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Kubicskó K, Farkas Ö. Quantum chemical (QM:MM) investigation of the mechanism of enzymatic reaction of tryptamine and N,N-dimethyltryptamine with monoamine oxidase A. Org Biomol Chem 2020; 18:9660-9674. [PMID: 33215182 DOI: 10.1039/d0ob01118e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The endogenous psychedelic (mind-altering) N,N-dimethyltryptamine (DMT) molecule has an important role in tissue protection, regeneration, and immunity via sigma-1 receptor activation as its natural ligand. The immunologic properties of DMT suggest this biogenic compound should be investigated thoroughly in other aspects as well. In our in silico project, we examined the metabolism of DMT and its primary analogue, the tryptamine (T), by the monoamine oxidase (MAO) flavoenzyme. MAO has two isoforms, MAO-A and MAO-B. MAOs perform the oxidation of various monoamines by their flavin adenine dinucleotide (FAD) cofactor. Two-layer QM:MM calculations at the ONIOM(M06-2X/6-31++G(d,p):UFF=QEq) level were performed including the whole enzyme to explore the potential energy surface (PES) of the reactions. Our findings reinforced that a hybrid mechanism, a mixture of pure H+ and H- transfer pathways, describes precisely the rate-determining step of amine oxidation as suggested by earlier works. Additionally, our results show that the oxidation of tertiary amine DMT requires a lower activation barrier than the primary amine T. This may reflect a general rule, thus we recommend further investigations. Furthermore, we demonstrated that at pH 7.4 the protonated form of these substrates enter the enzyme. As the deprotonation of substrates is crucial, we presumed protonated cofactor, FADH+, may form. Surprisingly, the activation barriers are much lower compared to FAD with both substrates. Therefore, we suggest further investigations in this direction.
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Affiliation(s)
- Károly Kubicskó
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.
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2
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Yasukawa K, Kawahara N, Motojima F, Nakano S, Asano Y. Porcine kidney d-amino acid oxidase-derived R-amine oxidases with new substrate specificities. Enzymes 2020; 47:117-136. [PMID: 32951821 DOI: 10.1016/bs.enz.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An R-stereoselective amine oxidase and variants with markedly altered substrate specificity toward (R)-amines were generated from porcine d-amino acid oxidase (pkDAO), based on the X-ray crystallographic analysis of the wild-type enzyme. The new R-amine oxidase, a pkDAO variant (Y228L/R283G), acted on α-MBA and its derivatives, α-ethylbenzylamine, alkylamine, and cyclic secondary amines, totally losing the activities toward the original substrates, d-amino acids. The variant is enantiocomplementary to the flavin-type S-stereoselective amine oxidase variant from Aspergillus niger. Moreover, we solved the structure of pkDAO variants and successfully applied the obtained information to generate more variants through rational protein engineering, and used them in the synthesis of pharmaceutically attractive chiral compounds. The pkDAO variant Y228L/R283G and a variant I230A/R283G were used to synthesize (S)-amine and (R)-4-CBHA through deracemization, from racemic α-methylbenzylamine and benzhydrylamine, respectively, by selective oxidation of one of the enantiomers in the presence of a chemical reductant such as NaBH4. From a mechanistic point of view, we speculated that the imine intermediate, synthesized by oxidases or dehydrogenases, could be converted into primary α-aminonitrile by nucleophilic addition of cyanide in aqueous solutions. Nitriles and some unnatural amino acids were synthesized through a cascade reaction by oxidative cyanation reaction with the variant and a wide substrate specificity nitrilase.
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Affiliation(s)
- Kazuyuki Yasukawa
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Nobuhiro Kawahara
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Fumihiro Motojima
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Shogo Nakano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Toyama, Japan.
