Investigation of interaction between enolase and phosphoglycerate mutase using molecular dynamics simulation.
Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae have been chosen to detect complex formation between active centers (a/c), using molecular dynamics simulation. Enzymes have been separated by 10 A distance and placed in a water box of size 173 x 173 x 173 A. Three different orientations where a/c of PGM and enolase were positioned toward each other have been used for investigation. The two initial 3-phosphoglycerate substrates at near active centers of initial structure of PGM have been replaced with final 2-phosphoglycerate products. 150mM of NaCl have been added to the system to observe binding activity in the near physiological conditions. Analysis of interaction energies and conformation changes for 3ns simulation indicates that PGM and enolase do show binding affinity between their near active regions. Moreover the similarity between final conformations of the first two orientations with the initial conformation of the third orientation suggests that complex formation between a/c of enzymes is not confined only by discussed orientations. Clear interaction of enolase with C-terminal tail of PGM has been recorded. These results suggest that substrate direct transfer mechanism may exist between enzymes.
Hakobyan
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D
Institute of Molecular Biology, National Academy of Sciences of Armenia, Hasratyan 7, Yerevan 375014, Armenia.
Nazaryan
K
K
D001665:Binding Sites; D020134:Catalytic Domain; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D010736:Phosphoglycerate Mutase / Q000737:chemistry / Q000378:metabolism*; D010751:Phosphopyruvate Hydratase / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation
D010751:Phosphopyruvate Hydratase; D010736:Phosphoglycerate Mutase