Παρασκευή, 15 Δεκεμβρίου 2017

N-terminal prion protein peptides (PrP(120-144)) form parallel in-register {beta}-sheets via multiple nucleation-dependent pathways. [Additions and Corrections]

VOLUME 291 (2016) PAGES 22093–22105In the “Materials and Methods” section, the conversion of the reduced time unit to a real time unit (Δt* = 0.072 ns) was incorrect. The correct value should be Δt* = 0.96 ns. Thus, the longest time accessed in the single DMD simulation should have been 672 μs, which corresponds to 2000 billion collisions. The simulation times (x axes) in Figs. 1, 6, 7, and 9 and Figs. S1–S5 and Table 2 as well as in other places in the context of the article should all be multiplied by a factor of 29. The correct calculation procedures are described below.The way that we relate the reduced time unit to the real time unit is to compare the self-diffusion coefficient of Aβ(16–22) peptide obtained from DMD simulation (DDMD) and atomistic molecular dynamics (MD) simulation (DMD) at T = 298 K. The reduced temperature of the self-diffusion coefficient measurement in DMD simulation is chosen to be T* = 0.181, which corresponds to room temperature (T = 298 K) according to temperature scaling (Wang, Y., Shao, Q., and Hall, C. K. (2016) N-terminal prion protein peptides (PrP(120–144)) form parallel in-register β-sheets via multiple nucleation-dependent pathways. J. Biol. Chem. 291, 22093–22105), T* = (T + 115.79)/2288.46 = (298 + 115.79)/2288.46 = 0.181.The self-diffusion coefficients in both DMD and MD simulation are calculated using the Einstein equation. We plotted the mean square displacement (MSD) of N Aβ(16–22) peptides versus time for both atomistic MD simulation (N = 1) and DMD simulation...

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