Bond Bundle Analysis of Ketosteroid Isomerase

25 October 2022, Version 6
This content is a preprint and has not undergone peer review at the time of posting.


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.


bond bundle
bond wedge
gradient bundle analysis
gradient bundle decomposition
enzymatic catalysis
enzyme design
electron density analysis

Supplementary materials

Supplementary information
• 3D depictions of some of the regions discussed in the manuscript • Coordinates and energies of ab-initio calculations • Atomic basin, bond bundle, and bond wedge tabulated integration values with many more properties than are included in this manuscript • Mmulti-variable bar charts of simplified regional property correlations • Plots of fits of each region and property with reaction barrier energy • Correlations among regional properties

Supplementary weblinks


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