Docking and molecular dynamics approach for enzyme selection for α, β-reduction of enoate moiety: Toward renewable production of adipic acid
September 24-28, 2017
Production of adipic acid from renewable sources has been gaining attention in strive on moving from an oil-based economy to a biobased economy. We target a metabolic pathway that relies on conversion of lysine to adipic acid. One of the enzymatic steps in this conversion pathway is an α, β-reduction of an unsaturated bond in an enoate moiety and so far no enzymes able to specifically make this conversion on trans-2-hexenoic acid have been identified. We evaluate Escherichia coli NemA, Bacillus subtilis YqjM and Saccharomyces pastorianus Oye1 (Old Yellow Enzyme 1) for their potential capability to carry out the desired α, β-reduction. Here, we build homology models for E. coli NemA and we carry out molecular docking studies of trans-2-hexenoic acid and trans-2-hexenal to the candidate enzyme models including NemA, YqjM and Oye1. Binding stability is assessed by molecular dynamics simulations. Docking studies accompanied by MD simulations revealed reasonably stable and possible docking conformations. Here we propose that NemA from E. coli and YqjM from B. subtilis, both belonging to Old yellow enzyme family, are possibly suitable for the α,β-reduction reaction of enoate moieties. However, protein engineering of both NemA and YqjM would be necessary for these enzymes to perform the targeted reactions efficiently.
Jaeho Shin, "Docking and molecular dynamics approach for enzyme selection for α, β-reduction of enoate moiety: Toward renewable production of adipic acid" in "Enzyme Engineering XXIV", Pierre Monsan, Toulouse White Biotechnology, France Magali Remaud-Simeon, LISBP-INSA, University of Toulouse, France Eds, ECI Symposium Series, (2017). https://dc.engconfintl.org/enzyme_xxiv/53