Computational simulation of ligand docking to L-type pyruvate kinase subunit |
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| Affiliation: | 1. Key Laboratory of Coordination Chemistry and Functional Materials in Universities of Shandong, Dezhou College, Dezhou, Shandong 253023, PR China;2. Department of Chemistry, The University of Cincinnati, Cincinnati, OH 45221, USA;3. Key Laboratory of Novel Thin Film Solar Cells, Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China;1. Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Kamýcká 129, 165 21 Prague 6, Czech Republic;2. Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic;3. Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy;1. Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, 7021 Zarzouna, Tunisia;2. Youngstown State University, Department of Chemistry, One University Plaza, Youngstown, OH 44555-3663, USA;3. Cristallographie, Résonance Magnétique et Modélisations, (CRM2), UMR CNRS 7036, Institut Jean Barriol, Universitéde Lorraine, BP 70239, Bd des Aiguillettes, 54506 Vandoeuvre-les-Nancy, France;4. Laboratoire de Chimie Organometallique de Surface (LCOMS), Ecole Superieure de Chimie Physique Electronique, 69622 Villeurbanne Cedex, France |
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| Abstract: | Computational blind docking approach was used for mapping of possible binding sites in L-type pyruvate kinase subunit for peptides, RRASVA and the phosphorylated derivative RRAS(Pi)VA, which model the phosphorylatable N-terminal regulatory domain of the enzyme. In parallel, the same docking analysis was done for both substrates of this enzyme, phosphoenolpyruvate (PEP) and adenosine diphosphate (ADP), and for docking of fructose 1,6-bisphosphate (FBP), which is the allosteric activator of the enzyme. The binding properties of the entire surface of the protein were scanned and several possible binding sites were identified in domains A and C of the protein, while domain B revealed no docking sites for peptides or for substrates or the allosteric regulator. It was found that the docking sites of different ligands were partially overlapping, pointing to the possibility that some regulatory effects, observed in the case of L-type pyruvate kinase, may be caused by the competition of different ligands for the same binding sites. |
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| Keywords: | L-type pyruvate kinase N-terminal domain docking in protein Regulatory phosphorylation Putative N-terminal docking sites Substrate affinity regulation Switching in cooperativity |
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