Bond Bundle Analysis of Ketosteroid Isomerase

25 August 2022, Version 5
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 that accompanies either enhancement or inhibition of KSI catalytic activity. In two examples—using direct inspection of bond bundle regional properties, and using correlations between those properties and reaction barrier height—we arrive at similar conclusions, that catalytic enhancement results from promoting electron density redistribution between bonds within the KSI-docked substrate molecule in a way that closely resembles our mechanistic understanding of the forward catalyzed reaction. The catalyzing charge redistribution between bond bundles is prevalent in KSI systems catalyzed via electric fields or via amino acid mutation, and are thus suggestive of a general catalytic role.


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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