Abstract
Molecular dynamics (MD) simulations on the complexes of glucoamylase II (471) from Aspergillus awamori var. X100 with two powerful inhibitors, 1-deoxynojirimycin and (+)-lentiginosine, have been performed, in order to build a model for these complexes in solution and to clarify the structure-activity relationship.
MD calculations were carried out for 105 ps, over a 15 Å sphere centered on the inhibitors. A 8 Å residue-based cut-off was used, and the calculations were performed with explicit inclusion of solvent molecules. The MD structure of the complex 1-deoxynojirimycin-glucoamylase shows only minor deviations from the available X-ray structure. The MD structure of the complex of (+)-lentiginosine-glucoamylase, obtained by docking the inhibitor into the active site, suggests us a suitable orientation for the molecule into the enzyme cavity, which can rationalize the high inhibition activity found for (+)-lentiginosine towards amyloglucosidase from A. niger.
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Received: 28 February 1997 / Accepted: 7 July 1997 / Published: 17 July 1997
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Cardona, F., Goti, A., Brandi, A. et al. Molecular Dynamics Simulations on the Complexes of Glucoamylase II (471) from Aspergillus awamori var. X100 with 1-Deoxynojirimycin and Lentiginosine. J Mol Med 3, 249–260 (1997). https://doi.org/10.1007/s008940050037
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DOI: https://doi.org/10.1007/s008940050037