1
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Fitzpatrick PF. Conservation of mechanism in flavoprotein-catalyzed amine oxidation. Arch Biochem Biophys 2025; 764:110242. [PMID: 39613287 DOI: 10.1016/j.abb.2024.110242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 11/19/2024] [Accepted: 11/27/2024] [Indexed: 12/01/2024]
Abstract
The goals of this presentation are to summarize the present understanding of the mechanism of amine oxidation by flavoproteins and to examine the possibility that a member of the monoamine oxidase family catalyzes oxidation of a carbon-carbon bond. In the discussion of mechanism, the emphasis is on the protonation state of the amine substrate, since the once-controversial mechanism of oxidation appears to be resolved. The argument will be made that flavoproteins catalyzing amine oxidation preferentially bind the form of the substrate in which the reacting nitrogen is uncharged. The reaction of a member of L-6-hydroxynicotine oxidase, which has been proposed to oxidize a carbon-carbon bond in its substrate during nicotine catabolism, is then discussed. Analysis of the reaction product establishes that the enzyme catalyzes oxidation of a carbon-nitrogen. The effects of site-directed mutagenesis and analysis of the substrate specificity identify the key residues for substrate binding.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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2
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Khangkhachit W, Shirai S, Iwasaki G, Asano Y. Imine Synthesis by Engineered d-Amino Acid Oxidase from Porcine Kidney. ACS OMEGA 2025; 10:2212-2221. [PMID: 39866613 PMCID: PMC11755151 DOI: 10.1021/acsomega.4c09160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 12/28/2024] [Accepted: 12/30/2024] [Indexed: 01/28/2025]
Abstract
Various symmetric and asymmetric imines were synthesized using the novel amine oxidase, obtained as variants of d-amino acid oxidase (pkDAO) from porcine kidney (Y228L/R283G) and (I230A/R283G). Active primary imines produced as intermediates in the oxidation of methylbenzylamine (MBA) derivatives were trapped by aliphatic, aromatic amines and diamines as nucleophiles forming new imines. (R)-Fluoro-MBA was the best substrate for symmetric imine synthesis, providing almost stoichiometric conversion (100 mM) and achieving nearly 100% yield. Several (R)-MBA derivatives were used as substrates, and the corresponding symmetric and asymmetric imines were synthesized. The turnover number of N-benzylidenebenzylamine synthesis from benzylamine was calculated to be 1.61 × 105 (number of moles of reactant consumed per mole of catalyst/h), which is more than 103 higher than metal-, photo-, and organo-catalysts reported so far. The diastereomers of bis(1-phenylethyl)amine, the reduced products of (R)-MBA, were identified as a mixture of 84.9% (R,R)-bis(1-phenylethyl)amine and 15.1% (R,S)-bis(1-phenylethyl)amine to consider the reaction mechanism.
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Affiliation(s)
| | - Seiya Shirai
- Biotechnology Research Center
and Department of Biotechnology, Toyama
Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Genji Iwasaki
- Biotechnology Research Center
and Department of Biotechnology, Toyama
Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center
and Department of Biotechnology, Toyama
Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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3
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Rajić M, Prah A, Stare J. Deciphering the Two-Step Hydride Mechanism of Monoamine Oxidase Flavoenzymes. ACS OMEGA 2024; 9:43046-43057. [PMID: 39464429 PMCID: PMC11500147 DOI: 10.1021/acsomega.4c06575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/29/2024]
Abstract
The complete two-step hydride transfer mechanism of amine oxidation involved in the metabolism of monoamine neurotransmitters was scrutinized by DFT calculations. In living organisms, this process is catalyzed by monoamine oxidase enzymes. Herein, we focus on some intriguing aspects of the reaction that may have been previously noticed but have not been clarified to date. The first step of the reaction includes the C-H bond cleavage on the methylene group vicinal to the amino group of the monoamine substrate and the subsequent transfer of hydrogen to the N5 atom of the flavin prosthetic group of the enzyme. We confirmed the nature of this step to be hydride transfer by evaluation of the pertinent HOMO-LUMO gap together with analysis of orbital contours alongside the intrinsic reaction coordinate profile. Next, we investigated the rather peculiar intermediate adduct that may form between the amine substrate and the flavin molecule, featuring an unusually long C-N bond of ∼1.62 Å. Although this bond is quite stable in the gas phase, the presence of just a few explicit water molecules facilitates its dissociation almost without energy input so that the amine-flavin intermediate can form an ionic pair instead. We attribute the existence of the unusual C-N bond to a fragile balance between opposing electronic structure effects, as evaluated by the natural bond orbital analysis. In line with this, the intermediate in the solution or in the enzyme active site can exist in two energetically almost equivalent forms, namely, as a covalently bound complex or as an ion pair, as suggested by previous studies. Finally, we characterized the transformation of the intermediate to the fully reduced flavin and imine products via proton transfer from the amino group to the flavin N1 atom, completing the reductive part of the catalytic cycle. Although we found that explicit solvation substantially boosts the kinetics of this step, the corresponding barrier is significantly lower than that in the hydride transfer step, confirming hydrogen abstraction as the rate-limiting step of amine oxidation and validating the two-step hydride transfer mechanism of monoamine oxidases.
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Affiliation(s)
- Martina Rajić
- Theory Department, Laboratory for Computational
Biochemistry and Drug Design, National Institute
of Chemistry, Hajdrihova
19, Ljubljana SI-1000, Slovenia
| | - Alja Prah
- Theory Department, Laboratory for Computational
Biochemistry and Drug Design, National Institute
of Chemistry, Hajdrihova
19, Ljubljana SI-1000, Slovenia
| | - Jernej Stare
- Theory Department, Laboratory for Computational
Biochemistry and Drug Design, National Institute
of Chemistry, Hajdrihova
19, Ljubljana SI-1000, Slovenia
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4
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Yildiz I. Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase. Chemphyschem 2023; 24:e202300431. [PMID: 37540527 DOI: 10.1002/cphc.202300431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/05/2023]
Abstract
D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.
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Affiliation(s)
- Ibrahim Yildiz
- Khalifa University, Chemistry Department and Applied Material Chemistry Center (AMCC), PO Box, 127788, Abu Dhabi, UAE
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5
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Sobrado P, Neira JL. Paul F. Fitzpatrick: A life of editorial duties and elucidating the mechanism of enzyme action. Arch Biochem Biophys 2023; 742:109635. [PMID: 37209767 DOI: 10.1016/j.abb.2023.109635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023]
Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, VA, 24061, USA.
| | - José Luis Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018, Zaragoza, Spain.
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6
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Brunner syndrome caused by point mutation explained by multiscale simulation of enzyme reaction. Sci Rep 2022; 12:21889. [PMID: 36536002 PMCID: PMC9763434 DOI: 10.1038/s41598-022-26296-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Brunner syndrome is a disorder characterized by intellectual disability and impulsive, aggressive behavior associated with deficient function of the monoamine oxidase A (MAO-A) enzyme. These symptoms (along with particularly high serotonin levels) have been reported in patients with two missense variants in MAO-A (p.R45W and p.E446K). Herein, we report molecular simulations of the rate-limiting step of MAO-A-catalyzed serotonin degradation for these variants. We found that the R45W mutation causes a 6000-fold slowdown of enzymatic function, whereas the E446K mutation causes a 450-fold reduction of serotonin degradation rate, both of which are practically equivalent to a gene knockout. In addition, we thoroughly compared the influence of enzyme electrostatics on the catalytic function of both the wild type MAO-A and the p.R45W variant relative to the wild type enzyme, revealing that the mutation represents a significant electrostatic perturbation that contributes to the barrier increase. Understanding genetic disorders is closely linked to understanding the associated chemical mechanisms, and our research represents a novel attempt to bridge the gap between clinical genetics and the underlying chemical physics.
