SAPPHIRE plot of the conformational disorder at the tips of a disease-relevant Aβ42 amyloid fibril

The progress index corresponds to the reordering of the snapshots according to pairwise structural similarity (see Disorder at the tips of a disease-relevant Aβ42 amyloid fibril: A molecular dynamics study). The cut function (red line) is constructed by counting transitions along the simulations such that its local minima and maxima correspond to states that are highly populated and barriers that are visited sporadically, respectively. The dynamic trace (red dots with legend on y-axis on the right) localizes the time development of the simulated system along the progress index and cut function. In other words, the dynamic trace reflects the sequence of events as it illustrates the visits to individual states and crossing of barriers for each simulation run where individual runs are separated by horizontal dotted lines.(Middle) Cα–Cα distances in nm between peptides A (red) and B (pink). These distances were used for the progress index metric. The structural annotation is binned into seven distances where the shortest (dark blue) corresponds to the optimal interstrand distance and the largest (green) to values larger than 2.4 nm. (Top) Intrapeptide Cβ–Cβ distances in nm. For K28-A42, the N of the side chain and the carboxyl carbon atom were used. These distances were not used for constructing the progress index.