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3
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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: 6] [Impact Index Per Article: 1.5] [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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4
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Ball J, Gannavaram S, Gadda G. Structural determinants for substrate specificity of flavoenzymes oxidizing d-amino acids. Arch Biochem Biophys 2018; 660:87-96. [PMID: 30312594 DOI: 10.1016/j.abb.2018.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022]
Abstract
The oxidation of d-amino acids is relevant to neurodegenerative diseases, detoxification, and nutrition in microorganisms and mammals. It is also important for the resolution of racemic amino acid mixtures and the preparation of chiral building blocks for the pharmaceutical and food industry. Considerable biochemical and structural knowledge has been accrued in recent years on the enzymes that carry out the oxidation of the Cα-N bond of d-amino acids. These enzymes contain FAD as a required coenzyme, share similar overall three-dimensional folds and highly conserved active sites, but differ in their specificity for substrates with neutral, anionic, or cationic side-chains. Here, we summarize the current biochemical and structural knowledge regarding substrate specificity on d-amino acid oxidase, d-aspartate oxidase, and d-arginine dehydrogenase for which a wealth of biochemical and structural studies is available.
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Affiliation(s)
- Jacob Ball
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Swathi Gannavaram
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Giovanni Gadda
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA; Departments of Biology, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302-3965, USA.
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5
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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: 1.0] [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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6
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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: 0.9] [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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7
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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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8
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Nakano S, Yasukawa K, Tokiwa T, Ishikawa T, Ishitsubo E, Matsuo N, Ito S, Tokiwa H, Asano Y. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase. J Phys Chem B 2016; 120:10736-10743. [DOI: 10.1021/acs.jpcb.6b09328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Nakano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuyuki Yasukawa
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takaki Tokiwa
- Department
of Chemistry, Graduate School of Science, Tohoku University, Aramaki,
Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeshi Ishikawa
- Department
of Molecular Microbiology and Immunology, Graduate School of Biomedical
Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Erika Ishitsubo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Naoya Matsuo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Sohei Ito
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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9
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Füller JJ, Röpke R, Krausze J, Rennhack KE, Daniel NP, Blankenfeldt W, Schulz S, Jahn D, Moser J. Biosynthesis of Violacein, Structure and Function of l-Tryptophan Oxidase VioA from Chromobacterium violaceum. J Biol Chem 2016; 291:20068-84. [PMID: 27466367 DOI: 10.1074/jbc.m116.741561] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 11/06/2022] Open
Abstract
Violacein is a natural purple pigment of Chromobacterium violaceum with potential medical applications as antimicrobial, antiviral, and anticancer drugs. The initial step of violacein biosynthesis is the oxidative conversion of l-tryptophan into the corresponding α-imine catalyzed by the flavoenzyme l-tryptophan oxidase (VioA). A substrate-related (3-(1H-indol-3-yl)-2-methylpropanoic acid) and a product-related (2-(1H-indol-3-ylmethyl)prop-2-enoic acid) competitive VioA inhibitor was synthesized for subsequent kinetic and x-ray crystallographic investigations. Structures of the binary VioA·FADH2 and of the ternary VioA·FADH2·2-(1H-indol-3-ylmethyl)prop-2-enoic acid complex were resolved. VioA forms a "loosely associated" homodimer as indicated by small-angle x-ray scattering experiments. VioA belongs to the glutathione reductase family 2 of FAD-dependent oxidoreductases according to the structurally conserved cofactor binding domain. The substrate-binding domain of VioA is mainly responsible for the specific recognition of l-tryptophan. Other canonical amino acids were efficiently discriminated with a minor conversion of l-phenylalanine. Furthermore, 7-aza-tryptophan, 1-methyl-tryptophan, 5-methyl-tryptophan, and 5-fluoro-tryptophan were efficient substrates of VioA. The ternary product-related VioA structure indicated involvement of protein domain movement during enzyme catalysis. Extensive structure-based mutagenesis in combination with enzyme kinetics (using l-tryptophan and substrate analogs) identified Arg(64), Lys(269), and Tyr(309) as key catalytic residues of VioA. An increased enzyme activity of protein variant H163A in the presence of l-phenylalanine indicated a functional role of His(163) in substrate binding. The combined structural and mutational analyses lead to the detailed understanding of VioA substrate recognition. Related strategies for the in vivo synthesis of novel violacein derivatives are discussed.
