TY - JOUR
T1 - Bioinformatics analysis of oligosaccharide phosphorylation effect on the stabilization of the -amylase ligand complex
AU - Dudkiewicz, Małgorzata
AU - Simińska, Joanna
AU - Pawłowski, Krzysztof
AU - Orzechowski, Sławomir
N1 - Funding Information:
The authors thank the Polish Ministry of Science and Higher Education for financial support (Grant no. N302061134 to K.P. and S.O.).
PY - 2008/11
Y1 - 2008/11
N2 - 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.) -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.
AB - 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.) -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.
KW - Oligosaccharide phosphorylation
KW - Potato ß-amylase catalytic site structure
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U2 - 10.1080/07328300802547863
DO - 10.1080/07328300802547863
M3 - Article
AN - SCOPUS:57649200104
SN - 0732-8303
VL - 27
SP - 479
EP - 495
JO - Journal of Carbohydrate Chemistry
JF - Journal of Carbohydrate Chemistry
IS - 8-9
ER -