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7
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Prah A, Gavranić T, Perdih A, Sollner Dolenc M, Mavri J. Computational Insights into β-Carboline Inhibition of Monoamine Oxidase A. Molecules 2022; 27:molecules27196711. [PMID: 36235246 PMCID: PMC9571839 DOI: 10.3390/molecules27196711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2022] Open
Abstract
Monoamine oxidases (MAOs) are an important group of enzymes involved in the degradation of neurotransmitters and their imbalanced mode of action may lead to the development of various neuropsychiatric or neurodegenerative disorders. In this work, we report the results of an in-depth computational study in which we performed a static and a dynamic analysis of a series of substituted β-carboline natural products, found mainly in roasted coffee and tobacco smoke, that bind to the active site of the MAO-A isoform. By applying molecular docking in conjunction with structure-based pharmacophores and molecular dynamics simulations coupled with dynamic pharmacophores, we extensively investigated the geometric aspects of MAO-A binding. To gain insight into the energetics of binding, we used the linear interaction energy (LIE) method and determined the key anchors that allow productive β-carboline binding to MAO-A. The results presented herein could be applied in the rational structure-based design and optimization of β-carbolines towards preclinical candidates that would target the MAO-A enzyme and would be applicable especially in the treatment of mental disorders such as depression.
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Affiliation(s)
- Alja Prah
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Tanja Gavranić
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | | | - Janez Mavri
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Correspondence:
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8
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Prah A, Mavri J, Stare J. An electrostatic duel: subtle differences in the catalytic performance of monoamine oxidase A and B isoenzymes elucidated at the residue level using quantum computations. Phys Chem Chem Phys 2021; 23:26459-26467. [PMID: 34806105 DOI: 10.1039/d1cp03993h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of the immense catalytic power of enzymes remains one of the biggest unresolved questions in biochemistry, with electrostatics being one of the main contenders. Herein, we report results that not only confirm that electrostatics is the driving force behind enzyme catalysis, but also that it is capable of tuning subtle differences in the catalytic performance between structurally similar enzymes, as demonstrated using the example of isoenzymes, monoamine oxidases A and B. Using our own computationally efficient multiscale model [A. Prah, et al., ACS Catal., 2019, 9, 1231] we analyzed the rate-limiting step of the reaction between phenylethylamine and both isoenzymes and deduced that the electrostatic environment provided by isoenzyme B has a perceivably higher catalytic influence on all the considered parameters of the reaction (energy barrier, charge transfer, dipole moment, and HOMO-LUMO gap). This is in full agreement with the available experimental kinetic data and with our own simulations of the reaction in question. In-depth analysis of individual amino acid contributions of both isoenzymes to the barrier (based on the interaction between the electric field provided by the enzyme and the dipole moment of the reacting moiety) shows that the majority of the difference between the isoenzymes can be attributed to a small number of sizable differences between the aligned amino acid pairs, whereas in most of the pairs the difference in contribution to the barrier is vanishingly small. These results suggest that electrostatics largely controls the substrate selectivity of enzymes and validates our approach as being capable of discerning fine nuances in the selectivity of structurally related isoenzymes.
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Affiliation(s)
- Alja Prah
- Theory Department, National Institute of Chemistry, Slovenia. .,University of Ljubljana, Faculty of Pharmacy, Slovenia
| | - Janez Mavri
- Theory Department, National Institute of Chemistry, Slovenia.
| | - Jernej Stare
- Theory Department, National Institute of Chemistry, Slovenia.
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9
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Kiss DJ, Ferenczy GG. A detailed mechanism of the oxidative half-reaction of d-amino acid oxidase: another route for flavin oxidation. Org Biomol Chem 2020; 17:7973-7984. [PMID: 31407761 DOI: 10.1039/c9ob00975b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
d-Amino acid oxidase (DAAO) is a flavoenzyme whose inhibition is expected to have therapeutic potential in schizophrenia. DAAO catalyses hydride transfer from the substrate to the flavin in the reductive half-reaction, and the flavin is reoxidized by O2 in the oxidative half-reaction. Quantum mechanical/molecular mechanical calculations were performed and their results together with available experimental information were used to elucidate the detailed mechanism of the oxidative half-reaction. The reaction starts with a single electron transfer from FAD to O2, followed by triplet-singlet transition. FAD oxidation is completed by a proton coupled electron transfer to the oxygen species and the reaction terminates with H2O2 formation by proton transfer from the oxidized substrate to the oxygen species via a chain of water molecules. The substrate plays a double role by facilitating the first electron transfer and by providing a proton in the last step. The mechanism differs from the oxidative half-reaction of other oxidases.
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Affiliation(s)
- Dóra Judit Kiss
- Doctoral School of Chemistry, Eötvös Loránd University, Pázmány s 1/A, H-1117, Budapest, Hungary. and Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt 2, H-1117, Budapest, Hungary.
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt 2, H-1117, Budapest, Hungary.
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10
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Shoji M, Abe Y, Boero M, Shigeta Y, Nishiya Y. Reaction mechanism of N-cyclopropylglycine oxidation by monomeric sarcosine oxidase. Phys Chem Chem Phys 2020; 22:16552-16561. [DOI: 10.1039/d0cp01679a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction mechanism of monomeric sarcosine oxidase (MSOX) with N-cyclopropylglycine (CPG) is unravelled at the theoretical level of the hybrid quantum mechanics/molecular mechanical (QM/MM) method.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
- JST-PRESTO
| | | | - Mauro Boero
- University of Strasbourg
- Institut de Physique et Chimie des Matériaux de Strasbourg
- CNRS
- UMR 7504
- France
| | - Yasuteru Shigeta
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Yoshiaki Nishiya
- Department of Life Science
- Faculty of Science and Engineering
- Setsunan University
- Osaka 572-8508
- Japan
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11
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Prah A, Ogrin P, Mavri J, Stare J. Nuclear quantum effects in enzymatic reactions: simulation of the kinetic isotope effect of phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2020; 22:6838-6847. [DOI: 10.1039/d0cp00131g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By using computational techniques for quantizing nuclear motion one can accurately reproduce kinetic isotope effect of enzymatic reactions, as demonstrated for phenylethylamine oxidation catalyzed by the monoamine oxidase A enzyme.
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Affiliation(s)
- Alja Prah
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Peter Ogrin
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Janez Mavri
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jernej Stare
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
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12
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Wanninayake US, Subedi B, Fitzpatrick PF. pH and deuterium isotope effects on the reaction of trimethylamine dehydrogenase with dimethylamine. Arch Biochem Biophys 2019; 676:108136. [PMID: 31604072 DOI: 10.1016/j.abb.2019.108136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 11/24/2022]
Abstract
The flavoprotein trimethylamine dehydrogenase is a member of a small class of flavoproteins that catalyze amine oxidation and transfer the electrons through an Fe/S center to an external oxidant. The mechanism of amine oxidation by this family of enzymes has not been established. Here, we describe the use of pH and kinetic isotope effects with the slow substrate dimethylamine to study the mechanism. The data are consistent with the neutral amine being the form of the substrate that binds productively at the pH optimum, since the pKa seen in the kcat/Kamine pH profile for a group that must be unprotonated matches the pKa of dimethylamine. The D(kcat/Kamine) value decreases to unity as the pH decreases. This suggests the presence of an alternative pathway at low pH, in which the protonated substrate binds and is then deprotonated by an active-site residue prior to oxidation. The kcat and Dkcat values both decrease to limiting values at low pH with similar pKa values. This is consistent with a step other than amine oxidation becoming rate-limiting for turnover.
