title: Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine.
abstract: 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.
authors.affiliation: Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
authors.forename: Matej
authors.initials: M
authors.lastname: Repič
authors.forename: Robert
authors.initials: R
authors.lastname: Vianello
authors.forename: Miha
authors.initials: M
authors.lastname: Purg
authors.forename: Fernanda
authors.initials: F
authors.lastname: Duarte
authors.forename: Paul
authors.initials: P
authors.lastname: Bauer
authors.forename: Shina C L
authors.initials: SC
authors.lastname: Kamerlin
authors.forename: Janez
authors.initials: J
authors.lastname: Mavri
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D016000:Cluster Analysis; D030562:Databases, Protein; D004298:Dopamine / Q000737:chemistry / Q000378:metabolism*; D004735:Energy Transfer; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008995:Monoamine Oxidase / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D005182:Flavin-Adenine Dinucleotide; D008995:Monoamine Oxidase; D008239:Lysine; D004298:Dopamine
keywords: computational chemistry; enzyme catalysis; flavins; kinetics; neurotransmitters