Figure 1. Energy minimized models of DPC micelles (left) and A4W peptide (right). The whole systems were minimized in TIP3P explicit water molecules using AMBER9. The water molecules were represented as triangle with red (oxygen) and white (hydrogen) color, respectively. Hydrophilic headgroups and hydrophobic tails were shown by blue ball and green stick, respectively.
Figure 2. Snapshots at different times along the simulation of a system composed of DPC lipids, water molecules, and A4W peptide. Colors and representations are the same as Figure 1. The position of the peptide and lipids at initial stage (0 ps, left) and one of the positions of the peptide after a 20 ps simulation (right) were shown, respectively.
Figure 3. RMS difference for A4W-solvent-micelle system during molecular dynamics simulation. The least square fit of position of C-alpha was calculated in model after MD (left), and RMS fluctuation of A4W in solvent-micelle system was calculated in fs scale (right).
Figure 4. Total GROMACS energies (left) and partial densities (right) of A4W-solvent-micelle system were represented in ps time scale and in nm periodic box scale.
Table 1. Molecular systems used for molecular dynamics simulations.
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