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. 2020 Dec 26;12(6):2030–2038. doi: 10.1039/d0sc06008a

Fig. 1. (a) Native protein conformation of ubiquitin with a schematic illustration of its secondary structure.22 (b) Five β-strands are labeled with Roman numerals and the couplings between them are marked with B–D letters. We have used a binary notation to describe if the β-strand couplings B–E are broken or not, where 0 means connected and 1 means broken. For example, (*0100) denotes that only the C-coupling is broken. Letter A is reserved for the α-helix. (c) The process of unfolding of ubiquitin over time in the electric field E = 5 × 104 kV cm−1. Snapshots were taken at 0 ps, 4.47 ps, 7.95 ps and 19.35 ps after turning on the electric field. (d) Average root mean square displacement, RMSD, and standard deviation of the average value for the simulations in the four different electric fields. Each line represents a set of 100 independent simulations, and the RMSD is calculated at each time step comparing the 100 structures at this specific time in the simulations. A similar trend can be observed for the average radius of gyration, depicted in Fig. S1 in the ESI. The crosses mark the time points the structures in (c) were taken from. We used VMD software for the visualisation.23.

Fig. 1