Ensemble-function relationships to dissect mechanisms of enzyme catalysis
Abstract
Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.
- Authors:
-
[1];
[2];
[3];
[4];
[5];
[6]
- Stanford Univ., CA (United States); Bristol Myers Squibb, San Diego, CA (United States)
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
- Stanford Univ., CA (United States); Univ. of California, San Francisco, CA (United States)
- Univ. of California, San Francisco, CA (United States); Relay Therapeutics, Cambridge, MA (United States)
- Univ. of California, San Francisco, CA (United States)
- Stanford Univ., CA (United States)
- Publication Date:
- Research Org.:
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); National Science Foundation (NSF)
- OSTI Identifier:
- 1989366
- Grant/Contract Number:
- AC02-76SF00515; P41GM103393; MCB-1714723; GM123159
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Science Advances
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 41; Journal ID: ISSN 2375-2548
- Publisher:
- AAAS
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Citation Formats
Yabukarski, Filip, Doukov, Tzanko, Pinney, Margaux M., Biel, Justin T., Fraser, James S., and Herschlag, Daniel. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. United States: N. p., 2022.
Web. doi:10.1126/sciadv.abn7738.
Yabukarski, Filip, Doukov, Tzanko, Pinney, Margaux M., Biel, Justin T., Fraser, James S., & Herschlag, Daniel. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. United States. https://doi.org/10.1126/sciadv.abn7738
Yabukarski, Filip, Doukov, Tzanko, Pinney, Margaux M., Biel, Justin T., Fraser, James S., and Herschlag, Daniel. Fri .
"Ensemble-function relationships to dissect mechanisms of enzyme catalysis". United States. https://doi.org/10.1126/sciadv.abn7738. https://www.osti.gov/servlets/purl/1989366.
@article{osti_1989366,
title = {Ensemble-function relationships to dissect mechanisms of enzyme catalysis},
author = {Yabukarski, Filip and Doukov, Tzanko and Pinney, Margaux M. and Biel, Justin T. and Fraser, James S. and Herschlag, Daniel},
abstractNote = {Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.},
doi = {10.1126/sciadv.abn7738},
journal = {Science Advances},
number = 41,
volume = 8,
place = {United States},
year = {Fri Oct 14 00:00:00 EDT 2022},
month = {Fri Oct 14 00:00:00 EDT 2022}
}
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