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Automated docking of α‐(1→4)‐ and α‐(1→6)‐linked glucosyl trisaccharides and maltopentaose into the soybean β‐amylase active site
Author(s) -
Rockey William M.,
Laederach Alain,
Reilly Peter J.
Publication year - 2000
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/(sici)1097-0134(20000801)40:2<299::aid-prot100>3.0.co;2-g
Subject(s) - maltotriose , chemistry , stereochemistry , active site , residue (chemistry) , dock , substrate (aquarium) , hydrogen bond , maltose , enzyme , biochemistry , organic chemistry , molecule , biology , ecology
The Lamarckian genetic algorithm of AutoDock 3.0 was used to dock α‐maltotriose, methyl α‐panoside, methyl α‐isopanoside, methyl α‐isomaltotrioside, methyl α‐(6 1 ‐α‐glucopyranosyl)‐maltoside, and α‐maltopentaose into the closed and, except for α‐maltopentaose, into the open conformation of the soybean β‐amylase active site. In the closed conformation, the hinged flap at the mouth of the active site closes over the substrate. The nonreducing end of α‐maltotriose docks preferentially to subsites −2 or +1, the latter yielding nonproductive binding. Some ligands dock into less optimal conformations with the nonreducing end at subsite −1. The reducing‐end glucosyl residue of nonproductively‐bound α‐maltotriose is close to residue Gln194, which likely contributes to binding to subsite +3. In the open conformation, the substrate hydrogen‐bonds with several residues of the open flap. When the flap closes, the substrate productively docks if the nonreducing end is near subsites −2 or −1. Trisaccharides with α‐(1→6) bonds do not successfully dock except for methyl α‐isopanoside, whose first and second glucosyl rings dock exceptionally well into subsites −2 and −1. The α‐(1→6) bond between the second and third glucosyl units causes the latter to be improperly positioned into subsite +1; the fact that isopanose is not a substrate of β‐amylase indicates that binding to this subsite is critical for hydrolysis. Proteins 2000;40:299–309. © 2000 Wiley‐Liss, Inc.