Artículo

Romero, J.M.; Martin, M.; Ramirez, C.L.; Dumas, V.G.; Marti, M.A.; Karabencheva-Christova T. "Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases" (2015) Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, 2015. 100:33-65
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Abstract:

Determination of the free energy profile for an enzyme reaction mechanism is of primordial relevance, paving the way for our understanding of the enzyme's catalytic power at the molecular level. Although hybrid, mostly DFT-based, QM/MM methods have been extensively applied to this type of studies, achieving accurate and statistically converged results at a moderate computational cost is still an open challenge. Recently, we have shown that accurate results can be achieved in less computational time, combining Jarzynski's relationship with a hybrid differential relaxation algorithm (HyDRA), which allows partial relaxation of the solvent during the nonequilibrium steering of the reaction. In this work, we have applied this strategy to study two mycobacterial zinc hydrolases. Mycobacterium tuberculosis infections are still a worldwide problem and thus characterization and validation of new drug targets is an intense field of research. Among possible drug targets, recently two essential zinc hydrolases, MshB (Rv1170) and MA-amidase (Rv3717), have been proposed and structurally characterized. Although possible mechanisms have been proposed by analogy to the widely studied human Zn hydrolases, several key issues, particularly those related to Zn coordination sphere and its role in catalysis, remained unanswered. Our results show that mycobacterial Zn hydrolases share a basic two-step mechanism. First, the attacking water becomes deprotonated by the conserved base and establishes the new C-O bond leading to a tetrahedral intermediate. The intermediate requires moderate reorganization to allow for proton transfer to the amide N and C-N bond breaking to occur in the second step. Zn ion plays a key role in stabilizing the tetrahedral intermediate and balancing the negative charge of the substrate during hydroxide ion attack. Finally, comparative analysis of other Zn hydrolases points to a convergent mechanistic evolution. © 2015 Elsevier Inc. All rights reserved.

Registro:

Documento: Artículo
Título:Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases
Autor:Romero, J.M.; Martin, M.; Ramirez, C.L.; Dumas, V.G.; Marti, M.A.; Karabencheva-Christova T.
Filiación:Instituto de Química Física de Los Materiales Medio Ambiente y Energía, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
Palabras clave:Free energy; HyDRA; Jarzynski's relationship; M. tuberculosis; MshB; QM/MM; Rv1170; Rv3717; Zn hydrolases; amidase; amide; carbonyl derivative; hydrolase; hydroxide; MA amidase; MshB enzyme; unclassified drug; zinc ion; amidase; bacterial protein; divalent cation; n acetylmuramoylalanine amidase; N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase; proton; water; zinc; algorithm; catalysis; Conference Paper; crystal structure; enzyme analysis; human; Mycobacterium tuberculosis; nonhuman; priority journal; proton transport; reaction analysis; tuberculosis; algorithm; biocatalysis; chemistry; enzymology; molecular dynamics; Mycobacterium tuberculosis; protein secondary structure; protein tertiary structure; quantum theory; species difference; thermodynamics; Algorithms; Amidohydrolases; Bacterial Proteins; Biocatalysis; Cations, Divalent; Humans; Molecular Dynamics Simulation; Mycobacterium tuberculosis; N-Acetylmuramoyl-L-alanine Amidase; Protein Structure, Secondary; Protein Structure, Tertiary; Protons; Quantum Theory; Species Specificity; Thermodynamics; Water; Zinc
Año:2015
Volumen:100
Página de inicio:33
Página de fin:65
DOI: http://dx.doi.org/10.1016/bs.apcsb.2015.06.006
Título revista:Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, 2015
Título revista abreviado:Adv. Protein Chem. Struct. Biol.
ISSN:18761623
CAS:amidase, 9012-56-0; amide, 17655-31-1; hydrolase, 9027-41-2; hydroxide, 14280-30-9; zinc ion, 23713-49-7; n acetylmuramoylalanine amidase, 9013-25-6; proton, 12408-02-5, 12586-59-3; water, 7732-18-5; zinc, 7440-66-6, 14378-32-6; Amidohydrolases; Bacterial Proteins; Cations, Divalent; N-acetyl-1-D-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase; N-Acetylmuramoyl-L-alanine Amidase; Protons; Water; Zinc
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_18761623_v100_n_p33_Romero

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Citas:

---------- APA ----------
Romero, J.M., Martin, M., Ramirez, C.L., Dumas, V.G., Marti, M.A. & Karabencheva-Christova T. (2015) . Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases. Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, 2015, 100, 33-65.
http://dx.doi.org/10.1016/bs.apcsb.2015.06.006
---------- CHICAGO ----------
Romero, J.M., Martin, M., Ramirez, C.L., Dumas, V.G., Marti, M.A., Karabencheva-Christova T. "Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases" . Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, 2015 100 (2015) : 33-65.
http://dx.doi.org/10.1016/bs.apcsb.2015.06.006
---------- MLA ----------
Romero, J.M., Martin, M., Ramirez, C.L., Dumas, V.G., Marti, M.A., Karabencheva-Christova T. "Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases" . Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, 2015, vol. 100, 2015, pp. 33-65.
http://dx.doi.org/10.1016/bs.apcsb.2015.06.006
---------- VANCOUVER ----------
Romero, J.M., Martin, M., Ramirez, C.L., Dumas, V.G., Marti, M.A., Karabencheva-Christova T. Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases. Adv. Protein Chem. Struct. Biol. 2015;100:33-65.
http://dx.doi.org/10.1016/bs.apcsb.2015.06.006