Charge Density in Enzyme Active Site as a Descriptor of Electrostatic Preorganization

Journal of Chemical Information and Modeling
Jack FullerAnastassia N Alexandrova

Abstract

Large protein macromolecules in enzymatic catalysis have been shown to exert a specific electric field that reduces the reorganization energy upon barrier crossing and thus reduces the reaction free energy barrier. In this work we suggest that the charge density in the active site of an enzyme investigated using formalisms embodied by the quantum theory of atoms in molecules (QTAIM) provides a sensitive and quantum mechanically rigorous probe of electrostatic preorganization. We focus on the active site of ketosteroid isomerase, a well-studied enzyme for which electrostatic preorganization has been modeled theoretically and studied experimentally. We study the charge density in the active site and the reaction mechanism in the presence of small external electric fields of various directions and magnitudes. We show that the geometry of the full charge density is a sensitive reporter on the external field experienced by the active site. Changes are observed in the relative positions of critical points and amount of charge at critical points as a function of the field. At the same time, a subset of these features correlates linearly with the barrier of the first reaction step in catalysis. Small changes in the barrier, within 1-2 ...Continue Reading

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Citations

Jul 7, 2020·Quarterly Reviews of Biophysics·Kasper P Kepp
Feb 2, 2021·The Journal of Physical Chemistry. a·Matthew R Hennefarth, Anastassia N Alexandrova
Jul 20, 2021·Current Opinion in Structural Biology·Matthew R Hennefarth, Anastassia N Alexandrova
Apr 17, 2020·Journal of Chemical Information and Modeling·Richard T BradshawJonathan W Essex
Aug 21, 2021·ACS Catalysis·Daniel Bím, Anastassia N Alexandrova
May 28, 2019·Journal of Chemical Information and Modeling·Habibah A WahabZoe Cournia
Sep 4, 2021·Journal of Chemical Theory and Computation·Santiago VargasAnastassia N Alexandrova
Jan 20, 2022·Journal of Chemical Information and Modeling·Samuel J H GaughanChristof M Jäger

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