Table 3.
Mean energies and corresponding standard error of the mean (for P-P and P-W) and standard deviation (for S-S) for the 11 systems are calculated from the simulations
| Structure | P-P vdW (kcal/mol) | P-W vdW (kcal/mol) | S-S vdW (kcal/mol) | S-S FA vdW (kcal/mol) | S-S FA out vdW (kcal/mol) |
|---|---|---|---|---|---|
| Hexamer | −188 ± 18.9 | −84.7 ± 21.1 | −20 ± 4.5 | −44 ± 6.1 | — |
| Heptamer | − 200 ± 14.8 | −68.1 ± 19.3 | −37 ± 5.6 | −56 ± 4.7 | −23 ± 3.8 |
| Octamer | −187 ± 13.7 | −84.4 ± 18.0 | −21 ± 3.8 | −62 ± 4.1 | — |
| AA6_3ud | −185 ± 16.4 | −88.1 ± 22.1 | −4.6 ± 2.2 | −52 ± 7.1 | — |
| AA7_1ud | −191 ± 19.8 | −83.0 ± 22.4 | −12 ± 4.6 | −50 ± 4.7 | −38 ± 4.8 |
| AA8_4udp | −189 ± 15.1 | −86.8 ± 18.9 | −18 ± 3.1 | −55 ± 3.5 | — |
| AA8_4uds | −190 ± 16.5 | −85.3 ± 21.1 | −24 ± 3.6 | −54 ± 4.4 | — |
| AA7_glp1 | −160 ± 15.1 | −84.9 ± 19.0 | −23 ± 5.1 | −26 ± 5.0 | −29 ± 5.2 |
| Structure | P-P vdW (kcal/mol) | P-W vdW (kcal/mol) | S-S all FA out vdW (kcal/mol) | ||
| AA6_FAout | −171 ± 13.4 | −104 ± 21.5 | −23 ± 3.0 | ||
| AA7_FAout | −187 ± 18.9 | −86.5 ± 25.3 | −33 ± 3.0 | ||
| AA8_FAout | −176 ± 13.1 | −98.6 ± 22.8 | −35 ± 3.0 | ||
The vdW energies for the peptide-peptide (P-P), peptide-water (P-W), segment-segment (seg-seg) with FA pairs (S-S FA), seg-seg without FA pairs interacting (S-S), and—for the heptamer—seg-seg interactions for the monomer pairs including the monomer with the FA pointing outward (S-S FA out), are calculated. Energies are also calculated for the systems where all FA chains are pointing outward (S-S all FA out). The energies for the P-P and P-W interactions are normalized according to the number of monomers in the structure. MDENERGY from the program NAMD (http://www.ks.uiuc.edu/Research/namd/) was used to calculate the energies in intervals of 50 ps.