Table 2:
Mean values of total SASA, packing distance, number of intrachain, stacking and packing contacts, and frequency of native interchain and intrachain contacts. All values are averages over the final 50 ns of all trajectories of the respective systems. Note that we consider only for the experimentally resolved regions in our calculation of these quantities, i.e., ignoring the disordered and unresolved parts of the fibril models.
| system | SASA (Å2) | packing distance (Å) | intrachain contacts | stacking contacts | packing contacts | % of native interchain contacts | % of native intrachain contacts | |
|---|---|---|---|---|---|---|---|---|
| Rod fibril model (PDB-ID: 6CU7; residues 38–97) | control | 29472 (878) | 10.4 (0.7) | 56 (4) | 359 (4) | 27 (2) | 84 (6) | 60 (5) |
| with SK9 | 30490 (656) | 10.6 (0.7) | 53 (5) | 354 (5) | 23 (2) | 84 (6) | 60 (5) | |
| Extended rod fibril model (residues 38–120) | control | 22514 (423) | 10.0 (0.9) | 56 (3) | 350 (17) | 25 (3) | 82 (4) | 60 (4) |
| with SK9 | 27874 (685) | 10.6 (0.6) | 62 (7) | 332 (6) | 24 (2) | 77 (6) | 60 (4) | |
| Twister fibril model (PDB-ID: 6CU8; residues 43–83) | control | 20918 (615) | 10.6 (0.4) | 19 (2) | 221 (6) | 42 (2) | 80 (6) | 46 (4) |
| with SK9 | 21717 (485) | 10.3 (0.7) | 17 (3) | 220 (3) | 40 (1) | 81 (4) | 46 (4) | |
| Extended twister fibril model (residues 38–120) | control | 15008 (389) | 9.6 (0.8) | 21 (3) | 215 (5) | 38 (2) | 80 (6) | 44 (5) |
| with SK9 | 19882 (771) | 9.8 (0.8) | 13 (6) | 213 (10) | 38 (3) | 80 (6) | 35 (5) | |