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Affiliation(s)
| | - René Röpke
- the Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, and
| | - Joern Krausze
- the Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | | | | | - Wulf Blankenfeldt
- the Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig
| | - Stefan Schulz
- the Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, and
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Angiulli G, Lantella A, Forte E, Angelucci F, Colotti G, Ilari A, Malatesta F. Leishmania infantum trypanothione reductase is a promiscuous enzyme carrying an NADPH:O2 oxidoreductase activity shared by glutathione reductase. Biochim Biophys Acta Gen Subj 2015; 1850:1891-7. [PMID: 26033467 DOI: 10.1016/j.bbagen.2015.05.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/05/2015] [Accepted: 05/27/2015] [Indexed: 01/01/2023]
Abstract
BACKGROUND Leishmania infantum is a protozoan of the trypanosomatid family causing visceral leishmaniasis. Leishmania parasites are transmitted by the bite of phlebotomine sand flies to the human host and are phagocyted by macrophages. The parasites synthesize N1-N8-bis(glutationyl)-spermidine (trypanothione, TS2), which furnishes electrons to the tryparedoxin-tryparedoxin peroxidase couple to reduce the reactive oxygen species produced by macrophages. Trypanothione is kept reduced by trypanothione reductase (TR), a FAD-containing enzyme essential for parasite survival. METHODS The enzymatic activity has been studied by stopped-flow, absorption spectroscopy, and amperometric measurements. RESULTS The study reported here demonstrates that the steady-state parameters change as a function of the order of substrates addition to the TR-containing solution. In particular, when the reaction is carried out by adding NADPH to a solution containing the enzyme and trypanothione, the KM for NADPH decreases six times compared to the value obtained by adding TS2 as last reagent to start the reaction (1.9 vs. 12μM). More importantly, we demonstrate that TR is able to catalyze the oxidation of NADPH also in the absence of trypanothione. Thus, TR catalyzes the reduction of O2 to water through the sequential formation of C(4a)-(hydro)peroxyflavin and sulfenic acid intermediates. This NADPH:O2 oxidoreductase activity is shared by Saccharomyces cerevisiae glutathione reductase (GR). CONCLUSIONS TR and GR, in the absence of their physiological substrates, may catalyze the electron transfer reaction from NADPH to molecular oxygen to yield water. GENERAL SIGNIFICANCE TR and GR are promiscuous enzymes.
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Affiliation(s)
- Gabriella Angiulli
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Antonella Lantella
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Elena Forte
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Francesco Angelucci
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, University of L'Aquila, L'Aquila, Italy
| | - Gianni Colotti
- CNR-Institute of Molecular Biology and Pathology, c/o Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology, c/o Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.
| | - Francesco Malatesta
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy.
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11
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A comparative computational investigation on the proton and hydride transfer mechanisms of monoamine oxidase using model molecules. Comput Biol Chem 2013; 47:181-91. [PMID: 24121676 DOI: 10.1016/j.compbiolchem.2013.08.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022]
Abstract
Monoamine oxidase (MAO) enzymes regulate the level of neurotransmitters by catalyzing the oxidation of various amine neurotransmitters, such as serotonin, dopamine and norepinephrine. Therefore, they are the important targets for drugs used in the treatment of depression, Parkinson, Alzeimer and other neurodegenerative disorders. Elucidation of MAO-catalyzed amine oxidation will provide new insights into the design of more effective drugs. Various amine oxidation mechanisms have been proposed for MAO so far, such as single electron transfer mechanism, polar nucleophilic mechanism and hydride mechanism. Since amine oxidation reaction of MAO takes place between cofactor flavin and the amine substrate, we focus on the small model structures mimicking flavin and amine substrates so that three model structures were employed. Reactants, transition states and products of the polar nucleophilic (proton transfer), the water-assisted proton transfer and the hydride transfer mechanisms were fully optimized employing various semi-empirical, ab initio and new generation density functional theory (DFT) methods. Activation energy barriers related to these mechanisms revealed that hydride transfer mechanism is more feasible.
