Structure and Dynamics of the Enzyme-Substrate Complex of N-Acetylaspartylglutamate Synthase According to Computer Simulation Data

N-acetylaspartilglutamate is the most common dipeptide in brain cells, which is synthesized using the enzyme N-acetylaspartilglutamate synthase. Herein we utilize bioinformatics methods to predict the protein structure from the primary sequence of the coding gene, classical molecular dynamics to obtain a stable protein complex with N-acetylaspartate and glutamate ligands within the trajectory, as well as machine learning methods to analyze, describe and select potential reactive and non-reactive conformations of the model system describing the enzyme-substrate complex. Molecular dynamics simulations with combined quantum mechanics / molecular mechanics potentials were performed for a set of selected conformations and the potential reaction mechanism were characterized.