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. 2020 Jun 8;9:e56707. doi: 10.7554/eLife.56707

Figure 6. Distribution of mutational tolerance and temperature dependence of wtVIM-2 residues.

(A) Scatterplots comparing fitness scores under selection at 25°C and 37°C (128 µg/mL AMP). Variants within the classified positions are highlighted in dark blue while all variants are plotted in grey for reference. (B) Proportion of residues in the wtVIM-2 catalytic domain that have been classified into each behavioral category. (C–D) The wtVIM-2 crystal structure (PDB: 5yd7) is colored by the behavioral classifications, the active-site zinc ions are colored in lime green. (C) View of the spacial distribution of temperature dependence in wtVIM-2, with residues depicted as spheres. The upper row depicts all residues, while the lower row depicts only essential and temperature dependent residues. (D) Cartoon representation of wtVIM-2 with metal-binding residues shown as sticks. All classifications can be found in Supplementary file 2F. Additional analysis of temperature dependence can be found in Figure 6—figure supplement 1 (correlation of Rosetta ΔΔG with temperature dependence) and Figure 6—figure supplement 2 (proportion of sidechain-backbone hydrogen bonding by temperature dependence).

Figure 6.

Figure 6—figure supplement 1. Rosetta ΔΔG in relation to temperature dependence classifications.

Figure 6—figure supplement 1.

In each plot, Rosetta ΔΔG is correlated with fitness score for amino acid variants from the catalytic domain, in positions with the temperature dependence classification indicated at the top.
Figure 6—figure supplement 2. Hydrogen bonding behavior in relation to temperature dependence classifications.

Figure 6—figure supplement 2.

A comparison of proportion of h-bonding sidechains to the proportion of sidechain-backbone h-bonds within each temperature dependent classification (determined from the wtVIM-2 crystal structure, PDB: 5yd7). The black bars display the percentage of h-bonding sidechains within the wtVIM-2 catalytic domain (114 total) that fall within each temperature dependence classification. The white bars show the percentage of sidechain-backbone h-bonds (73 total) that are formed through sidechains of residues with the classification. All h-bonding in the 5yd7 structure can be found in Supplementary file 2G.