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Molecular simulations bring new insights into flavonoid/quercetinase interaction modes
Author(s) -
Fiorucci Sébastien,
Golebiowski Jérôme,
CabrolBass Daniel,
Antonczak Serge
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21380
Subject(s) - substrate (aquarium) , linker , chemistry , dioxygenase , active site , enzyme , allosteric regulation , flavonoid , stereochemistry , molecular dynamics , binding site , computational chemistry , biochemistry , biology , computer science , ecology , antioxidant , operating system
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. Proteins 2007. © 2007 Wiley‐Liss, Inc.