Molecular dynamics simulations have been performed for non-covalent complexes of phenyl β-xylobioside with the retaining endo-β-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. A trajectory initiated for the wild-type enzyme–substrate complex with the proximal xylose ring bound at the –1 subsite (adjacent to the scissile glycosidic bond) in the 4C1 chair conformation shows spontaneous transformation to the 2,5B boat conformation, and potential of mean force calculations indicate that the boat is 30 kJ mol−1 lower in free energy than the chair. Analogous simulations for the mutant lacking one oxygen atom confirm the key role of Tyr69 in stabilizing the boat in preference to the 4C1 chair conformation, with a relative free energy difference of about 20 kJ mol−1, by donating a hydrogen bond to the endocyclic oxygen of the proximal xylose ring. QM/MM MD simulations for phenyl β-xyloside in water, with and without a propionate/propionic acid pair to mimic the catalyticglutamate/glutamic acid pair of the enzyme, show the 4C1 chair to be stable, although a hydrogen bond between the OHgroup at C2 of xylose and the propionate moiety seems to provide some stabilization for the 2,5B conformation.
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Organic & Biomolecular Chemistry
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