Molecular dynamics simulation of interactions in glycolytic enzymes.
Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae, have been chosen to detect complex formation and possible channeling, using molecular dynamics simulation. The enzymes were separated by 10 angstroms distance and placed in a water-filled box of size 173 x 173 x 173 angstroms. Three different orientations have been investigated. The two initial 3-phosphoglycerate substrate molecules near the active centers of the initial structure of PGM have been replaced with final product (2-phosphoglycerate) molecules, and 150 mM NaCl together with three Mg2+ ions have been added to the system to observe post-catalytic activity under near-physiological conditions. Analysis of interaction energies and conformation changes for 3 nsec simulation indicates that PGM and enolase do show binding affinity between their near active regions, which is necessary for channeling to occur. Interaction of the C-terminal residues Ala239 and Val240 of PGM (which partially "cap" the 2-phosphoglycerate) with enolase also favors the existence of channeling.
Hakobyan
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Institute of Molecular Biology, National Academy of Sciences of Armenia, 375014 Yerevan, Armenia.
Nazaryan
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K
D001665:Binding Sites; D003198:Computer Simulation; D005988:Glyceric Acids / Q000737:chemistry / Q000378:metabolism; D006019:Glycolysis; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D009994:Osmolar Concentration; D010736:Phosphoglycerate Mutase / Q000737:chemistry* / Q000378:metabolism; D010751:Phosphopyruvate Hydratase / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D012965:Sodium Chloride / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D014867:Water / Q000737:chemistry / Q000378:metabolism
D005988:Glyceric Acids; D014867:Water; C008885:2-phosphoglycerate; D012965:Sodium Chloride; D010751:Phosphopyruvate Hydratase; D010736:Phosphoglycerate Mutase