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Hwang D, Wrigley LM, Lee M, Sobolewski AL, Domcke W, Schlenker CW. Local Hydrogen Bonding Determines Branching Pathways in Intermolecular Heptazine Photochemistry. J Phys Chem B 2023. [PMID: 37471476 DOI: 10.1021/acs.jpcb.3c01397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Heptazine is the molecular core of the widely studied photocatalyst carbon nitride. By analyzing the excited-state intermolecular proton-coupled electron-transfer (PCET) reaction between a heptazine derivative and a hydrogen-atom donor substrate, we are able to spectroscopically identify the resultant heptazinyl reactive radical species on a picosecond time scale. We provide detailed spectroscopic characterization of the tri-anisole heptazine:4-methoxyphenol hydrogen-bonded intermolecular complex (TAHz:MeOPhOH), using femtosecond transient absorption spectroscopy and global analysis, to reveal distinct product absorption signatures at ∼520, 1250, and 1600 nm. We assign these product peaks to the hydrogenated TAHz radical (TAHzH•) based on control experiments utilizing 1,4-dimethoxybenzene (DMB), which initiates electron transfer without concomitant proton transfer, i.e., no excited-state PCET. Additional control experiments with radical quenchers, protonation agents, and UV-vis-NIR spectroelectrochemistry also corroborate our product peak assignments. These spectral assignments allowed us to monitor the influence of the local hydrogen-bonding environment on the resulting evolution of photochemical products from excited-state PCET of heptazines. We observe that the preassociation of heptazine with the substrate in solution is extremely sensitive to the hydrogen-bond-accepting character of the solvent. This sensitivity directly influences which product signatures we detect with time-resolved spectroscopy. The spectral signature of the TAHzH• radical assigned in this work will facilitate future in-depth analysis of heptazine and carbon nitride photochemistry. Our results may also be utilized for designing improved PCET-based photochemical systems that will require precise control over local molecular environments. Examples include applications such as preparative synthesis involving organic photoredox catalysis, on-site solar water purification, as well as photocatalytic water splitting and artificial photosynthesis.
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Affiliation(s)
- Doyk Hwang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Liam M Wrigley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Micah Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Cody W Schlenker
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, Washington 98195-1652, United States
- Clean Energy Institute, University of Washington, Seattle, Washington 98195-1653, United States
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Reis RAG, Li H, Johnson M, Sobrado P. New frontiers in flavin-dependent monooxygenases. Arch Biochem Biophys 2021; 699:108765. [PMID: 33460580 DOI: 10.1016/j.abb.2021.108765] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of redox reactions in important biological processes and are responsible for the synthesis of highly complex natural products. Although much has been learned about FMO chemistry in the last ~80 years of research, several aspects of the reactions catalyzed by these enzymes remain unknown. In this review, we summarize recent advancements in the flavin-dependent monooxygenase field including aspects of flavin dynamics, formation and stabilization of reactive species, and the hydroxylation mechanism. Novel catalysis of flavin-dependent N-oxidases involving consecutive oxidations of amines to generate oximes or nitrones is presented and the biological relevance of the products is discussed. In addition, the activity of some FMOs have been shown to be essential for the virulence of several human pathogens. We also discuss the biomedical relevance of FMOs in antibiotic resistance and the efforts to identify inhibitors against some members of this important and growing family enzymes.
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Affiliation(s)
| | - Hao Li
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Maxim Johnson
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Blacksburg, VA, 24061, USA; Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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Beaupre BA, Reabe KR, Roman JV, Moran GR. Hydrogen movements in the oxidative half-reaction of kynurenine 3-monooxygenase from Pseudomonas fluorescens reveal the mechanism of hydroxylation. Arch Biochem Biophys 2020; 690:108474. [PMID: 32687799 DOI: 10.1016/j.abb.2020.108474] [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] [Received: 05/01/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 11/30/2022]
Abstract
Kynurenine 3-monoxygenase (KMO) catalyzes the conversion of l-kynurenine (L-Kyn) to 3-hydroxykynurenine (3-OHKyn) in the pathway for tryptophan catabolism. We have investigated the effects of pH and deuterium substitution on the oxidative half-reaction of KMO from P. fluorescens (PfKMO). The three phases observed during the oxidative half reaction are formation of the hydroperoxyflavin, hydroxylation and product release. The measured rate constants for these phases proved largely unchanging with pH, suggesting that the KMO active site is insulated from exchange with solvent during catalysis. A solvent inventory study indicated that a solvent isotope effect of 2-3 is observed for the hydroxylation phase and that two or more protons are in flight during this step. An inverse isotope effect of 0.84 ± 0.01 on the rate constant for the hydroxylation step with ring perdeutero-L-Kyn as a substrate indicates a shift from sp2 to sp3 hybridization in the transition state leading to the formation of a non-aromatic intermediate. The pH dependence of transient state data collected for the substrate analog meta-nitrobenzoylalanine indicate that groups proximal to the hydroperoxyflavin are titrated in the range pH 5-8.5 and can be described by a pKa of 8.8. That higher pH values do not slow the rate of hydroxylation precludes that the pKa measured pertains to the proton of the hydroperoxflavin. Together, these observations indicate that the C4a-hydroperoxyflavin has a pKa ≫ 8.5, that a non-aromatic species is the immediate product of hydroxylation and that at least two solvent derived protons are in-flight during oxygen insertion to the substrate aromatic ring. A unifying mechanistic proposal for these observations is proposed.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Karen R Reabe
