Fig. 2: In silico analyses for the substrate recognition mechanism of PcPAL. | Nature Communications

Fig. 2: In silico analyses for the substrate recognition mechanism of PcPAL.

From: Direct asymmetric synthesis of β-branched aromatic α-amino acids using engineered phenylalanine ammonia lyases

Fig. 2

a, b Gibbs energy diagram of the cMD simulations projected onto the distance from the amino N of MIO to the αC of the substrates (X-axis) and the angle between MIO and the double bond of the substrates (Y-axis) within the (CA)/(PcPAL-WT) complex and the (β-MeCA)/(PcPAL-WT) complex, respectively. c, d the pocket volumes detected during the cMD simulations of (CA)/(PcPAL-WT) complex and the (β-MeCA)/(PcPAL-WT) complex, respectively. e, f Optimized pre-reaction states of CA and β-MeCA in the PcPAL-WT using the Quantum Mechanics/Molecular Mechanics (QM/MM) methodology, respectively. Source data are provided in Source Data 3 to Source Data 5. CA: cinnamic acid; β-MeCA: β-methyl cinnamic acid; MIO: 3,5-dihydro-5-methylidene-4H-imidazol-4-one.

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