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

  • José Carlos Parada-Fabián
  • Humberto Hernández-Sánchez
  • Alfonso Méndez-Tenorio
Original Article
  • 14 Downloads

Abstract

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.

Keywords

Equilibrium molecular dynamics Ferulic acid decarboxylase Multiple sequence alignment Phenolic acid decarboxylase p-Coumaric acid decarboxylase 

Abbreviations

EMD

Equilibrium molecular dynamics

FAD

Ferulic acid decarboxylase

MSA

Multiple sequence alignment

PAD

Phenolic acid decarboxylase

PDC

p-Coumaric acid decarboxylase

RMSD

Root median square deviation

QMEAN4

Qualitative model energy analysis

GMQE

Global model quality estimation

Notes

Acknowledgement

To the memory of Ph. D. José Luis Muñoz-Sánchez, who started this project.

Compliance with ethical standards

Conflict of interest

Dr. Parada-Fabián, Dr. Sánchez-Hernández and Dr. Méndez Tenorio have nothing to disclose.

Supplementary material

13562_2018_466_MOESM1_ESM.doc (98 kb)
Supplementary material 1 (DOC 98 kb)
13562_2018_466_MOESM2_ESM.doc (136 kb)
Supplementary material 2 (DOC 136 kb)
13562_2018_466_MOESM3_ESM.doc (52 kb)
Supplementary material 3 (DOC 51 kb)

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2018

Authors and Affiliations

  1. 1.Laboratorio de Bioinformática y Biotecnología Genómica, Escuela Nacional de Ciencias Biológicas, Unidad Profesional Lázaro CárdenasInstituto Politécnico NacionalMexico CityMexico
  2. 2.Laboratorio de Biotecnología de Alimentos, Escuela Nacional de Ciencias Biológicas, Unidad Adolfo López MateosInstituto Politécnico NacionalMexico CityMexico

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