Artículo

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" (2016) Biochemistry. 55(42):5907-5916
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Abstract:

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.

Registro:

Documento: Artículo
Título:Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations
Autor:Issoglio, F.M.; Campolo, N.; Zeida, A.; Grune, T.; Radi, R.; Estrin, D.A.; Bartesaghi, S.
Filiación:Departamento de Química Inorgánica, Analítica y Química-Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
Departamento de Educación Médica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, Department of Molecular Toxicology, Arthur-Scheunert-Allee 114-116, Nuthetal, 14558, Germany
Palabras clave: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
Año:2016
Volumen:55
Número:42
Página de inicio:5907
Página de fin:5916
DOI: http://dx.doi.org/10.1021/acs.biochem.6b00822
Título revista:Biochemistry
Título revista abreviado:Biochemistry
ISSN:00062960
CODEN:BICHA
CAS:ammonia, 14798-03-9, 51847-23-5, 7664-41-7; glutamate ammonia ligase, 9023-70-5
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00062960_v55_n42_p5907_Issoglio

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Citas:

---------- APA ----------
Issoglio, F.M., Campolo, N., Zeida, A., Grune, T., Radi, R., Estrin, D.A. & Bartesaghi, S. (2016) . Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations. Biochemistry, 55(42), 5907-5916.
http://dx.doi.org/10.1021/acs.biochem.6b00822
---------- CHICAGO ----------
Issoglio, F.M., Campolo, N., Zeida, A., Grune, T., Radi, R., Estrin, D.A., et al. "Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations" . Biochemistry 55, no. 42 (2016) : 5907-5916.
http://dx.doi.org/10.1021/acs.biochem.6b00822
---------- MLA ----------
Issoglio, F.M., Campolo, N., Zeida, A., Grune, T., Radi, R., Estrin, D.A., et al. "Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations" . Biochemistry, vol. 55, no. 42, 2016, pp. 5907-5916.
http://dx.doi.org/10.1021/acs.biochem.6b00822
---------- VANCOUVER ----------
Issoglio, F.M., Campolo, N., Zeida, A., Grune, T., Radi, R., Estrin, D.A., et al. Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations. Biochemistry. 2016;55(42):5907-5916.
http://dx.doi.org/10.1021/acs.biochem.6b00822