Bioinformatics Analysis of Oligosaccharide Phosphorylation Effect on the Stabilization of the β-Amylase Ligand Complex

Abstract

Starch is the most abundant storage carbohydrate produced in plants. The beginning of transitory starch degradation in plants depends mainly on day cycle, posttranslational regulation of enzyme activity, and starch phosphorylation, but the molecular mechanism of these factors' influence is not yet precisely described. The aim of our analysis was to investigate the effect of phosphorylation on the intermolecular energies for stabilization of the complexes between the set of phosphorylated and nonphosphorylated carbohydrate ligands and Solanum tuberosum (L.) β-amylase model. For performing protein-ligand docking procedures and calculating the binding energies, the DOCK6 and Glide 4.5 program suites were applied. We have observed simultaneously the effect of chain elongation, phosphorylation, and chain branching. Results of flexible ligand docking show that phosphorylation as well as chain elongation increase the stabilization of the ligand-protein complex.

Keywords:

• Potato β-amylase catalytic site structure
• Oligosaccharide phosphorylation

ACKNOWLEDGMENTS

The authors thank the Polish Ministry of Science and Higher Education for financial support (Grant no. N302061134 to K.P. and S.O.).