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. Author manuscript; available in PMC: 2019 Jun 7.
Published in final edited form as: J Phys Chem B. 2018 May 21;122(22):5845–5850. doi: 10.1021/acs.jpcb.8b03000

Figure 4.

Figure 4.

DMD/PRIME20 simulations of P3. (A) A plot of potential energy of P3 peptide aggregation versus simulation time. Also shown are simulation snapshots of eight random coil P3 peptides aggregating to form a disordered oligomer (top panel corresponding to the red curve) and a U-shaped P3 protofilament (bottom panel corresponding to the black curve). Each of the eight peptides has a distinct color. (B) and (C) are final simulation snapshots of the disordered P3 oligomer and U-shaped P3 protofilament, respectively. (D) The schematic representation of peptide conformation in the U-shaped P3 protofilaments. Hydrophobic and polar residues are shown in white and green, respectively.