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Automated docking of glucosyl disaccharides in the glucoamylase active site

✍ Scribed by Pedro M. Coutinho; Michael K. Dowd; Peter J. Reilly

Publisher: John Wiley and Sons
Year: 1997
Tongue: English
Weight: 321 KB
Volume: 28
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(199706)28:2<162::aid-prot5>3.0.co;2-h

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✦ Synopsis

To better understand the molecular basis of glucomylase selectivity, lowenergy conformers of glucosyl disaccharides obtained from relaxed-residue conformational mapping were flexibly docked into the glucoamylase active site using AutoDock 2.2. This procedure ensures that significant conformational space is searched and can produce bound structures comparable to those obtained by protein crystallography. a-Linked glucosyl disaccharides except a,a-trehalose dock easily into the active site while exclusively b-linked disaccharides do not, explaining why only the former are glucoamylase substrates. The optimized docking modes are similar at the nonreducing end of the different substrates. Individual atomic energies of intermolecular interaction allow the definite identification of key hydroxyl groups for each substrate. This approach confirmed the versatility of the second subsite of the glucoamylase active site in binding different substrates. Proteins 28:162-173, 1997.

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