Amylose chain behavior in an interacting context II. Molecular modeling ofa maltopentaose fragment in the barley alpha-amylase catalytic site

In the first paper of this series, the tools necessary to evaluate the cons equences of glucopyranose ring deformations in terms of glycosidic torsion angle shifts, and amylose chain propagation have been created. In this seco nd paper the modeling of amylose fragments into the catalytic region of bar ley barley alpha-amylase has been performed by a systematic approach. From the crystal data of the acarbose/amylase complex, maltotriose and maltopent aose fragments have been docked in the catalytic cleft. It has been found t hat for the trisaccharide, no substrate ring deformation is needed to respe ct stacking interactions (with Y51 and W206) characteristic of the substrat e 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 residu es have been listed, which is of great importance for the understanding of the cleavage mechanism or any further biochemical modification. The best en ergy docking solution that was found is consistent with experimental data. (C) 1999 John Wiley & Sons, Inc.