Biomaterial Database

Molecular dynamics simulation of interactions in glycolytic enzymes. 2006

D Hakobyan, and K Nazaryan

Institute of Molecular Biology, National Academy of Sciences of Armenia, 375014 Yerevan, Armenia.

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.

UI	MeSH Term	Description	Entries
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D008968	Molecular Conformation	The characteristic three-dimensional shape of a molecule.	Molecular Configuration,3D Molecular Structure,Configuration, Molecular,Molecular Structure, Three Dimensional,Three Dimensional Molecular Structure,3D Molecular Structures,Configurations, Molecular,Conformation, Molecular,Conformations, Molecular,Molecular Configurations,Molecular Conformations,Molecular Structure, 3D,Molecular Structures, 3D,Structure, 3D Molecular,Structures, 3D Molecular
D009994	Osmolar Concentration	The concentration of osmotically active particles in solution expressed in terms of osmoles of solute per liter of solution. Osmolality is expressed in terms of osmoles of solute per kilogram of solvent.	Ionic Strength,Osmolality,Osmolarity,Concentration, Osmolar,Concentrations, Osmolar,Ionic Strengths,Osmolalities,Osmolar Concentrations,Osmolarities,Strength, Ionic,Strengths, Ionic
D010736	Phosphoglycerate Mutase	An enzyme that catalyzes the conversion of 2-phospho-D-glycerate to 3-phospho-D-glycerate.	Glycerate (3-2)-Phosphomutase,Phosphoglyceromutase,Phosphoglycerate Phosphomutase,Mutase, Phosphoglycerate,Phosphomutase, Phosphoglycerate
D010751	Phosphopyruvate Hydratase	A hydro-lyase that catalyzes the dehydration of 2-phosphoglycerate to form PHOSPHOENOLPYRUVATE. Several different isoforms of this enzyme exist, each with its own tissue specificity.	Enolase,Neuron-Specific Enolase,2-Phospho-D-Glycerate Hydro-Lyase,2-Phospho-D-Glycerate Hydrolase,2-Phosphoglycerate Dehydratase,Enolase 2,Enolase 3,Muscle-Specific Enolase,Nervous System-Specific Enolase,Non-Neuronal Enolase,alpha-Enolase,beta-Enolase,gamma-Enolase,2 Phospho D Glycerate Hydro Lyase,2 Phospho D Glycerate Hydrolase,2 Phosphoglycerate Dehydratase,Dehydratase, 2-Phosphoglycerate,Enolase, Muscle-Specific,Enolase, Nervous System-Specific,Enolase, Neuron-Specific,Enolase, Non-Neuronal,Hydratase, Phosphopyruvate,Hydro-Lyase, 2-Phospho-D-Glycerate,Muscle Specific Enolase,Nervous System Specific Enolase,Neuron Specific Enolase,Non Neuronal Enolase,System-Specific Enolase, Nervous,alpha Enolase,beta Enolase,gamma Enolase
D011485	Protein Binding	The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.	Plasma Protein Binding Capacity,Binding, Protein
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D005988	Glyceric Acids	Three-carbon SUGAR ACIDS with the formula HOCH2(CHOH)COOH.	Acids, Glyceric