Bond Bundle Analysis of Ketosteroid Isomerase

• Published in: The journal of physical chemistry. B 2022-11, Vol.126 (46), p.9443-9456
• Main Authors: Wilson, Timothy R., Morgenstern, Amanda, Alexandrova, Anastassia N., Eberhart, M.E.
• Format: Article
• Language: English
• Subjects: B: Biophysical and Biochemical Systems and Processes; Catalysis; Catalytic Domain - genetics; Hydrogen Bonding; Isomerases - metabolism; Ketosteroids - chemistry; Ketosteroids - metabolism; Steroid Isomerases - chemistry
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.2c03638

Bond bundle analysis is used to investigate enzymatic catalysis in the ketosteroid isomerase (KSI) active site. We identify the unique bonding regions in five KSI systems, including those exposed to applied oriented electric fields and those with amino acid mutations, and calculate the precise redistribution of electron density and other regional properties that accompanies either enhancement or inhibition of KSI catalytic activity. We find that catalytic enhancement results from promoting both inter- and intra-molecular electron density redistribution, between bond bundles and bond wedges within the KSI-docked substrate molecule, in the forward direction of the catalyzed reaction. Though the redistribution applies to both types of perturbed systems and is thus suggestive of a general catalytic role, we observe that bond properties (e.g., volume vs energy vs electron count) can respond independently and disproportionately depending on the type of perturbation. We conclude that the resulting catalytic enhancement/inhibition proceeds via different mechanisms, where some bond properties are utilized more by one type of perturbation than the other. Additionally, we find that the correlations between bond wedge properties and catalyzed reaction barrier energies are additive to predict those of bond bundles and atomic basins, providing a rigorous grounding for connecting changes in local charge density to resulting shifts in reaction barrier energy.