Fig. 4: PtdChos and albumin interaction analysis in all-atoms molecular dynamics simulations.
From: Small molecule modulation of protein corona for deep plasma proteome profiling
a Total linear interaction energies between albumin and various number of ligands systems over simulation time. The total energy represents the sum of Lennard-Jones and Coulombic energies. b Effective free energy of binding terms for the different systems over the entire simulation. From left to right, we have poses 1, 2, and 3 of the 1 ligand systems and the 3, 5, and 10 ligands systems. GGAS represents the energy of the gas phase, GSOLV, is the energy of solvation, and TOTAL is the sum of the two. For each simulation, the energies of 1000 frames were averaged, and the error bars show SD. c Average root mean square fluctuation of albumin residues for the four systems. d Root mean square deviation of PtdChos over time for the four types of systems. e Bond types present within each simulation. The y-axis represents the bond types, and the x-axis represents the percentage of simulation timestamps when each type of bond is present.
