Amylose chain behavior in an interacting context II. Molecular modeling of a maltopentaose fragment in the barley α‐amylase catalytic site

In the first paper of this series, the tools necessary to evaluate the consequences of glucopyranose ring deformations in terms of glycosidic torsion angle shifts, and amylose chain propagation have been created. In this second paper, the modeling of amylose fragments into the catalytic region of barley α‐amylase has been performed by a systematic approach. From the crystal data of the acarbose/amylase complex, maltotriose and maltopentaose fragments have been docked in the catalytic cleft. It has been found that for the trisaccharide, no substrate ring deformation is needed to respect stacking interactions (with Y51 and W206) characteristic of the substrate binding. However, for the pentasaccharide the deformations of rings A and C (from chair { C } toward half‐chair { H2 } and skew { S4 }, respectively) are essential conditions to fit this amylose fragment into the narrow catalytic site. Within five contiguous binding subsites, all important enzyme residues have been listed, which is of great importance for the understanding of the cleavage mechanism or any further biochemical modification. The best energy docking solution that was found is consistent with experimental data. © 1999 John Wiley & Sons, Inc. Biopoly 49: 107–119, 1999