Article
Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine
Matej Repič,
Robert Vianello,
Miha Purg,
Fernanda Duarte,
Paul Bauer,
Shina C. L. Kamerlin,
Janez Mavri,
Matej Repič
Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Search for more papers by this authorRobert Vianello
Quantum Organic Chemistry Group, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
Search for more papers by this authorMiha Purg
Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Search for more papers by this authorFernanda Duarte
Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden
Search for more papers by this authorPaul Bauer
Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden
Search for more papers by this authorCorresponding Author
Shina C. L. Kamerlin
Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden
Correspondence to: Shina C. L. Kamerlin, Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden. E-mail: [email protected] and Janez Mavri, Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia. E-mail: [email protected]Search for more papers by this authorCorresponding Author
Janez Mavri
Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Correspondence to: Shina C. L. Kamerlin, Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden. E-mail: [email protected] and Janez Mavri, Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia. E-mail: [email protected]Search for more papers by this authorMatej Repič,
Robert Vianello,
Miha Purg,
Fernanda Duarte,
Paul Bauer,
Shina C. L. Kamerlin,
Janez Mavri,
Matej Repič
Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Search for more papers by this authorRobert Vianello
Quantum Organic Chemistry Group, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
Search for more papers by this authorMiha Purg
Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Search for more papers by this authorFernanda Duarte
Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden
Search for more papers by this authorPaul Bauer
Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden
Search for more papers by this authorCorresponding Author
Shina C. L. Kamerlin
Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden
Correspondence to: Shina C. L. Kamerlin, Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden. E-mail: [email protected] and Janez Mavri, Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia. E-mail: [email protected]Search for more papers by this authorCorresponding Author
Janez Mavri
Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
Correspondence to: Shina C. L. Kamerlin, Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, SE-751 24 Uppsala, Sweden. E-mail: [email protected] and Janez Mavri, Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia. E-mail: [email protected]Search for more papers by this authorABSTRACT
Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines such as dopamine, serotonin and noradrenaline. In this work, we present a comprehensive study of the rate-limiting step of dopamine degradation by MAO B, which consists in the hydride transfer from the methylene group of the substrate to the flavin moiety of the FAD prosthetic group. This article builds on our previous quantum chemical study of the same reaction using a cluster model (Vianello et al., Eur J Org Chem 2012; 7057), but now considering the full dimensionality of the hydrated enzyme with extensive configurational sampling. We show that MAO B is specifically tuned to catalyze the hydride transfer step from the substrate to the flavin moiety of the FAD prosthetic group and that it lowers the activation barrier by 12.3 kcal mol−1 compared to the same reaction in aqueous solution, a rate enhancement of more than nine orders of magnitude. Taking into account the deprotonation of the substrate prior to the hydride transfer reaction, the activation barrier in the enzyme is calculated to be 16.1 kcal mol−1, in excellent agreement with the experimental value of 16.5 kcal mol−1. Additionally, we demonstrate that the protonation state of the active site residue Lys296 does not have an influence on the hydride transfer reaction. Proteins 2014; 82:3347–3355. © 2014 Wiley Periodicals, Inc.
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