: The structure and physical properties of a packaged bacteriophage particle
a, Explicit solvent all-atom MD simulations of internal pressure in a DNA array50. Color indicates bulk electrolyte molarity: 20 mM Mg2+/200 mM Na+ (cyan), 250 mM Na+ (orange), and 2 mM Sm4+/200 mM Na+ (red). Using CUFIX corrections to non-bonded interactions63 was essential to achieve quantitative agreement with experiment. b, CG simulations of DNA array pressure at multiple resolutions. The internal pressure matches experimental values regardless of the resolution of the model. The CG simulations were performed using the mrDNA model77. c, Calibration of DNA–protein interactions. In each simulation, a DNA molecule was pushed against a flat cross-section of the viral capsid by an external force corresponding to a 20 bar pressure. The grid-based representation of the protein capsid was tuned to match the average DNA–protein distance seen in the all-atom simulation. Image in a adapted from ref. 50, Oxford Univ. Press.
