Figure 8: Cα-atom root mean square fluctuations of all simulated variants.
From: De novo active sites for resurrected Precambrian enzymes
Shown here are the root mean square fluctuations (RMSF, Å) of all Cα atoms during our simulations of (a) wild-type and (b) variant forms of the TEM-1 (blue), Bacillus licheniformis (purple), GNCAMP (red), GNCA4 (orange), ENCA (dark green) and PNCA (light green) β-lactamases. In the case of the variant forms, the simulations were performed both in the absence of the transition-state analogue (TSA) or in complex with the TSA, 5(6)-nitrobenzotriazole. The simulations shown in (b) were all performed in the absence of the TSA, and a corresponding comparison of the Cα RMSF values of the ancestral enzymes both with and without the TSA present are shown in Supplementary Fig. 29. All values shown here are averages over the last 60 ns of three independent trajectories (180 ns total simulation time), which were obtained as described in the Methods section.