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Affiliation(s)
- Udayanga S Wanninayake
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Bishnu Subedi
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA.
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13
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Jones HBL, Crean RM, Mullen A, Kendrick EG, Bull SD, Wells SA, Carbery DR, MacMillan F, van der Kamp MW, Pudney CR. Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B. Biochemistry 2019; 58:2362-2372. [PMID: 30964996 DOI: 10.1021/acs.biochem.9b00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is an increasing realization that structure-based drug design may show improved success by understanding the ensemble of conformations accessible to an enzyme and how the environment affects this ensemble. Human monoamine oxidase B (MAO-B) catalyzes the oxidation of amines and is inhibited for the treatment of both Parkinson's disease and depression. Despite its clinical importance, its catalytic mechanism remains unclear, and routes to drugging this target would be valuable. Evidence of a radical in either the transition state or the resting state of MAO-B is present throughout the literature and is suggested to be a flavin semiquinone, a tyrosyl radical, or both. Here we see evidence of a resting-state flavin semiquinone, via absorption redox studies and electron paramagnetic resonance, suggesting that the anionic semiquinone is biologically relevant. On the basis of enzyme kinetic studies, enzyme variants, and molecular dynamics simulations, we find evidence for the importance of the membrane environment in mediating the activity of MAO-B and that this mediation is related to the protein dynamics of MAO-B. Further, our MD simulations identify a hitherto undescribed entrance for substrate binding, membrane modulated substrate access, and indications for half-site reactivity: only one active site is accessible to binding at a time. Our study combines both experimental and computational evidence to illustrate the subtle interplay between enzyme activity and protein dynamics and the immediate membrane environment. Understanding key biomedical enzymes to this level of detail will be crucial to inform strategies (and binding sites) for rational drug design for these targets.
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Affiliation(s)
| | | | - Anna Mullen
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | | | | | | | | | - Fraser MacMillan
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry , University of Bristol , Biomedical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
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14
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Szilágyi B, Ferenczy GG, Keserű GM. Drug discovery strategies and the preclinical development of D-amino-acid oxidase inhibitors as antipsychotic therapies. Expert Opin Drug Discov 2018; 13:973-982. [DOI: 10.1080/17460441.2018.1524459] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Bence Szilágyi
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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15
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Discovery of d-amino acid oxidase inhibitors based on virtual screening against the lid-open enzyme conformation. Bioorg Med Chem Lett 2018; 28:1693-1698. [DOI: 10.1016/j.bmcl.2018.04.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 11/20/2022]
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16
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Pregeljc D, Jug U, Mavri J, Stare J. Why does the Y326I mutant of monoamine oxidase B decompose an endogenous amphetamine at a slower rate than the wild type enzyme? Reaction step elucidated by multiscale molecular simulations. Phys Chem Chem Phys 2018; 20:4181-4188. [PMID: 29360121 DOI: 10.1039/c7cp07069a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This work investigates the Y326I point mutation effect on the kinetics of oxidative deamination of phenylethylamine (PEA) catalyzed by the monoamine oxidase B (MAO B) enzyme. PEA is a neuromodulator capable of affecting the plasticity of the brain and is responsible for the mood enhancing effect caused by physical exercise. Due to a similar functionality, PEA is often regarded as an endogenous amphetamine. The rate limiting step of the deamination was simulated at the multiscale level, employing the Empirical Valence Bond approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field. A comparison of the reaction free energy profiles delivered by simulation of the reaction in the wild type MAO B and its Y326I mutant yields an increase in the barrier by 1.06 kcal mol-1 upon mutation, corresponding to a roughly 6-fold decrease in the reaction rate. This is in excellent agreement with the experimental kinetic studies. Inspection of simulation trajectories reveals possible sources of the point mutation effect, namely vanishing favorable electrostatic interactions between PEA and a Tyr326 side chain and an increased amount of water molecules at the active site due to the replacement of tyrosine by a less spacious isoleucine residue, thereby increasing the dielectric shielding of the catalytic environment provided by the enzyme.
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Affiliation(s)
- Domen Pregeljc
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia.
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17
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Chow C, Hegde S, Blanchard JS. Mechanistic Characterization of Escherichia coli l-Aspartate Oxidase from Kinetic Isotope Effects. Biochemistry 2017; 56:4044-4052. [PMID: 28700220 DOI: 10.1021/acs.biochem.7b00307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
l-Aspartate oxidase, encoded by the nadB gene, is the first enzyme in the de novo synthesis of NAD+ in bacteria. This FAD-dependent enzyme catalyzes the oxidation of l-aspartate to generate iminoaspartate and reduced flavin. Distinct from most amino acid oxidases, it can use either molecular oxygen or fumarate to reoxidize the reduced enzyme. Sequence alignments and the three-dimensional crystal structure have revealed that the overall fold and catalytic residues of NadB closely resemble those of the succinate dehydrogenase/fumarate reductase family rather than those of the prototypical d-amino acid oxidases. This suggests that the enzyme can catalyze amino acid oxidation via typical amino acid oxidase chemistry, involving the removal of protons from the α-amino group and the transfer of the hydride from C2, or potentially deprotonation at C3 followed by transfer of the hydride from C2, similar to chemistry occurring during succinate oxidation. We have investigated this potential mechanistic ambiguity using a combination of primary, solvent, and multiple deuterium kinetic isotope effects in steady state experiments. Our results indicate that the chemistry is similar to that of typical amino acid oxidases in which the transfer of the hydride from C2 of l-aspartate to FAD is rate-limiting and occurs in a concerted manner with respect to deprotonation of the α-amine. Together with previous kinetic and structural data, we propose that NadB has structurally evolved from succinate dehydrogenase/fumarate reductase-type enzymes to gain the new functionality of oxidizing amino acids while retaining the ability to reduce fumarate.
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Affiliation(s)
- Carmen Chow
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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18
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Trimmer EE, Wanninayake US, Fitzpatrick PF. Mechanistic Studies of an Amine Oxidase Derived from d-Amino Acid Oxidase. Biochemistry 2017; 56:2024-2030. [PMID: 28355481 DOI: 10.1021/acs.biochem.7b00161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The flavoprotein d-amino acid oxidase has long served as a paradigm for understanding the mechanism of oxidation of amino acids by flavoproteins. Recently, a mutant d-amino acid oxidase (Y228L/R283G) that catalyzed the oxidation of amines rather than amino acids was described [Yasukawa, K., et al. (2014) Angew. Chem., Int. Ed. 53, 4428-4431]. We describe here the use of pH and kinetic isotope effects with (R)-α-methylbenzylamine as a substrate to determine whether the mutant enzyme utilizes the same catalytic mechanism as the wild-type enzyme. The effects of pH on the steady-state and rapid-reaction kinetics establish that the neutral amine is the substrate, while an active-site residue, likely Tyr224, must be uncharged for productive binding. There is no solvent isotope effect on the kcat/Km value for the amine, consistent with the neutral amine being the substrate. The deuterium isotope effect on the kcat/Km value is pH-independent, with an average value of 5.3, similar to values found with amino acids as substrates for the wild-type enzyme and establishing that there is no commitment to catalysis with this substrate. The kcat/KO2 value is similar to that seen with amino acids as the substrate, consistent with the oxidative half-reaction being unperturbed by the mutation and with flavin oxidation preceding product release. All of the data are consistent with the mutant enzyme utilizing the same mechanism as the wild-type enzyme, transfer of hydride from the neutral amine to the flavin.
