Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations

Glutamine synthetase is an important enzyme that catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. In mammals, it plays a key role in preventing excitotoxicity in the brain and detoxifying ammonia in the liver. In plants and bacteria, it is fundamental for nitrogen metab...

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Autores principales:	Issoglio, F.M., Campolo, N., Zeida, A., Grune, T., Radi, R., Estrin, D.A., Bartesaghi, S.
Formato:	JOUR
Materias:	Amino acids Ammonia Catalysis Energy barriers Molecular dynamics Molecular modeling Quantum theory Reaction intermediates Reaction kinetics Thermodynamics Acid-base equilibria Catalytic mechanisms Classical molecular dynamics Glutamine synthetase Post-translational modifications Quantum mechanics/molecular mechanics Reaction free energy Thermodynamics and kinetics Free energy ammonia enzyme gamma glutamyl phosphate glutamate ammonia ligase unclassified drug Article catalysis computer simulation enzyme structure human molecular dynamics nitrogen metabolism nucleophilicity priority journal quantum mechanics reaction analysis
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_00062960_v55_n42_p5907_Issoglio
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_00062960_v55_n42_p5907_Issoglio
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spelling	todo:paper_00062960_v55_n42_p5907_Issoglio2023-10-03T14:04:37Z Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations Issoglio, F.M. Campolo, N. Zeida, A. Grune, T. Radi, R. Estrin, D.A. Bartesaghi, S. Amino acids Ammonia Catalysis Energy barriers Molecular dynamics Molecular modeling Quantum theory Reaction intermediates Reaction kinetics Thermodynamics Acid-base equilibria Catalytic mechanisms Classical molecular dynamics Glutamine synthetase Post-translational modifications Quantum mechanics/molecular mechanics Reaction free energy Thermodynamics and kinetics Free energy ammonia enzyme gamma glutamyl phosphate glutamate ammonia ligase unclassified drug Article catalysis computer simulation enzyme structure human molecular dynamics nitrogen metabolism nucleophilicity priority journal quantum mechanics reaction analysis Glutamine synthetase is an important enzyme that catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. In mammals, it plays a key role in preventing excitotoxicity in the brain and detoxifying ammonia in the liver. In plants and bacteria, it is fundamental for nitrogen metabolism, being critical for the survival of the organism. In this work, we show how the use of classical molecular dynamics simulations and multiscale quantum mechanics/molecular mechanics simulations allowed us to examine the structural properties and dynamics of human glutamine synthetase (HsGS), as well as the reaction mechanisms involved in the catalytic process with atomic level detail. Our results suggest that glutamine formation proceeds through a two-step mechanism that includes a first step in which the γ-glutamyl phosphate intermediate forms, with a 5 kcal/mol free energy barrier and a -8 kcal/mol reaction free energy, and then a second rate-limiting step involving the ammonia nucleophilic attack, with a free energy barrier of 19 kcal/mol and a reaction free energy of almost zero. A detailed analysis of structural features within each step exposed the relevance of the acid-base equilibrium related to protein residues and substrates in the thermodynamics and kinetics of the reactions. These results provide a comprehensive study of HsGS dynamics and establish the groundwork for further analysis regarding changes in HsGS activity, as occur in natural variants and post-translational modifications. © 2016 American Chemical Society. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_00062960_v55_n42_p5907_Issoglio
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Amino acids Ammonia Catalysis Energy barriers Molecular dynamics Molecular modeling Quantum theory Reaction intermediates Reaction kinetics Thermodynamics Acid-base equilibria Catalytic mechanisms Classical molecular dynamics Glutamine synthetase Post-translational modifications Quantum mechanics/molecular mechanics Reaction free energy Thermodynamics and kinetics Free energy ammonia enzyme gamma glutamyl phosphate glutamate ammonia ligase unclassified drug Article catalysis computer simulation enzyme structure human molecular dynamics nitrogen metabolism nucleophilicity priority journal quantum mechanics reaction analysis
spellingShingle	Amino acids Ammonia Catalysis Energy barriers Molecular dynamics Molecular modeling Quantum theory Reaction intermediates Reaction kinetics Thermodynamics Acid-base equilibria Catalytic mechanisms Classical molecular dynamics Glutamine synthetase Post-translational modifications Quantum mechanics/molecular mechanics Reaction free energy Thermodynamics and kinetics Free energy ammonia enzyme gamma glutamyl phosphate glutamate ammonia ligase unclassified drug Article catalysis computer simulation enzyme structure human molecular dynamics nitrogen metabolism nucleophilicity priority journal quantum mechanics reaction analysis Issoglio, F.M. Campolo, N. Zeida, A. Grune, T. Radi, R. Estrin, D.A. Bartesaghi, S. Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
topic_facet	Amino acids Ammonia Catalysis Energy barriers Molecular dynamics Molecular modeling Quantum theory Reaction intermediates Reaction kinetics Thermodynamics Acid-base equilibria Catalytic mechanisms Classical molecular dynamics Glutamine synthetase Post-translational modifications Quantum mechanics/molecular mechanics Reaction free energy Thermodynamics and kinetics Free energy ammonia enzyme gamma glutamyl phosphate glutamate ammonia ligase unclassified drug Article catalysis computer simulation enzyme structure human molecular dynamics nitrogen metabolism nucleophilicity priority journal quantum mechanics reaction analysis
description	Glutamine synthetase is an important enzyme that catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. In mammals, it plays a key role in preventing excitotoxicity in the brain and detoxifying ammonia in the liver. In plants and bacteria, it is fundamental for nitrogen metabolism, being critical for the survival of the organism. In this work, we show how the use of classical molecular dynamics simulations and multiscale quantum mechanics/molecular mechanics simulations allowed us to examine the structural properties and dynamics of human glutamine synthetase (HsGS), as well as the reaction mechanisms involved in the catalytic process with atomic level detail. Our results suggest that glutamine formation proceeds through a two-step mechanism that includes a first step in which the γ-glutamyl phosphate intermediate forms, with a 5 kcal/mol free energy barrier and a -8 kcal/mol reaction free energy, and then a second rate-limiting step involving the ammonia nucleophilic attack, with a free energy barrier of 19 kcal/mol and a reaction free energy of almost zero. A detailed analysis of structural features within each step exposed the relevance of the acid-base equilibrium related to protein residues and substrates in the thermodynamics and kinetics of the reactions. These results provide a comprehensive study of HsGS dynamics and establish the groundwork for further analysis regarding changes in HsGS activity, as occur in natural variants and post-translational modifications. © 2016 American Chemical Society.
format	JOUR
author	Issoglio, F.M. Campolo, N. Zeida, A. Grune, T. Radi, R. Estrin, D.A. Bartesaghi, S.
author_facet	Issoglio, F.M. Campolo, N. Zeida, A. Grune, T. Radi, R. Estrin, D.A. Bartesaghi, S.
author_sort	Issoglio, F.M.
title	Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
title_short	Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
title_full	Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
title_fullStr	Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
title_full_unstemmed	Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
title_sort	exploring the catalytic mechanism of human glutamine synthetase by computer simulations
url	http://hdl.handle.net/20.500.12110/paper_00062960_v55_n42_p5907_Issoglio
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Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations

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