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12
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Akyüz MA, Erdem SS. Computational modeling of the direct hydride transfer mechanism for the MAO catalyzed oxidation of phenethylamine and benzylamine: ONIOM (QM/QM) calculations. J Neural Transm (Vienna) 2013; 120:937-45. [PMID: 23619993 DOI: 10.1007/s00702-013-1027-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 04/15/2013] [Indexed: 11/28/2022]
Abstract
Monoamine oxidases are two isozymic flavoenzymes which are the important targets for drugs used in the treatment of depression, Parkinson and Alzheimer's diseases. The catalytic reaction taking place between the cofactor FAD and amine substrate is still not completely understood. Herein we employed quantum chemical methods on the recently proposed direct hydride transfer mechanism including full active site residues of MAO isoforms in the calculations. Activation free energy barriers of direct hydride transfer mechanism for MAO-A and MAO-B were calculated by ONIOM (our own n-layered integrated molecular orbital + molecular mechanics) method with QM/QM (quantum mechanics:quantum mechanics) approach employing several density functional theory functionals, B3LYP, WB97XD, CAM-B3LYP and M06-2X, for the high layer. The formation of very recently proposed αC-flavin N5 adduct inside the enzyme has been investigated. ONIOM (M06-2X/6-31+G(d,p):PM6) results revealed that such an adduct may form only in MAO-B suggesting slightly different hydride transfer mechanisms for MAO-A and MAO-B.
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Affiliation(s)
- Mehmet Ali Akyüz
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, Göztepe, 34722, Istanbul, Turkey
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13
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MICAL, the flavoenzyme participating in cytoskeleton dynamics. Int J Mol Sci 2013; 14:6920-59. [PMID: 23535333 PMCID: PMC3645671 DOI: 10.3390/ijms14046920] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 03/02/2013] [Accepted: 03/11/2013] [Indexed: 01/01/2023] Open
Abstract
MICAL (from the Molecule Interacting with CasL) indicates a family of recently discovered cytosolic, multidomain proteins, which uniquely couple an N-terminal FAD-containing monooxygenase-like domain to typical calponine homology, LIM and coiled-coil protein-interaction modules. Genetic and cell biology approaches have demonstrated an essential role of the catalytic activity of the monooxygenase-like domain in transducing the signal initiated by semaphorins interaction with their plexin receptors, which results in local actin cytoskeleton disassembly as part of fundamental processes that include differentiation, migration and cell-cell contacts in neuronal and non-neuronal cell types. This review focuses on the structure-function relations of the MICAL monooxygenase-like domain as they are emerging from the available in vitro studies on mouse, human and Drosophila MICAL forms that demonstrated a NADPH-dependent actin depolymerizing activity of MICAL. With Drosophila MICAL forms, actin depolymerization was demonstrated to be associated to conversion of Met44 to methionine sulfone through a postulated hydroxylating reaction. Arguments supporting the concept that MICAL effect on F-actin may be reversible will be discussed.