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Affiliation(s)
- Elizabeth E Trimmer
- Department of Chemistry, Grinnell College , Grinnell, Iowa 50112, United States
| | - Udayanga S Wanninayake
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center , San Antonio, Texas 78229, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center , San Antonio, Texas 78229, United States
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19
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Stare J. Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27894a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.
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Affiliation(s)
- Jernej Stare
- Department of Computational Biochemistry and Drug Design
- National Institute of Chemistry
- SI-1000 Ljubljana
- Slovenia
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20
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Zhang S, Wei Q, Shang Y, Zhang Q, Wang Q. d-Serine enzymatic metabolism induced formation of a powder-remoldable PAAM–CS hydrogel. Chem Commun (Camb) 2017; 53:12270-12273. [PMID: 29067380 DOI: 10.1039/c7cc06733j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metabolism of d-serine by d-amino acid oxidase was developed to induce radical polymerization and formation of a powder-remoldable PAAM–CS hydrogel.
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Affiliation(s)
- Shuang Zhang
- School of Chemical Science and Engineering, Tongji University
- Shanghai 200092
- China
| | - Qingcong Wei
- School of Chemistry and Chemical Engineering, Henan Normal University
- Xinxiang 453007
- China
| | - Yinghui Shang
- School of Chemical Science and Engineering, Tongji University
- Shanghai 200092
- China
| | - Qi Zhang
- School of Chemical Science and Engineering, Tongji University
- Shanghai 200092
- China
| | - Qigang Wang
- School of Chemical Science and Engineering, Tongji University
- Shanghai 200092
- China
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21
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Abe Y, Shoji M, Nishiya Y, Aiba H, Kishimoto T, Kitaura K. The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods. Phys Chem Chem Phys 2017; 19:9811-9822. [DOI: 10.1039/c6cp08172j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monomeric sarcosine oxidase (MSOX) is a flavoprotein that oxidizes sarcosine to the corresponding imine product and is widely used in clinical diagnostics to test renal function.
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Affiliation(s)
| | - Mitsuo Shoji
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Yoshiaki Nishiya
- Department of Life Science
- Faculty of Science and Engineering
- Setsunan University
- Neyagawa
- Japan
| | - Hiroshi Aiba
- Tsuruga Institute of Biotechnology
- TOYOBO Co., Ltd
- Tsuruga
- Japan
| | | | - Kazuo Kitaura
- Fukui Institute for Fundamental Chemistry
- Kyoto University
- Sakyou-ku
- Japan
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22
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Tormos JR, Suarez MB, Fitzpatrick PF. 13C kinetic isotope effects on the reaction of a flavin amine oxidase determined from whole molecule isotope effects. Arch Biochem Biophys 2016; 612:115-119. [PMID: 27815088 PMCID: PMC5257176 DOI: 10.1016/j.abb.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
A large number of flavoproteins catalyze the oxidation of amines. Because of the importance of these enzymes in metabolism, their mechanisms have previously been studied using deuterium, nitrogen, and solvent isotope effects. While these results have been valuable for computational studies to distinguish among proposed mechanisms, a measure of the change at the reacting carbon has been lacking. We describe here the measurement of a 13C kinetic isotope effect for a representative amine oxidase, polyamine oxidase. The isotope effect was determined by analysis of the isotopic composition of the unlabeled substrate, N, N'-dibenzyl-1,4-diaminopropane, to obtain a pH-independent value of 1.025. The availability of a 13C isotope effect for flavoprotein-catalyzed amine oxidation provides the first measure of the change in bond order at the carbon involved in this carbon-hydrogen bond cleavage and will be of value to understanding the transition state structure for this class of enzymes.
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Affiliation(s)
- José R Tormos
- Department of Chemistry and Biochemistry, St. Mary's University, San Antonio, TX 78228, United States
| | - Marina B Suarez
- Department of Geological Sciences, University of Texas-San Antonio, San Antonio, TX 78249, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, United States.
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23
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Mauve C, Giraud N, Boex-Fontvieille ERA, Antheaume I, Tea I, Tcherkez G. Kinetic commitment in the catalysis of glutamine synthesis by GS1 from Arabidopsis using 14N/ 15N and solvent isotope effects. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:203-211. [PMID: 27448794 DOI: 10.1016/j.plaphy.2016.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/12/2016] [Indexed: 05/26/2023]
Abstract
Glutamine synthetase (GS, EC 6.3.1.2) catalyzes the production of glutamine from glutamate, ammonium and ATP. Although being essential in plants for N assimilation and recycling, kinetic commitments and transition states of the reaction have not been clearly established yet. Here, we examined 12C/13C, 14N/15N and H2O/D2O isotope effects in Arabidopsis GS1 catalysis and compared to the prokaryotic (Escherichia coli) enzyme. A14N/15N isotope effect (15V/K ≈ 1.015, with respect to substrate NH4+) was observed in the prokaryotic enzyme, indicating that ammonium utilization (deprotonation and/or amidation) was partially rate-limiting. In the plant enzyme, the isotope effect was inverse (15V/K = 0.965), suggesting that the reaction intermediate is involved in an amidation-deamidation equilibrium favoring 15N. There was no 12C/13C kinetic isotope effect (13V/K = 1.000), suggesting that the amidation step of the catalytic cycle involves a transition state with minimal alteration of overall force constants at the C-5 carbon. Surprisingly, the solvent isotope effect was found to be inverse, that is, with a higher turn-over rate in heavy water (DV ≈ 0.5), showing that restructuration of the active site due to displacement of H2O by D2O facilitates the processing of intermediates.
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Affiliation(s)
- Caroline Mauve
- Plateforme Métabolisme-Métabolome, Institute of Plant Science of Saclay (IPS2), Université Paris-Sud, 91405, Orsay Cedex, France
| | - Nicolas Giraud
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris-Sud, 91405, Orsay Cedex, France
| | - Edouard R A Boex-Fontvieille
- Laboratoire de Biotechnologies végétales appliquées aux Plantes aromatiques et médicinales, Université Jean Monnet, 42023, Saint Etienne Cedex 2, France
| | - Ingrid Antheaume
- Laboratoire de Géologie de Lyon Terre, Planètes, Environnement. UMR 5276, Université de Lyon, 69361, Lyon Cedex 07, France
| | - Illa Tea
- Chimie Et Interdisciplinarité: Synthèse, Analyse, Modélisation, UMR 6230, Université de Nantes, Nantes Cedex 3, 44322, France; John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, Australian National University, Canberra ACT, 2601, Australia
| | - Guillaume Tcherkez
- Research School of Biology, ANU College of Medicine, Biology and Environment, Australian National University, Canberra ACT, 2601, Australia.
