Single Htt-1-19 peptide in 100 mM KCl at neutral pH |
|
Soluble and disordered but with ~10–30% helical propensity according to circular dichroism spectra that peaks at residues 14–18[45].
|
ff14SB-TIP3P |
1 × ~ 10 µs |
Helix propensity too high (45%), highest for residues 3–12. |
CHARMM36m-TIP3P* |
1 × ~ 10 µs |
22% helix propensity, highest for residues 9–15. |
a99SBdisp-TIP4PD |
1 × ~ 10 µs |
28% helix propensity, highest for residues 3–14. |
ff19SB-OPC |
1 × ~ 10 µs |
29% helix propensity, highest for residues 4–11. |
|
3 ubiquitin molecules around 5 mM, in 100 mM KCl at neutral pH |
|
Soluble but undergoing weak dimerization through a favored interface (residues 4–12, 42–51 and 62–71), exchanging in the microsecond timescale[40].
|
ff14SB-TIP3P |
3 × ~ 1.7 µs |
Aggregation into dimers and then trimers that get increasingly more compact. |
CHARMM36m-TIP3P* |
3 × ~ 2 µs |
Aggregation into dimers and then trimers but less compact than with ff14SB-TIP3P. |
a99SBdisp-TIP4PD |
3 × ~ 1.9 µs |
Soluble with a few short-lived encounters that do not match the NMR data; no trimers. |
ff19SB-OPC |
3 × ~ 2.2 us |
Dimers lasting for tens to few hundreds nanoseconds, contacts most consistent with NMR data yet not perfect; no trimers. |
|
9 ubiquitin molecules around 5 mM, in 100 mM KCl at neutral pH |
|
Soluble but undergoing weak dimerization through a favored interface (residues 4–12, 42–51 and 62–71), exchanging in the microsecond timescale[40].
|
ff14SB-TIP3P |
1 × ~ 0.95 µs |
Aggregates form and grow bigger and more compact. |
CHARMM36m-TIP3P* |
1 × ~ 0.88 µs |
Aggregates form and grow bigger, but less compact than ff14SB-TIP3P. |
a99SBdisp-TIP4PD |
1 × ~ 1.1 µs |
Highly soluble, only collisions through no preferred surface. |
ff19SB-OPC |
1 × ~ 1.1 us |
Some dimers form that then grow into bigger aggregates, but slower than C36m. |
|
10 Aβ 16–22 molecules at around 10 mM, in 50 mM KCl at neutral pH |
|
Totally insoluble in water. Forms β-rich fibrils and amorphous aggregates depending on conditions and concentration[41].
|
ff14SB-TIP3P |
1 × ~ 1.8 µs |
Aggregate of large β content |
CHARMM36m-TIP3P* |
1 × ~ 1.8 µs |
Aggregate of large β content |
a99SBdisp-TIP4PD |
1 × ~ 2 µs |
Remains soluble, some reversible formation of different pairs of strands |
ff19SB-OPC |
1 × 1.95 us |
Largely soluble, with small aggregates of β content |
|
Fiber stretch of 10 Aβ-40 strands from PDB 2LNQ, in 50 mM KCl at neutral pH |
|
Totally insoluble fiber that does not dissociate in water[51].
|
ff14SB-TIP3P |
3 × ~ 3 µs |
Rigid, max Cα RMSD 5–6 Å |
CHARMM36m-TIP3P* |
3 × ~ 3 µs |
Less rigid than ff14SB, max Cα RMSD 8–10 Å. |
a99SBdisp-TIP4PD |
3 × ~ 3 µs |
Similar to CHARMM36m, max Cα RMSD 8–10 Å. |
ff19SB-OPC |
3 × ~ 3 us |
As rigid as ff14SB-TIP3P, max Cα RMSD 5–6 Å |