Extended Data Fig. 9: MD simulation of mutation of key residues in active cavity of PycR1. | Nature Chemistry

Extended Data Fig. 9: MD simulation of mutation of key residues in active cavity of PycR1.

From: Tandem intermolecular [4 + 2] cycloadditions are catalysed by glycosylated enzymes for natural product biosynthesis

Extended Data Fig. 9: MD simulation of mutation of key residues in active cavity of PycR1.

(a) MD simulations of the Y176A mutant with pyc-TS1. It shows a representative structure of pyc-TS1 in Y176A. The results indicate that removal of the phenyl group destabilizes the hydrogen bond between Oxygen 2 in 7 and R94. (b) MD simulation of pyc-TS3 with the N341K mutant. The structure was obtained upon docking and after minimization and equilibrium processing. (c) MD simulations of the S242M mutant with pyc-TS3. It shows the representative structure of pyc-TS3 in S242M PycR1. Introduction of the bulky thiomethyl group change the loop near V225, making V225 far apart from Oxygen 4 in 2’, and breaking this hydrogen bond. (d) MD simulations of the S242Q mutant with pyc-TS1 (left) and eup-TS1 (right). Diene 7 is omitted for clarity. The left is an overlay of the representative structures of S242Q-4’ (green) and WT-4’ (cyan). The right presents structures of S242Q-4 (green) and WT-4’ (cyan). The 4’ in pyc-TS1 appears to adopt a highly distorted conformation, suggesting substantial destabilization of pyc-TS1. The calculated distortion energies also show that this conformation is unfavored compared to eup-TS1 (by about 6.4 kcal/mol). The distortion energy for S242Q-4’ is defined as the electronic energy difference between the representative conformation of 4’ in simulation and pyc-TS1, which represents the energy required to distort the 4’ into geometry in enzyme environment.

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