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24
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Vianello R, Domene C, Mavri J. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes. Front Neurosci 2016; 10:327. [PMID: 27471444 PMCID: PMC4945635 DOI: 10.3389/fnins.2016.00327] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/28/2016] [Indexed: 01/17/2023] Open
Abstract
HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic activities and their inhibition. As an illustrative example, the later will focus on the monoamine oxidase family of enzymes, which catalyze the degradation of amine neurotransmitters in various parts of the brain, the imbalance of which is associated with the development and progression of a range of neurodegenerative disorders. Inhibitors that act mainly on MAO A are used in the treatment of depression, due to their ability to raise serotonin concentrations, while MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Our results give strong support that both MAO isoforms, A and B, operate through the hydride transfer mechanism. Relevance of MAO catalyzed reactions and MAO inhibition in the context of neurodegeneration will be discussed.
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Affiliation(s)
- Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković InstituteZagreb, Croatia
| | - Carmen Domene
- Department of Chemistry, King's College LondonLondon, UK
- Chemistry Research Laboratory, University of OxfordOxford, UK
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of ChemistryLjubljana, Slovenia
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25
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Oanca G, Purg M, Mavri J, Shih JC, Stare J. Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2016; 18:13346-56. [PMID: 27121693 DOI: 10.1039/c6cp00098c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier.
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Affiliation(s)
- Gabriel Oanca
- Laboratory of Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia.
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26
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Mould DP, McGonagle AE, Wiseman DH, Williams EL, Jordan AM. Reversible inhibitors of LSD1 as therapeutic agents in acute myeloid leukemia: clinical significance and progress to date. Med Res Rev 2015; 35:586-618. [PMID: 25418875 DOI: 10.1002/med.21334] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the 10 years since the discovery of lysine-specific demethylase 1 (LSD1), this epigenetic eraser has emerged as an important target of interest in oncology. More specifically, research has demonstrated that it plays an essential role in the self-renewal of leukemic stem cells in acute myeloid leukemia (AML). This review will cover clinical aspects of AML, the role of epigenetics in the disease, and discuss the research that led to the first irreversible inhibitors of LSD1 entering clinical trials for the treatment of AML in 2014. We also review recent achievements and progress in the development of potent and selective reversible inhibitors of LSD1. These compounds differ in their mode of action from tranylcypromine derivatives and could facilitate novel biochemical studies to probe the pathways mediated by LSD1. In this review, we will critically evaluate the strengths and weaknesses of published series of reversible LSD1 inhibitors. Overall, while the development of reversible inhibitors to date has been less fruitful than that of irreversible inhibitors, there is still the possibility for their use to facilitate further research into the roles and functions of LSD1 and to expand the therapeutic applications of LSD1 inhibitors in the clinic.
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Affiliation(s)
- Daniel P Mould
- Department of Drug Discovery, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
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27
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Zenn RK, Abad E, Kästner J. Influence of the Environment on the Oxidative Deamination of p-Substituted Benzylamines in Monoamine Oxidase. J Phys Chem B 2015; 119:3678-86. [DOI: 10.1021/jp512470a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Roland K. Zenn
- Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Enrique Abad
- Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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28
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Dellero Y, Mauve C, Boex-Fontvieille E, Flesch V, Jossier M, Tcherkez G, Hodges M. Experimental evidence for a hydride transfer mechanism in plant glycolate oxidase catalysis. J Biol Chem 2014; 290:1689-98. [PMID: 25416784 DOI: 10.1074/jbc.m114.618629] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In plants, glycolate oxidase is involved in the photorespiratory cycle, one of the major fluxes at the global scale. To clarify both the nature of the mechanism and possible differences in glycolate oxidase enzyme chemistry from C3 and C4 plant species, we analyzed kinetic parameters of purified recombinant C3 (Arabidopsis thaliana) and C4 (Zea mays) plant enzymes and compared isotope effects using natural and deuterated glycolate in either natural or deuterated solvent. The (12)C/(13)C isotope effect was also investigated for each plant glycolate oxidase protein by measuring the (13)C natural abundance in glycolate using natural or deuterated glycolate as a substrate. Our results suggest that several elemental steps were associated with an hydrogen/deuterium isotope effect and that glycolate α-deprotonation itself was only partially rate-limiting. Calculations of commitment factors from observed kinetic isotope effect values support a hydride transfer mechanism. No significant differences were seen between C3 and C4 enzymes.
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Affiliation(s)
- Younès Dellero
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Caroline Mauve
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France, Plateforme Métabolisme-Métabolome, Saclay Plant Sciences, Institut de Biologie des Plantes, Bâtiment 630, 91405 Orsay Cedex, France, and
| | - Edouard Boex-Fontvieille
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Valérie Flesch
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Mathieu Jossier
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Guillaume Tcherkez
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France, Plateforme Métabolisme-Métabolome, Saclay Plant Sciences, Institut de Biologie des Plantes, Bâtiment 630, 91405 Orsay Cedex, France, and Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Michael Hodges
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France,
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29
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Fitzpatrick PF. Combining solvent isotope effects with substrate isotope effects in mechanistic studies of alcohol and amine oxidation by enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1746-55. [PMID: 25448013 DOI: 10.1016/j.bbapap.2014.10.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
Abstract
Oxidation of alcohols and amines is catalyzed by multiple families of flavin- and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78212, USA.
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30
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Abad E, Zenn RK, Kästner J. Reaction Mechanism of Monoamine Oxidase from QM/MM Calculations. J Phys Chem B 2013; 117:14238-46. [DOI: 10.1021/jp4061522] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Enrique Abad
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Roland K. Zenn
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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31
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Cheng C, Wu SC. A Combined Effect of Thermal and Enzymatic Racemization ford-Aspartic Acid tol-Aspartic Acid by High-Performance Liquid Chromatography Assay. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200200158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Flavin-dependent enzymes in cancer prevention. Int J Mol Sci 2012; 13:16751-68. [PMID: 23222680 PMCID: PMC3546718 DOI: 10.3390/ijms131216751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/26/2012] [Accepted: 12/04/2012] [Indexed: 12/13/2022] Open
Abstract
Statistical studies have demonstrated that various agents may reduce the risk of cancer's development. One of them is activity of flavin-dependent enzymes such as flavin-containing monooxygenase (FMO)(GS-OX1), FAD-dependent 5,10-methylenetetrahydrofolate reductase and flavin-dependent monoamine oxidase. In the last decade, many papers concerning their structure, reaction mechanism and role in the cancer prevention were published. In our work, we provide a more in-depth analysis of flavin-dependent enzymes and their contribution to the cancer prevention. We present the actual knowledge about the glucosinolate synthesized by flavin-containing monooxygenase (FMO)(GS-OX1) and its role in cancer prevention, discuss the influence of mutations in FAD-dependent 5,10-methylenetetrahydrofolate reductase on the cancer risk, and describe FAD as an important cofactor for the demethylation of histons. We also present our views on the role of riboflavin supplements in the prevention against cancer.
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33
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Tormos JR, Pozzi MH, Fitzpatrick PF. Mechanistic studies of the role of a conserved histidine in a mammalian polyamine oxidase. Arch Biochem Biophys 2012; 528:45-9. [PMID: 22959971 PMCID: PMC3483376 DOI: 10.1016/j.abb.2012.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 11/21/2022]
Abstract
Polyamine oxidases are peroxisomal flavoproteins that catalyze the oxidation of an endo carbon nitrogen bond of N1-acetylspermine in the catabolism of polyamines. While no structure has been reported for a mammalian polyamine oxidase, sequence alignments of polyamine oxidizing flavoproteins identify a conserved histidine residue. Based on the structure of a yeast polyamine oxidase, Saccharomyces cerevisiae Fms1, this residue has been proposed to hydrogen bond to the reactive nitrogen in the polyamine substrate. The corresponding histidine in mouse polyamine oxidase, His64, has been mutated to glutamine, asparagine, and alanine to determine if this residue plays a similar role in the mammalian enzymes. The kinetics of the mutant enzymes were examined with N1-acetylspermine and the slow substrates spermine and N,N'-dibenzyl-1,4-diaminobutane. On average the mutations result in a decrease of ~15-fold in the rate constant for amine oxidation. Rapid-reaction kinetic analyses established that amine oxidation is rate-limiting with spermine as substrate for the wild-type and mutant enzymes and for the H64N enzyme with N1-acetylspermine as substrate. The k(cat)/K(O(2)) value was unaffected by the mutations with N1-acetylspermine as substrate, but decreased ~55-fold with the two slower substrates. The results are consistent with this residue assisting in properly positioning the amine substrate for oxidation.