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14
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Nueangaudom A, Lugsanangarm K, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F. The mechanism of photoinduced electron transfer in the d-amino acid oxidase–benzoate complex from pig kidney: Electron transfer in the inverted region. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Nueangaudom A, Lugsanangarm K, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F. Structural basis for the temperature-induced transition of d-amino acid oxidase from pig kidney revealed by molecular dynamic simulation and photo-induced electron transfer. Phys Chem Chem Phys 2012; 14:2567-78. [DOI: 10.1039/c2cp23001a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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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: 1.2] [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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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: 3.2] [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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18
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Saam J, Rosini E, Molla G, Schulten K, Pollegioni L, Ghisla S. O2 reactivity of flavoproteins: dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase. J Biol Chem 2010; 285:24439-46. [PMID: 20498362 DOI: 10.1074/jbc.m110.131193] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular dynamics simulations and implicit ligand sampling methods have identified trajectories and sites of high affinity for O(2) in the protein framework of the flavoprotein D-amino-acid oxidase (DAAO). A specific dynamic channel for the diffusion of O(2) leads from solvent to the flavin Si-side (amino acid substrate and product bind on the Re-side). Based on this, amino acids that flank the putative O(2) high affinity sites have been exchanged with bulky residues to introduce steric constraints. In G52V DAAO, the valine side chain occupies the site that in wild-type DAAO has the highest O(2) affinity. In this variant, the reactivity of the reduced enzyme with O(2) is decreased >or=100-fold and the turnover number approximately 1000-fold thus verifying the concept. In addition, the simulations have identified a chain of three water molecules that might serve in relaying a H(+) from the product imino acid =NH(2)(+) group bound on the flavin Re-side to the developing peroxide on the Si-side. This function would be comparable with that of a similarly located histidine in the flavoprotein glucose oxidase.
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Affiliation(s)
- Jan Saam
- Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA
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19
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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: 166] [Impact Index Per Article: 11.1] [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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Tabacchi G, Zucchini D, Caprini G, Gamba A, Lederer F, Vanoni MA, Fois E. L-lactate dehydrogenation in flavocytochrome b2: a first principles molecular dynamics study. FEBS J 2009; 276:2368-80. [PMID: 19348008 DOI: 10.1111/j.1742-4658.2009.06969.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
First principles molecular dynamics studies on active-site models of flavocytochrome b2 (L-lactate : cytochrome c oxidoreductase, Fcb2), in complex with the substrate, were carried out for the first time to contribute towards establishing the mechanism of the enzyme-catalyzed L-lactate oxidation reaction, a still-debated issue. In the calculated enzyme-substrate model complex, the L-lactate alpha-OH hydrogen is hydrogen bonded to the active-site base H373 Nepsilon, whereas the Halpha is directed towards flavin N5, suggesting that the reaction is initiated by alpha-OH proton abstraction. Starting from this structure, simulation of L-lactate oxidation led to formation of the reduced enzyme-pyruvate complex by transfer of a hydride from lactate to flavin mononucleotide, without intermediates, but with alpha-OH proton abstraction preceding Halpha transfer and a calculated free energy barrier (12.1 kcal mol(-1)) consistent with that determined experimentally (13.5 kcal mol(-1)). Simulation results also revealed features that are of relevance to the understanding of catalysis in Fcb2 homologs and in a number of flavoenzymes. Namely, they highlighted the role of: (a) the flavin mononucleotide-ribityl chain 2'OH group in maintaining the conserved K349 in a geometry favoring flavin reduction; (b) an active site water molecule belonging to a S371-Wat-D282-H373 hydrogen-bonded chain, conserved in the structures of Fcb2 family members, which modulates the reactivity of the key catalytic histidine; and (c) the flavin C4a-C10a locus in facilitating proton transfer from the substrate to the active-site base, favoring the initial step of the lactate dehydrogenation reaction.
