(426m) Toward the Transition State: Further Docking Studies on Family 47 Alpha-1,2-Mannosidases
AIChE Annual Meeting
2005
2005 Annual Meeting
Food, Pharmaceutical & Bioengineering Division
Poster Session: Biocatalysis & Protein Engineering
Wednesday, November 2, 2005 - 4:30pm to 7:30pm
Alpha-1,2-Mannosidase
from the endoplasmic reticulum (ERMan), a Family 47 glycosyl hydrolase, is a
key enzyme in the N-glycan
synthesis pathway. Catalytic-domain crystal structures of human and yeast
ERMans have been determined, the former without ligands, with the inhibitors
1-deoxymannojirimycin and kifunensine, and with a thiodisaccharide substrate
analog. Both inhibitors were bound at the base of the funnel-shaped active site
as the unusual 1C4
conformer, while the substrate analog glycone is a 3S1 conformer. In the current
study, AutoDock was used to dock alpha-D-mannopyranosyl-(1,2)-alpha-D-mannopyranose with its glycone in chair
(1C4,
4C1),
half-chair (3H2,3H4,4H3),
skew-boat (OS2,3S1,5S1),
boat (2,5B,
3,OB, B1,4, B2,5), and envelope (3E, 4E, E3,E4) conformations into the
yeast ERMan active site. Both docked energies and forces on docked ligand atoms
were calculated to determine how the ligand distorts to the transition state.
From these, we can conclude that 1) both 1C4 and OS2 can be the starting
conformers; 2) the most likely binding pathways are 1C4 to3H2 toOS2 to3,OB to 3S1 to 3E and OS2 to3,OB to 3S1
to3E
with 1C4
and OS2
as starting conformers, respectively; 3) the transition state is likely
to be close to a 3E conformation.