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Affiliation(s)
- José R. Tormos
- Department of Biochemistry, University of Texas Health Science Center, San Antonio TX 78229
| | | | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio TX 78229
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34
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Adachi MS, Taylor AB, Hart PJ, Fitzpatrick PF. Mechanistic and structural analyses of the roles of active site residues in yeast polyamine oxidase Fms1: characterization of the N195A and D94N enzymes. Biochemistry 2012; 51:8690-7. [PMID: 23034052 PMCID: PMC3548949 DOI: 10.1021/bi3011434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Flavoprotein Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine in the biosynthetic pathway for pantothenic acid. The same reaction is catalyzed by the mammalian polyamine and spermine oxidases. The active site of Fms1 contains three amino acid residues positioned to interact with the polyamine substrate, His67, Asn195, and Asp94. These three residues form a hydrogen-bonding triad with Asn195 being the central residue. Previous studies of the effects of mutating His67 are consistent with that residue being important both for interacting with the substrate and for maintaining the hydrogen bonds in the triad [Adachi, M. S., Taylor, A. B., Hart, P. J., and Fitzpatrick, P. F. (2012) Biochemistry 51, 4888-4897]. The N195A and D94N enzymes have now been characterized to evaluate their roles in catalysis. Both mutations primarily affect the reductive half-reaction. With N(1)-acetylspermine as the substrate, the rate constant for flavin reduction decreases ~450-fold for both mutations; the effects with spermine as the substrate are smaller, 20-40-fold. The k(cat)/K(amine)- and k(cat)-pH profiles with N(1)-acetylspermine are only slightly changed from the profiles for the wild-type enzyme, consistent with the pK(a) values arising from the amine substrate or product and not from active site residues. The structure of the N195A enzyme was determined at a resolution of 2.0 Å. The structure shows a molecule of tetraethylene glycol in the active site and establishes that the mutation has no effect on the protein structure. Overall, the results are consistent with the role of Asn195 and Asp94 being to properly position the polyamine substrate for oxidation.
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Affiliation(s)
- Mariya S. Adachi
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Alexander B. Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - P. John Hart
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
- Department of Veterans Affairs, Audie Murphy Division, Geriatric Research, Education, and Clinical Center, South Texas Veterans Health Care System, San Antonio, TX 78229
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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35
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Vianello R, Repič M, Mavri J. How are Biogenic Amines Metabolized by Monoamine Oxidases? European J Org Chem 2012. [DOI: 10.1002/ejoc.201201122] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Gaweska HM, Roberts KM, Fitzpatrick PF. Isotope effects suggest a stepwise mechanism for berberine bridge enzyme. Biochemistry 2012; 51:7342-7. [PMID: 22931234 DOI: 10.1021/bi300887m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The flavoprotein Berberine Bridge Enzyme (BBE) catalyzes the regioselective oxidative cyclization of (S)-reticuline to (S)-scoulerine in an alkaloid biosynthetic pathway. A series of solvent and substrate deuterium kinetic isotope effect studies were conducted to discriminate between a concerted mechanism, in which deprotonation of the substrate phenol occurs before or during the transfer of a hydride from the substrate to the flavin cofactor and substrate cyclization, and a stepwise mechanism, in which hydride transfer results in the formation of a methylene iminium ion intermediate that is subsequently cyclized. The substrate deuterium isotope effect of 3.5 on k(red), the rate constant for flavin reduction, is pH-independent, indicating that C-H bond cleavage is rate-limiting during flavin reduction. Solvent isotope effects on k(red) are equal to 1 for both wild-type BBE and the E417Q mutant, indicating that solvent exchangeable protons are not in flight during or before flavin reduction, thus eliminating a fully concerted mechanism as a possibility for catalysis by BBE. An intermediate was not detected by rapid chemical quench or continuous-flow mass spectrometry experiments, indicating that it must be short-lived.
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Affiliation(s)
- Helena M Gaweska
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, United States
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37
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Yuan H, Xin Y, Hamelberg D, Gadda G. Insights on the Mechanism of Amine Oxidation Catalyzed by d-Arginine Dehydrogenase Through pH and Kinetic Isotope Effects. J Am Chem Soc 2011; 133:18957-65. [DOI: 10.1021/ja2082729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongling Yuan
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Yao Xin
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Donald Hamelberg
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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38
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Kong X, Ouyang S, Liang Z, Lu J, Chen L, Shen B, Li D, Zheng M, Li KK, Luo C, Jiang H. Catalytic mechanism investigation of lysine-specific demethylase 1 (LSD1): a computational study. PLoS One 2011; 6:e25444. [PMID: 21984927 PMCID: PMC3184146 DOI: 10.1371/journal.pone.0025444] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/05/2011] [Indexed: 12/13/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is a flavin-dependent amine oxidase which specifically demethylates mono- or dimethylated H3K4 and H3K9 via a redox process. It participates in a broad spectrum of biological processes and is of high importance in cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. To date, as a potential drug target for discovering anti-tumor drugs, the medical significance of LSD1 has been greatly appreciated. However, the catalytic mechanism for the rate-limiting reductive half-reaction in demethylation remains controversial. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, the catalytic mechanism of dimethylated H3K4 demethylation by LSD1 was characterized in details. The three-dimensional (3D) model of the complex was composed of LSD1, CoREST, and histone substrate. A 30-ns MD simulation of the model highlights the pivotal role of the conserved Tyr761 and lysine-water-flavin motif in properly orienting flavin adenine dinucleotide (FAD) with respect to substrate. The synergy of the two factors effectively stabilizes the catalytic environment and facilitated the demethylation reaction. On the basis of the reasonable consistence between simulation results and available mutagenesis data, QM/MM strategy was further employed to probe the catalytic mechanism of the reductive half-reaction in demethylation. The characteristics of the demethylation pathway determined by the potential energy surface and charge distribution analysis indicates that this reaction belongs to the direct hydride transfer mechanism. Our study provides insights into the LSD1 mechanism of reductive half-reaction in demethylation and has important implications for the discovery of regulators against LSD1 enzymes.
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Affiliation(s)
- Xiangqian Kong
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Sisheng Ouyang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhongjie Liang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junyan Lu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liang Chen
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Jiangsu, China
| | - Donghai Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Jiangsu Diabetes Research Center, Nanjing University, Nanjing, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Keqin Kathy Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (CL); (KKL)
| | - Cheng Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Center for Systems Biology, Soochow University, Jiangsu, China
- * E-mail: (CL); (KKL)
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
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MacMillar S, Edmondson DE, Matsson O. Nitrogen kinetic isotope effects for the monoamine oxidase B-catalyzed oxidation of benzylamine and (1,1-(2)H2)benzylamine: nitrogen rehybridization and CH bond cleavage are not concerted. J Am Chem Soc 2011; 133:12319-21. [PMID: 21786798 DOI: 10.1021/ja205629b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen kinetic isotope effects for the oxidation of benzylamine and (1,1-(2)H(2))benzylamine by recombinant human monoamine oxidase B show that cleavage of the CH bond is not concerted with rehybridization of the nitrogen atom.
