title: Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation.
abstract: The flavoenzyme pyranose dehydrogenase (PDH) from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation. This promiscuous substrate specificity makes PDH a promising catalyst for bioelectrochemical applications. A generalized approach to simulate all 32 possible aldohexopyranoses in the course of one or a few molecular dynamics (MD) simulations is reported. Free energy calculations according to the one-step perturbation (OSP) method revealed the solvation free energies (ΔGsolv) of all 32 aldohexopyranoses in water, which have not yet been reported in the literature. The free energy difference between β- and α-anomers (ΔGβ-α) of all d-stereoisomers in water were compared to experimental values with a good agreement. Moreover, the free-energy differences (ΔG) of the 32 stereoisomers bound to PDH in two different poses were calculated from MD simulations. The relative binding free energies (ΔΔGbind) were calculated and, where available, compared to experimental values, approximated from Km values. The agreement was very good for one of the poses, in which the sugars are positioned in the active site for oxidation at C1 or C2. Distance analysis between hydrogens of the monosaccharide and the reactive N5-atom of the flavin adenine dinucleotide (FAD) revealed that oxidation is possible at HC1 or HC2 for pose A, and at HC3 or HC4 for pose B. Experimentally detected oxidation products could be rationalized for the majority of monosaccharides by combining ΔΔGbind and a reweighted distance analysis. Furthermore, several oxidation products were predicted for sugars that have not yet been tested experimentally, directing further analyses. This study rationalizes the relationship between binding free energies and substrate promiscuity in PDH, providing novel insights for its applicability in bioelectrochemistry. The results suggest that a similar approach could be applied to study promiscuity of other enzymes.
authors.affiliation: Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
authors.forename: Michael M H
authors.initials: MM
authors.lastname: Graf
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhixiong
authors.affiliation: Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria; Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia.
authors.forename: Urban
authors.initials: U
authors.lastname: Bren
authors.affiliation: Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
authors.forename: Dietmar
authors.initials: D
authors.lastname: Haltrich
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland.
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
authors.affiliation: Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
mesh_terms: D000364:Agaricus / Q000201:enzymology; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009005:Monosaccharides / Q000737:chemistry* / Q000378:metabolism*; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D005656:Fungal Proteins; D009005:Monosaccharides; D010088:Oxidoreductases