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Minimization of dynamic effects in the evolution of dihydrofolate reductase

Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase...

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Autores principales: Ruiz-Pernía, J. Javier, Behiry, Enas, Luk, Louis Y. P., Loveridge, E. Joel, Tuñón, Iñaki, Moliner, Vicent, Allemann, Rudolf K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Royal Society of Chemistry 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006479/
https://www.ncbi.nlm.nih.gov/pubmed/29997817
http://dx.doi.org/10.1039/c5sc04209g
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author Ruiz-Pernía, J. Javier
Behiry, Enas
Luk, Louis Y. P.
Loveridge, E. Joel
Tuñón, Iñaki
Moliner, Vicent
Allemann, Rudolf K.
author_facet Ruiz-Pernía, J. Javier
Behiry, Enas
Luk, Louis Y. P.
Loveridge, E. Joel
Tuñón, Iñaki
Moliner, Vicent
Allemann, Rudolf K.
author_sort Ruiz-Pernía, J. Javier
collection PubMed
description Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase (DHFR) from the mesophile Escherichia coli (EcDHFR). Comparison of DHFRs from organisms adapted to survive at a wide range of temperatures suggests that dynamic coupling in DHFR catalysis has been minimized during evolution; it arises from reorganizational motions needed to facilitate charge transfer events. Contrary to the behaviour observed for the DHFR from the moderate thermophile Geobacillus stearothermophilus (BsDHFR), the chemical transformation catalyzed by the cold-adapted bacterium Moritella profunda (MpDHFR) is only weakly affected by protein isotope substitutions at low temperatures, but the isotopically substituted enzyme is a substantially inferior catalyst at higher, non-physiological temperatures. QM/MM studies revealed that this behaviour is caused by the enzyme’s structural sensitivity to temperature changes, which enhances unfavorable dynamic coupling at higher temperatures by promoting additional recrossing trajectories on the transition state dividing surface. We postulate that these motions are minimized by fine-tuning DHFR flexibility through optimization of the free energy surface of the reaction, such that a nearly static reaction-ready configuration with optimal electrostatic properties is maintained under physiological conditions.
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spelling pubmed-60064792018-07-11 Minimization of dynamic effects in the evolution of dihydrofolate reductase Ruiz-Pernía, J. Javier Behiry, Enas Luk, Louis Y. P. Loveridge, E. Joel Tuñón, Iñaki Moliner, Vicent Allemann, Rudolf K. Chem Sci Chemistry Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins. Previous investigations have indicated that dynamic coupling is detrimental to catalysis by dihydrofolate reductase (DHFR) from the mesophile Escherichia coli (EcDHFR). Comparison of DHFRs from organisms adapted to survive at a wide range of temperatures suggests that dynamic coupling in DHFR catalysis has been minimized during evolution; it arises from reorganizational motions needed to facilitate charge transfer events. Contrary to the behaviour observed for the DHFR from the moderate thermophile Geobacillus stearothermophilus (BsDHFR), the chemical transformation catalyzed by the cold-adapted bacterium Moritella profunda (MpDHFR) is only weakly affected by protein isotope substitutions at low temperatures, but the isotopically substituted enzyme is a substantially inferior catalyst at higher, non-physiological temperatures. QM/MM studies revealed that this behaviour is caused by the enzyme’s structural sensitivity to temperature changes, which enhances unfavorable dynamic coupling at higher temperatures by promoting additional recrossing trajectories on the transition state dividing surface. We postulate that these motions are minimized by fine-tuning DHFR flexibility through optimization of the free energy surface of the reaction, such that a nearly static reaction-ready configuration with optimal electrostatic properties is maintained under physiological conditions. Royal Society of Chemistry 2016-05-01 2016-02-03 /pmc/articles/PMC6006479/ /pubmed/29997817 http://dx.doi.org/10.1039/c5sc04209g Text en This journal is © The Royal Society of Chemistry 2016 http://creativecommons.org/licenses/by/3.0/ This article is freely available. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence (CC BY 3.0)
spellingShingle Chemistry
Ruiz-Pernía, J. Javier
Behiry, Enas
Luk, Louis Y. P.
Loveridge, E. Joel
Tuñón, Iñaki
Moliner, Vicent
Allemann, Rudolf K.
Minimization of dynamic effects in the evolution of dihydrofolate reductase
title Minimization of dynamic effects in the evolution of dihydrofolate reductase
title_full Minimization of dynamic effects in the evolution of dihydrofolate reductase
title_fullStr Minimization of dynamic effects in the evolution of dihydrofolate reductase
title_full_unstemmed Minimization of dynamic effects in the evolution of dihydrofolate reductase
title_short Minimization of dynamic effects in the evolution of dihydrofolate reductase
title_sort minimization of dynamic effects in the evolution of dihydrofolate reductase
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006479/
https://www.ncbi.nlm.nih.gov/pubmed/29997817
http://dx.doi.org/10.1039/c5sc04209g
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