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Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis
[Image: see text] Substrate inhibition, whereby enzymatic activity decreases with excess substrate after reaching a maximum turnover rate, is among the most elusive phenomena in enzymatic catalysis. Here, based on a dynamic energy landscape model, we investigate the underlying mechanism by performin...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9483917/ https://www.ncbi.nlm.nih.gov/pubmed/36044985 http://dx.doi.org/10.1021/acs.jpcb.2c03832 |
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author | Zhang, Yangyang Chen, Mingchen Lu, Jiajun Li, Wenfei Wolynes, Peter G. Wang, Wei |
author_facet | Zhang, Yangyang Chen, Mingchen Lu, Jiajun Li, Wenfei Wolynes, Peter G. Wang, Wei |
author_sort | Zhang, Yangyang |
collection | PubMed |
description | [Image: see text] Substrate inhibition, whereby enzymatic activity decreases with excess substrate after reaching a maximum turnover rate, is among the most elusive phenomena in enzymatic catalysis. Here, based on a dynamic energy landscape model, we investigate the underlying mechanism by performing molecular simulations and frustration analysis for a model enzyme adenylate kinase (AdK), which catalyzes the phosphoryl transfer reaction ATP + AMP ⇋ ADP + ADP. Intriguingly, these reveal a kinetic repartitioning mechanism of substrate inhibition, whereby excess substrate AMP suppresses the population of an energetically frustrated, but kinetically activated, catalytic pathway going through a substrate (ATP)-product (ADP) cobound complex with steric incompatibility. Such a frustrated pathway plays a crucial role in facilitating the bottleneck product ADP release, and its suppression by excess substrate AMP leads to a slow down of product release and overall turnover. The simulation results directly demonstrate that substrate inhibition arises from the rate-limiting product-release step, instead of the steps for populating the catalytically competent complex as often suggested in previous works. Furthermore, there is a tight interplay between the enzyme conformational equilibrium and the extent of substrate inhibition. Mutations biasing to more closed conformations tend to enhance substrate inhibition. We also characterized the key features of single-molecule enzyme kinetics with substrate inhibition effect. We propose that the above molecular mechanism of substrate inhibition may be relevant to other multisubstrate enzymes in which product release is the bottleneck step. |
format | Online Article Text |
id | pubmed-9483917 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-94839172022-09-20 Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis Zhang, Yangyang Chen, Mingchen Lu, Jiajun Li, Wenfei Wolynes, Peter G. Wang, Wei J Phys Chem B [Image: see text] Substrate inhibition, whereby enzymatic activity decreases with excess substrate after reaching a maximum turnover rate, is among the most elusive phenomena in enzymatic catalysis. Here, based on a dynamic energy landscape model, we investigate the underlying mechanism by performing molecular simulations and frustration analysis for a model enzyme adenylate kinase (AdK), which catalyzes the phosphoryl transfer reaction ATP + AMP ⇋ ADP + ADP. Intriguingly, these reveal a kinetic repartitioning mechanism of substrate inhibition, whereby excess substrate AMP suppresses the population of an energetically frustrated, but kinetically activated, catalytic pathway going through a substrate (ATP)-product (ADP) cobound complex with steric incompatibility. Such a frustrated pathway plays a crucial role in facilitating the bottleneck product ADP release, and its suppression by excess substrate AMP leads to a slow down of product release and overall turnover. The simulation results directly demonstrate that substrate inhibition arises from the rate-limiting product-release step, instead of the steps for populating the catalytically competent complex as often suggested in previous works. Furthermore, there is a tight interplay between the enzyme conformational equilibrium and the extent of substrate inhibition. Mutations biasing to more closed conformations tend to enhance substrate inhibition. We also characterized the key features of single-molecule enzyme kinetics with substrate inhibition effect. We propose that the above molecular mechanism of substrate inhibition may be relevant to other multisubstrate enzymes in which product release is the bottleneck step. American Chemical Society 2022-08-31 2022-09-15 /pmc/articles/PMC9483917/ /pubmed/36044985 http://dx.doi.org/10.1021/acs.jpcb.2c03832 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Zhang, Yangyang Chen, Mingchen Lu, Jiajun Li, Wenfei Wolynes, Peter G. Wang, Wei Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis |
title | Frustration and
the Kinetic Repartitioning Mechanism
of Substrate Inhibition in Enzyme Catalysis |
title_full | Frustration and
the Kinetic Repartitioning Mechanism
of Substrate Inhibition in Enzyme Catalysis |
title_fullStr | Frustration and
the Kinetic Repartitioning Mechanism
of Substrate Inhibition in Enzyme Catalysis |
title_full_unstemmed | Frustration and
the Kinetic Repartitioning Mechanism
of Substrate Inhibition in Enzyme Catalysis |
title_short | Frustration and
the Kinetic Repartitioning Mechanism
of Substrate Inhibition in Enzyme Catalysis |
title_sort | frustration and
the kinetic repartitioning mechanism
of substrate inhibition in enzyme catalysis |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9483917/ https://www.ncbi.nlm.nih.gov/pubmed/36044985 http://dx.doi.org/10.1021/acs.jpcb.2c03832 |
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