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Affiliation(s)
- Susanna MacMillar
- Department of Biochemistry and Organic Chemistry, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
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40
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Elucidation of the mechanism of N-demethylation catalyzed by cytochrome P450 monooxygenase is facilitated by exploiting nitrogen-15 heavy isotope effects. Arch Biochem Biophys 2011; 510:35-41. [DOI: 10.1016/j.abb.2011.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/12/2011] [Accepted: 03/14/2011] [Indexed: 11/19/2022]
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41
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Study on the decrease of renal d-amino acid oxidase activity in the rat after renal ischemia by chiral ligand exchange capillary electrophoresis. Amino Acids 2010; 42:337-45. [DOI: 10.1007/s00726-010-0811-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/08/2010] [Indexed: 01/25/2023]
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42
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Pozzi MH, Fitzpatrick PF. A lysine conserved in the monoamine oxidase family is involved in oxidation of the reduced flavin in mouse polyamine oxidase. Arch Biochem Biophys 2010; 498:83-8. [PMID: 20417173 PMCID: PMC2880204 DOI: 10.1016/j.abb.2010.04.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 04/19/2010] [Accepted: 04/20/2010] [Indexed: 10/19/2022]
Abstract
Lysine 315 of mouse polyamine amine oxidase corresponds to a lysine residue that is conserved in the flavoprotein amine oxidases of the monoamine oxidase structural family. In several structures, this lysine residue forms a hydrogen bond to a water molecule that is hydrogen-bonded to the flavin N(5). Mutation of Lys315 in polyamine oxidase to methionine was previously shown to have no effect on the kinetics of the reductive half-reaction of the enzyme (M. Henderson Pozzi, V. Gawandi, P.F. Fitzpatrick, Biochemistry 48 (2009) 1508-1516). In contrast, the mutation does affect steps in the oxidative half-reaction. The k(cat) value is unaffected by the mutation; this kinetic parameter likely reflects product release. At pH 10, the k(cat)/K(m) value for oxygen is 25-fold lower in the mutant enzyme. The k(cat)/K(O2) value is pH-dependent for the wild-type enzyme, decreasing below a pK(a) of 7.0, while this kinetic parameter for the mutant enzyme is pH-independent. This is consistent with the neutral form of Lys315 being required for more rapid flavin oxidation. The solvent isotope effect on the k(cat)/K(O2) value increases from 1.4 in the wild-type enzyme to 1.9 in the mutant protein, and the solvent inventory changes from linear to bowed. The effects of the mutation can be explained by the lysine orienting the bridging water so that it can accept the proton from the flavin N(5) during flavin oxidation. In the mutant enzyme the lysine amine would be replaced by a water chain.
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Affiliation(s)
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, San Antonio TX 78229-3900
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43
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Sucharitakul J, Wongnate T, Chaiyen P. Kinetic Isotope Effects on the Noncovalent Flavin Mutant Protein of Pyranose 2-Oxidase Reveal Insights into the Flavin Reduction Mechanism. Biochemistry 2010; 49:3753-65. [DOI: 10.1021/bi100187b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Patumwan, Bangkok 10330, Thailand
| | - Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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44
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Adachi MS, Juarez PR, Fitzpatrick PF. Mechanistic studies of human spermine oxidase: kinetic mechanism and pH effects. Biochemistry 2010; 49:386-92. [PMID: 20000632 PMCID: PMC2810717 DOI: 10.1021/bi9017945] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In mammalian cells, the flavoprotein spermine oxidase (SMO) catalyzes the oxidation of spermine to spermidine and 3-aminopropanal. Mechanistic studies have been conducted with the recombinant human enzyme. The initial velocity pattern in which the ratio between the concentrations of spermine and oxygen is kept constant establishes the steady-state kinetic pattern as ping-pong. Reduction of SMO by spermine in the absence of oxygen is biphasic. The rate constant for the rapid phase varies with the substrate concentration, with a limiting value (k(3)) of 49 s(-1) and an apparent K(d) value of 48 microM at pH 8.3. The rate constant for the slow step is independent of the spermine concentration, with a value of 5.5 s(-1), comparable to the k(cat) value of 6.6 s(-1). The kinetics of the oxidative half-reaction depend on the aging time after the spermine and enzyme are mixed in a double-mixing experiment. At an aging time of 6 s, the reaction is monophasic with a second-order rate constant of 4.2 mM(-1) s(-1). At an aging time of 0.3 s, the reaction is biphasic with two second-order constants equal to 4.0 and 40 mM(-1) s(-1). Neither is equal to the k(cat)/K(O(2)) value of 13 mM(-1) s(-1). These results establish the existence of more than one pathway for the reaction of the reduced flavin intermediate with oxygen. The k(cat)/K(M) value for spermine exhibits a bell-shaped pH profile, with an average pK(a) value of 8.3. This profile is consistent with the active form of spermine having three charged nitrogens. The pH profile for k(3) shows a pK(a) value of 7.4 for a group that must be unprotonated. The pK(i)-pH profiles for the competitive inhibitors N,N'-dibenzylbutane-1,4-diamine and spermidine show that the fully protonated forms of the inhibitors and the unprotonated form of an amino acid residue with a pK(a) of approximately 7.4 in the active site are preferred for binding.
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Affiliation(s)
- Maria S. Adachi
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX 78229
| | - Paul R. Juarez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Center for Biomedical Neuroscience, University of Texas Health Science Center, San Antonio, TX 78229
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45
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Tcherkez G. Natural 15N/ 14N isotope composition in C 3 leaves: are enzymatic isotope effects informative for predicting the 15N-abundance in key metabolites? FUNCTIONAL PLANT BIOLOGY : FPB 2010; 38:1-12. [PMID: 32480857 DOI: 10.1071/fp10091] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 10/24/2010] [Indexed: 06/11/2023]
Abstract
Although nitrogen isotopes are viewed as important tools for understanding plant N acquisition and allocation, the current interpretation of natural 15N-abundances (δ15N values) is often impaired by substantial variability among individuals or between species. Such variability is likely to stem from the fact that 15N-abundance of assimilated N is not preserved during N metabolism and redistribution within the plant; that is, 14N/15N isotope effects associated with N metabolic reactions are certainly responsible for isotopic shifts between organic-N (amino acids) and absorbed inorganic N (nitrate). Therefore, to gain insights into the metabolic origin of 15N-abundance in plants, the present paper reviews enzymatic isotope effects and integrates them into a metabolic model at the leaf level. Using simple steady-state equations which satisfactorily predict the δ15N value of amino acids, it is shown that the sensitivity of δ15N values to both photorespiratory and N-input (reduction by nitrate reductase) rates is quite high. In other words, the variability in δ15N values observed in nature might originate from subtle changes in metabolic fluxes or environment-driven effects, such as stomatal closure that in turn changes v0, the Rubisco-catalysed oxygenation rate.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay Cedex, France. Email
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46
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Pozzi MH, Gawandi V, Fitzpatrick PF. Mechanistic studies of para-substituted N,N'-dibenzyl-1,4-diaminobutanes as substrates for a mammalian polyamine oxidase. Biochemistry 2009; 48:12305-13. [PMID: 19911805 PMCID: PMC2797579 DOI: 10.1021/bi901694s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The kinetics of oxidation of a series of para-substituted N,N'-dibenzyl-1,4-diaminobutanes by the flavoprotein polyamine oxidase from mouse have been determined to gain insight into the mechanism of amine oxidation by this member of the monoamine oxidase structural family. The k(cat)/K(m) values are maximal at pH 9, consistent with the singly charged substrate being the active form. The rate constant for flavin reduction, k(red), by N,N'-dibenzyl-1,4-diaminobutane decreases about 5-fold below a pK(a) of approximately 8; this is attributed to the need for a neutral nitrogen at the site of oxidation. The k(red) and k(cat) values are comparable for each of the N,N'-dibenzyl-1,4-diaminobutanes, consistent with rate-limiting reduction. The deuterium kinetic isotope effects on k(red) and k(cat) are identical for each of the N,N'-dibenzyl-1,4-diaminobutanes, consistent with rate-limiting cleavage of the substrate CH bond. The k(red) values for seven different para-substituted N,N'-dibenzyl-1,4-diaminobutanes correlate with a combination of the van der Waals volume and sigma value of the substrates, with rho values of -0.59 at pH 8.6 and -0.09 at pH 6.6. These results are consistent with direct transfer of a hydride from the neutral CN bond of the substrate to the flavin as the mechanism of polyamine oxidase.
