1997
DOI: 10.1002/(sici)1097-0134(199702)27:2<235::aid-prot10>3.0.co;2-n
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Automated docking of monosaccharide substrates and analogues and methyl α-Acarviosinide in the glucoamylase active site

Abstract: Glucoamylase is an important industrial glucohydrolase with a large specificity range. To investigate its interaction with the monosaccharides D-glucose, D-mannose, and D-galactose and with the substrate analogues 1-deoxynojirimycin, D-glucono-1,5-lactone, and methyl alpha-acarviosinide, MM3(92)-optimized structures were docked into its active site using AutoDock 2.1. The results were compared to structures of glucoamylase complexes obtained by protein crystallography. Charged forms of some substrate analogues… Show more

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Cited by 36 publications
(30 citation statements)
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“…We have used AutoDock (Scripps Research Institute; La Jolla, CA)14 to explain how the 2 domains collaborate to separate cellulose chains from the crystal and then to cleave them. AutoDock is a small‐molecule docking program that searches the ligand conformational space for the conformer with the lowest sum of its internal energy plus its interaction energy with the enzyme, and we have used it to supplement knowledge of the structure and function of glucoamylase,15 β‐amylase,16 α‐1,2‐mannosidase,17 surfactant protein D,18 and phospholipase D 19. In this work, docking energies of and forces on cello‐oligosaccharides docked to the H. jecorina Cel 7A CD and CBD were computed to help explain its processive action and ability to disrupt crystalline cellulose.…”
Section: Introductionmentioning
confidence: 99%
“…We have used AutoDock (Scripps Research Institute; La Jolla, CA)14 to explain how the 2 domains collaborate to separate cellulose chains from the crystal and then to cleave them. AutoDock is a small‐molecule docking program that searches the ligand conformational space for the conformer with the lowest sum of its internal energy plus its interaction energy with the enzyme, and we have used it to supplement knowledge of the structure and function of glucoamylase,15 β‐amylase,16 α‐1,2‐mannosidase,17 surfactant protein D,18 and phospholipase D 19. In this work, docking energies of and forces on cello‐oligosaccharides docked to the H. jecorina Cel 7A CD and CBD were computed to help explain its processive action and ability to disrupt crystalline cellulose.…”
Section: Introductionmentioning
confidence: 99%
“…The methyl R-and S-α-acarviosinide maps are generally similar to the previously published MM3 map that combined the energies for both forms, but the maps for the protonated form have some important differences. 25 Those MM3 maps were based on a much smaller number of starting geometries as well as a lower dielectric constant. The pure MM3 map for the protonated form has a global minimum at φ = 67° and ψ = 42° (after converting from φ H and ψ H ), whereas the global minimum on the hybrid map is near φ = 70°, ψ = −140°.…”
Section: α-14 Glycosidic Bondsmentioning
confidence: 99%
“…Dextrozyme is a mixture of glucoamylase and pullulanase. Glucoamylase degrades oligosaccharides from the nonreducing end of a sugar molecule releasing glucose [4,15,16], but at the same time it catalyzes the condensation of glucose to maltose and isomaltose without the formation of other oligosaccharides [17,18]. Pullulanase (debranching enzyme) prevents the reverse reaction of condensation [19], and it is therefore possible to achieve the complete conversion of substrate to glucose.…”
Section: Introductionmentioning
confidence: 99%