Substrate specificity of the phenolic acid decarboxylase from Lactobacillus plantarum and related bacteria analyzed by molecular dynamics and docking

The phenolic acid decarboxylase (PAD) is a 44 kDa homodimeric, thermolabile and acid-resistant enzyme that some bacteria have developed as a detoxification system against phenolic acids produced by plants. It seems that the specificity of the PAD for their different substrates may be determined by an initial binding of the substrate to a cavity located in the vicinity of the active site. In order to test this hypothesis, PAD structures from Lactobacillus plantarum and 10 phylogenetically related bacteria were modeled and used for blind docking assays with p-coumaric acid as well as with 3 p-coumaric analogs and 42 property-matched decoys, to evaluate both the efficiency as the specificity with which the substrate can bind to the cavity. We show that both the efficiency and the specificity are low with raw models (not optimized) of the protein structures, but they are significantly increased when an equilibrium molecular dynamics simulation of the model of the protein in explicit solvent is previously conducted to the docking assay. The docking results showed that the binding efficiencies for the cis and trans conformations of the p-coumaric acid are different and suggest that the affinity of this substrate in the PADs from different bacteria may depend on the presence of charged amino acid residues in the cavity.