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Affiliation(s)
| | - Vijay Gawandi
- Department of Biochemistry and Biophysics Texas A&M University, College Station TX 77843-2128
| | - Paul F. Fitzpatrick
- Department of Biochemistry University of Texas Health Science Center at San Antonio, San Antonio TX 78229-3900
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47
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Oxidation of amines by flavoproteins. Arch Biochem Biophys 2009; 493:13-25. [PMID: 19651103 DOI: 10.1016/j.abb.2009.07.019] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 07/27/2009] [Accepted: 07/29/2009] [Indexed: 11/21/2022]
Abstract
Many flavoproteins catalyze the oxidation of primary and secondary amines, with the transfer of a hydride equivalent from a carbon-nitrogen bond to the flavin cofactor. Most of these amine oxidases can be classified into two structural families, the D-amino acid oxidase/sarcosine oxidase family and the monoamine oxidase family. This review discusses the present understanding of the mechanisms of amine and amino acid oxidation by flavoproteins, focusing on these two structural families.
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48
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Gaweska H, Henderson Pozzi M, Schmidt DMZ, McCafferty DG, Fitzpatrick PF. Use of pH and kinetic isotope effects to establish chemistry as rate-limiting in oxidation of a peptide substrate by LSD1. Biochemistry 2009; 48:5440-5. [PMID: 19408960 DOI: 10.1021/bi900499w] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mechanism of oxidation of a peptide substrate by the flavoprotein lysine-specific demethylase (LSD1) has been examined using the effects of pH and isotopic substitution on steady-state and rapid-reaction kinetic parameters. The substrate contained the 21 N-terminal residues of histone H3, with a dimethylated lysyl residue at position 4. At pH 7.5, the rate constant for flavin reduction, k(red), equals k(cat), establishing the reductive half-reaction as rate-limiting at physiological pH. Deuteration of the lysyl methyls results in identical kinetic isotope effects of 3.1 +/- 0.2 on the k(red), k(cat), and k(cat)/K(m) values for the peptide, establishing C-H bond cleavage as rate-limiting with this substrate. No intermediates between oxidized and reduced flavin can be detected by stopped-flow spectroscopy, consistent with the expectation for a direct hydride transfer mechanism. The k(cat)/K(m) value for the peptide is bell-shaped, consistent with a requirement that the nitrogen at the site of oxidation be uncharged and that at least one of the other lysyl residues be charged for catalysis. The (D)(k(cat)/K(m)) value for the peptide is pH-independent, suggesting that the observed value is the intrinsic deuterium kinetic isotope effect for oxidation of this substrate.
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Affiliation(s)
- Helena Gaweska
- Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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49
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Edmondson DE, Binda C, Wang J, Upadhyay AK, Mattevi A. Molecular and mechanistic properties of the membrane-bound mitochondrial monoamine oxidases. Biochemistry 2009; 48:4220-30. [PMID: 19371079 DOI: 10.1021/bi900413g] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The past decade has brought major advances in our knowledge of the structures and mechanisms of MAO A and MAO B, which are pharmacological targets for specific inhibitors. In both enzymes, crystallographic and biochemical data show their respective C-terminal transmembrane helices anchor the enzymes to the outer mitochondrial membrane. Pulsed EPR data show both enzymes are dimeric in their membrane-bound forms with agreement between distances measured in their crystalline forms. Distances measured between active site-directed spin-labels in membrane preparations show excellent agreement with those estimated from crystallographic data. Our knowledge of requirements for development of specific reversible MAO B inhibitors is in a fairly mature status. Less is known regarding the structural requirements for highly specific reversible MAO A inhibitors. In spite of their 70% level of sequence identity and similarities of C(alpha) folds, the two enzymes exhibit significant functional and structural differences that can be exploited in the ultimate goal of the development of highly specific inhibitors. This review summarizes the current structural and mechanistic information available that can be utilized in the development of future highly specific neuroprotectants and cardioprotectants.
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Affiliation(s)
- Dale E Edmondson
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA.
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50
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Pozzi MH, Gawandi V, Fitzpatrick PF. pH dependence of a mammalian polyamine oxidase: insights into substrate specificity and the role of lysine 315. Biochemistry 2009; 48:1508-16. [PMID: 19199575 PMCID: PMC2752350 DOI: 10.1021/bi802227m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian polyamine oxidases (PAOs) catalyze the oxidation of N1-acetylspermine and N1-acetylspermidine to produce N-acetyl-3-aminopropanaldehyde and spermidine or putrescine. Structurally, PAO is a member of the monoamine oxidase family of flavoproteins. The effects of pH on the kinetic parameters of mouse PAO have been determined to provide insight into the protonation state of the polyamine required for catalysis and the roles of ionizable residues in the active site in amine oxidation. For N1-acetylspermine, N1-acetylspermidine, and spermine, the k(cat)/K(amine)-pH profiles are bell-shaped. In each case, the profile agrees with that expected if the productive form of the substrate has a single positively charged nitrogen. The pK(i)-pH profiles for a series of polyamine analogues are most consistent with the nitrogen at the site of oxidation being neutral and one other nitrogen being positively charged in the reactive form of the substrate. With N1-acetylspermine as the substrate, the value of k(red), the limiting rate constant for flavin reduction, is pH-dependent, decreasing below a pK(a) value of 7.3, again consistent with the requirement for an uncharged nitrogen for substrate oxidation. Lys315 in PAO corresponds to a conserved active site residue found throughout the monoamine oxidase family. Mutation of Lys315 to methionine has no effect on the k(cat)/K(amine) profile for spermine; the k(red) value with N1-acetylspermine is only 1.8-fold lower in the mutant protein, and the pK(a) in the k(red)-pH profile with N1-acetylspermine shifts to 7.8. These results rule out Lys315 as a source of a pK(a) in the k(cat)/K(amine) or k(cat)/k(red) profiles. They also establish that this residue does not play a critical role in amine oxidation by PAO.
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Affiliation(s)
| | - Vijay Gawandi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77843-2128
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77843-2128
- Department of Chemistry, Texas A&M University, College Station TX 77843-2128
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