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 Angstrom sphere centered on the inhibitors. A 8 Angstrom 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.

F., C., A., G., A., B., M., S., Niccolai, N., & Mangani, S. (1997). Molecular dynamics simulations on the complexes of glucoamylase II (471) from Asgergillus awamori var. X100 with 1-deoxynojirimycin and lentiginosine. JOURNAL OF MOLECULAR MODELING, 3, 249-260 [10.1007/s008940050037].

Molecular dynamics simulations on the complexes of glucoamylase II (471) from Asgergillus awamori var. X100 with 1-deoxynojirimycin and lentiginosine

NICCOLAI, NERI;MANGANI, STEFANO
1997

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 Angstrom sphere centered on the inhibitors. A 8 Angstrom 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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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11365/35173
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