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Affiliation(s)
- Gloria Tabacchi
- Dipartimento di Scienze Chimiche ed Ambientali and INSTM, Università dell'Insubria, Como, Italy
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21
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Stability and stabilization of D-amino acid oxidase from the yeast Trigonopsis variabilis. Biochem Soc Trans 2007; 35:1588-92. [DOI: 10.1042/bst0351588] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of DAO (D-amino acid oxidase) for the conversion of cephalosporin C has provided a significant case for the successful implementation of an O2-dependent biocatalyst on an industrial scale. Improvement of the operational stability of the immobilized oxidase is, however, an important goal of ongoing process optimization. We have examined DAO from the yeast Trigonopsis variabilis with the aim of developing a rational basis for the stabilization of the enzyme activity at elevated temperature and under conditions of substrate turnover. Loss of activity in the resting enzyme can occur via different paths of denaturation. Partial thermal unfolding and release of the FAD cofactor, kinetically coupled with aggregation, contribute to the overall inactivation rate of the oxidase at 50°C. Oxidation of Cys108 into a stable cysteine sulfinic acid causes both decreased activity and stability of the enzyme. Strategies to counteract each of the denaturation steps in DAO are discussed. Fusion to a pull-down domain is a novel approach to produce DAO as protein-based insoluble particles that display high enzymatic activity per unit mass of catalyst.
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Tabacchi G, Vanoni MA, Gamba A, Fois E. Does Negative Hyperconjugation Assist Enzymatic Dehydrogenations? Chemphyschem 2007; 8:1283-8. [PMID: 17506039 DOI: 10.1002/cphc.200700085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gloria Tabacchi
- Dipartimento di Scienze Chimiche ed Ambientali and INSTM, Università degli Studi dell'Insubria, Via Lucini 3, I-22100 Como, Italy
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23
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Spanó E, Tabacchi G, Gamba A, Fois E. On the role of Ti(IV) as a Lewis acid in the chemistry of titanium zeolites: Formation, structure, reactivity, and aging of Ti-peroxo oxidizing intermediates. A first principles study. J Phys Chem B 2007; 110:21651-61. [PMID: 17064121 DOI: 10.1021/jp065494m] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ethylene epoxidation cycle in a H2O2/H2O-loaded Ti zeolite has been simulated by a Car-Parrinello approach. Results indicate a process where the zeolitic framework is the active oxygen mediator. The dissociative chemisorption of H2O2 leads, via a transient Ti-hydroperoxo species, to H2O and a Ti-peroxo zeolite intermediate. Transfer of active oxygen to ethylene follows, giving the epoxide and recovering the catalyst. A thorough theoretical characterization indicates that the active oxidizing species is an asymmetric eta2-Ti-peroxo, absorbing in the visible range. The lability of the intermediate is found related to eta2 <--> eta1 interconversions of the Ti-peroxo structure. The interconversions, triggered by water molecules, could account for the experimentally found reduced catalytic activity in aged TS-1 catalysts. The results provide a microscopic picture of the reactivity and dehydration/aging processes of the catalyst fully consistent with experiments and highlight the fundamental role of the Lewis acid character of Ti in the formation, reactivity, and degradation of the active oxidizing species.
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Affiliation(s)
- Eleonora Spanó
- Dipartimento di Scienze Chimiche ed Ambientali, University of Insubria at Como, and INSTM udr Como, Via Lucini 3, I-22100 Como, Italy
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24
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Fitzpatrick PF. Carbanion versus hydride transfer mechanisms in flavoprotein-catalyzed dehydrogenations. Bioorg Chem 2004; 32:125-39. [PMID: 15110192 DOI: 10.1016/j.bioorg.2003.02.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2003] [Indexed: 11/26/2022]
Abstract
The present understanding of the mechanisms by which flavoproteins oxidize amino acid or hydroxy acids to the respective imino or keto acids is reviewed. The observation that many of these enzymes catalyze the elimination of HBr or HCl from the appropriate beta-halogenated substrate was long considered evidence for a carbanion intermediate. Recent structural and mechanistic studies are not compatible with the intermediacy of carbanions in the reactions catalyzed by d-amino acid oxidase and flavocytochrome b(2). In contrast, the data are most consistent with mechanisms involving direct hydride transfer.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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25
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Tilocca A, Selloni A. Reaction pathway and free energy barrier for defect-induced water dissociation on the (101) surface of TiO2-anatase. J Chem Phys 2003. [DOI: 10.1063/1.1607306] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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