Fig 1.
Backbone RMSD for simulations of Al-Aβ16, Al-Aβ40 and Al-Aβ42.
Table 1.
Equilibration point for simulations (ns).
Table 2.
RMSD statistics for post-equilibration simulations (Å).
Fig 2.
(a) RDF and (b) integrated RDF of Al-oxygen distances in Al-Aβ42.
Fig 3.
Rg plots for Al-Aβ16, Al-Aβ40 and Al-Aβ42 simulations.
Table 3.
Rg statistics for post-equilibration simulations (Å).
Fig 4.
RMSF plots, by residue, for Al-Aβ16, Al-Aβ40 and Al-Aβ42.
Fig 5.
Ramachandran plots for simulations of Al-Aβ16, Al-Aβ40 and Al-Aβ42.
Fig 6.
Peptide secondary structure percentage, by residue, for Al-Aβ16, Al-Aβ40 and Al-Aβ42.
Table 4.
Total secondary structure character for Al-Aβ16, Al-Aβ40 and Al-Aβ42.
Fig 7.
Hydrogen bond incidence plots for Al-Aβ16, Al-Aβ40 and Al-Aβ42 simulations.
Black circles indicate more than one type of hydrogen bond between the relevant residues.
Table 5.
Hydrogen bond statistics for Al-Aβ16, Al-Aβ40 and Al-Aβ42 simulations.
Fig 8.
Salt bridge incidence plots (%) for Al-Aβ16, Al-Aβ40 and Al-Aβ42 simulations.
Fig 9.
Cα–Cα contact maps for Al-Aβ16, Al-Aβ40 and Al-Aβ42.
Fig 10.
Most populated clusters for Al-Aβ16, Al-Aβ40 and Al-Aβ42 simulations.
Al(III) is shown as a cyan sphere, selected atoms of Glu3, Asp7 and Glu11 as wireframe, and the remainder of the peptide as a ribbon, coloured by secondary structure (red = helix, blue = turn, white = coil).