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. 2011 May 19;7(5):e1002051. doi: 10.1371/journal.pcbi.1002051

Figure 6. Structures obtained for the 20-mer preliminary simulations.

Figure 6

The stable 20-mer structures obtained from OPEP's preliminary simulation 20OPp are shown on the left-hand side panel. The final primary clusters obtained from the OPEP structures with all-atom MD or all-atom REMD are displayed on the right-hand side panel. 20OPp-A,-B,-C and -D were extracted at 283.4 K. The color code is the same as in Figure 5. 20OPp-A is composed of 2 perpendicular β-sheets. 20OPp-B is a twisted β-sandwich fibril-like structure. 20OPp-C is made of 2 sheets on top of one another. 20OPp-D consists of a folded sheet (green) facing another shorter sheet (red). During the all-atom MD simulation the structures tend to be more globular with the strands seeing some exchange between the β-sheets, i.e. the red and green β-sheets from the OPEP structures dissociate and re-associate during the all-atom MD simulations except for structures 20GRp-D1 and -D2.