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Igor V. Polyakov I. V., Alexandra V. Krivitskaya, Maria G. Khrenova
Structure and
dynamics of the enzyme-substrate complex of N-acetylaspartylglutamate synthase
according to computer simulation data
Abstract
Abstract. 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.
Key words: enzymatic catalysis, molecular modeling, QM/MM, N-acetylaspartilglutamate synthase
Copyright (C) Chemistry Dept., Moscow State University, 2002
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