Fig. 5: MD analysis for WT, Com1-WT, and Com2-WT. | Nature Communications

Fig. 5: MD analysis for WT, Com1-WT, and Com2-WT.

From: Machine learning-guided evolution of pyrrolysyl-tRNA synthetase for improved incorporation efficiency of diverse noncanonical amino acids

Fig. 5

a The MmPylRS structure predicted by Alphafold 3. b The reaction distance between the 3′-OH of tRNA A76 and the Ca atom of amino acid Pyl, calculated through analysis of 10 ns equilibrated trajectories. c The number of snapshots with a distance shorter than 4 Å. d Hydrogen bonds occupancy in WT, Com1-WT, Com2-WT, calculated through analysis of 10 ns equilibrated trajectories. e The binding free energy of amino acids within 4 Å of the tRNA as ligand and the tRNA bases. f Dynamics cross-correlation map for the Cα atom and tRNA P atom pairs within MmPylRS and variants calculated with the last 150 ns MD trajectory. Protein contains 454 amino acids, and the tRNA contains 72 bases (Supplementary Fig. 34). The correlation coefficient (Cij) was shown in different colors. Cij with values from 0 to 1 represents positive correlations, whereas Cij with values from −1 to 0 represents negative correlations.

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