Molecular simulations bring new insights into flavonoid/quercetinase interaction modes.
Molecular dynamics simulations, using the AMBER force field, were performed to study Quercetin 2,3-Dioxygenase enzyme (Quercetinase or 2,3QD). We have analyzed the structural modifications of the active site and of the linker region between the native enzyme and the enzyme-substrate complex. New structural informations, such as an allosteric effect in the presence of the substrate, as well as description of the enzyme-substrate interactions and values of binding free energies were brought out. All these results confirm the idea that the linker encloses the substrate in the active site and also enlighten the recognition role of the substrate B-ring by the enzyme. Moreover, a specific interaction scheme has been proposed to explain the relative degradation rate of various flavonoid compounds under the oxygenolysis reaction catalyzed by the Quercetin 2,3-Dioxygenase enzyme.
Fiorucci
Sébastien
S
Laboratoire de Chimie des Molécules Bioactives et des Arômes, UMR-CNRS 6001, Faculté des Sciences, Université de Nice-Sophia Antipolis, 06108 Nice Cedex 2, France.
Golebiowski
Jérôme
J
Cabrol-Bass
Daniel
D
Antonczak
Serge
S
D003198:Computer Simulation; D049308:Dioxygenases / Q000737:chemistry* / Q000378:metabolism*; D005419:Flavonoids / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D014867:Water / Q000737:chemistry
D005419:Flavonoids; D014867:Water; D049308:Dioxygenases; C003281:quercetin 2,3-dioxygenase