Glycosaminoglycan-Phospholipid Interactions

HA, CS-4 and CS-6 structure modification with YASARA Structure software (Vienna, Austria) [11 (link)] is described in [12 (link)]. Three types of phospholipids—DPPC, DPPE, and SPH (Figure 3)—were used to look at their interactions with the abovementioned glycosaminoglycans. Molecules were placed randomly in a simulation box that was followed by system minimization with a time step of 1 fs. Next, water molecules were added, followed with another 1000-step minimization with a 1-fs time step. The total number of atoms in all the cases was ~150,000, including water molecules (4400 of GAGs, and 7500 of PL). Isothermal–isobaric ensemble all-atom simulations were performed under the following conditions: temperature 310 K, pH = 7.0 in 0.9% NaCl (0.154 M) aqueous solution (a four-site (TIP3P) model of water [13 (link)]), with a timestep of 2 fs. Berendsen barostat [14 (link)] with a relaxation time of 1 fs were used to maintain constant temperature and pressure. The final concentrations of HA and CS were the same, C_CS = C_HA= 5·10⁻⁷ M, and both molecules were of the same weight—40 kDa. Concentrations used were chosen to enable PL molecules to bind to GAGs in a relatively short time, and thus they do not refer to any value taken from the literature.