Fig. 2: Molecular dynamics simulations of a 22-mer PAR polymer.
From: Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose)
A Initial configuration of a typical simulation system. One 22-mer PAR polymer is placed in electrolyte solution (semitransparent molecular surface) containing 50 mM of NaCl. B End-to-end distance (REE, in red) and radius of gyration (Rg, in blue) of a PAR molecule as a function of time simulated in 50 mM NaCl electrolyte. C, E, G Average equilibrium end-to-end distance (circles) and radius of gyration (squares) of the 22-unit PAR polymer at various ion conditions. Dashed lines connect the points to guide the eye. Each data point represents a 250-ns trajectory average after exclusion of the first 50 ns in each simulation where the molecule started in an extended state. Error bars denote S.D. from the average value. D, F, H Representative snapshots of PAR conformation at the end of a 300 ns equilibration performed at the specified ion concentration conditions. The O3′, C3′, C4′, C5′, and O5′ atoms of PAR are shown in green, whereas all other atoms are in blue. Na+ (yellow), Cl− (green) and Mg2+ (pink) ions located within 6 Å of PAR are shown as spheres. The ends of the PAR chains are depicted in red.
