To better understand the molecular basis of glucomylase selectivity, l
ow-energy conformers of glucosyl disaccharides obtained from relaxed-r
esidue conformational mapping were flexibly docked into the glucoamyla
se active site using AutoDock 2.2. This procedure ensures that signifi
cant conformational space is searched and can produce bound structures
comparable to those obtained by protein crystallography, alpha-linked
glucosyl disaccharides except alpha,alpha-trehalose dock easily into
the active site while exclusively beta-linked disaccharides do not, ex
plaining why only the former are glucoamylase substrates. The optimize
d docking modes are similar at the nonreducing end of the different su
bstrates. Individual atomic energies of intermolecular interaction all
ow the definite identification of key hydroxyl groups for each substra
te. This approach confirmed the versatility of the second subsite of t
he glucoamylase active site in binding different substrates. (C) 1997
Wiley-Liss, Inc.