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI, 53211-3029, USA
| | - Joseph V Roman
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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Tweedy SE, Rodríguez Benítez A, Narayan ARH, Zimmerman PM, Brooks CL, Wymore T. Hydroxyl Radical-Coupled Electron-Transfer Mechanism of Flavin-Dependent Hydroxylases. J Phys Chem B 2019; 123:8065-8073. [PMID: 31532200 DOI: 10.1021/acs.jpcb.9b08178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Class A flavin-dependent hydroxylases (FdHs) catalyze the hydroxylation of organic compounds in a site- and stereoselective manner. In stark contrast, conventional synthetic routes require environmentally hazardous reagents and give modest yields. Thus, understanding the detailed mechanism of this class of enzymes is essential to their rational manipulation for applications in green chemistry and pharmaceutical production. Both electrophilic substitution and radical intermediate mechanisms have been proposed as interpretations of FdH hydroxylation rates and optical spectra. While radical mechanistic steps are often difficult to examine directly, modern quantum chemistry calculations combined with statistical mechanical approaches can yield detailed mechanistic models providing insights that can be used to differentiate reaction pathways. In the current work, we report quantum mechanical/molecular mechanical (QM/MM) calculations on the fungal TropB enzyme that shows an alternative reaction pathway in which hydroxylation through a hydroxyl radical-coupled electron-transfer mechanism is significantly favored over electrophilic substitution. Furthermore, QM/MM calculations on several modified flavins provide a more consistent interpretation of the experimental trends in the reaction rates seen experimentally for a related enzyme, para-hydroxybenzoate hydroxylase. These calculations should guide future enzyme and substrate design strategies and broaden the scope of biological spin chemistry.
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Control of catalysis in flavin-dependent monooxygenases. Arch Biochem Biophys 2010; 493:26-36. [DOI: 10.1016/j.abb.2009.11.028] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Revised: 11/17/2009] [Accepted: 11/17/2009] [Indexed: 11/17/2022]
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Ridder L, Harvey JN, Rietjens IMCM, Vervoort J, Mulholland AJ. Ab Initio QM/MM Modeling of the Hydroxylation Step in p-Hydroxybenzoate Hydroxylase. J Phys Chem B 2003. [DOI: 10.1021/jp026213n] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lars Ridder
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom, Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands, and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Jeremy N. Harvey
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom, Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands, and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Ivonne M. C. M. Rietjens
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom, Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands, and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Jacques Vervoort
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom, Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands, and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Adrian J. Mulholland
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom, Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands, and Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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Ridder L, Mulholland AJ, Rietjens IM, Vervoort J. Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase. J Mol Graph Model 1999; 17:163-75, 214. [PMID: 10736773 DOI: 10.1016/s1093-3263(99)00027-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the C4a-hydroperoxyflavin intermediate in the PHBH reaction cycle was built on the basis of the crystal structure coordinates of the enzyme-substrate complex. A reaction pathway for the subsequent hydroxylation step was calculated by imposing a reaction coordinate that involves cleavage of the peroxide oxygen-oxygen bond and formation of the carbon-oxygen bond between the C3 atom of the substrate and the distal oxygen of the peroxide moiety of the cofactor. The geometric changes and the Mulliken charge distributions along the calculated reaction pathway are in line with an electrophilic aromatic substitution type of mechanism. The energy barrier of the calculated reaction is considerably lower when the substrate hydroxyl moiety is deprotonated, in comparison with the barrier found with a protonated hydroxyl moiety. This effect of the protonation state of the substrate on the calculated energy barrier supports experimental observations that deprotonation is required for hydroxylation of the substrate. A notable event in the calculated reaction pathway is a lengthening of the peroxide oxygen-oxygen bond at an intermediate stage. Further analysis of the reaction pathway indicates that this oxygen-oxygen bond elongation is accompanied by an increase in electrophilic reactivity on the distal oxygen of the peroxide moiety, which may assist the C-O bond formation in the reaction of the C4a-hydroperoxyflavin intermediate with the substrate. Analysis of the effect of individual active site residues on the reaction reveals a specific transition state stabilization by the backbone carbonyl moiety of Pro293. The crystal water 717 appears to drive the hydroxylation step through a stabilizing hydrogen bond interaction to the proximal oxygen of the C4a-hydroperoxyflavin intermediate, which increases in strength as the hydroperoxyflavin cofactor converts to the anionic (deprotonated) hydroxyflavin.
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Affiliation(s)
- L Ridder
- Laboratory of Biochemistry, Wageningen University, The Netherlands.
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Peräkylä M, Pakkanen TA. Ab initio molecular orbital study on reactivity of phenol, biphenyl, benzoate and p-hydroxybenzoate in the ˙OH addition reaction and stability of the corresponding ˙H and ˙OH cyclohexadienyl adducts. ACTA ACUST UNITED AC 1995. [DOI: 10.1039/p29950001405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Peelen S, Rietjens IM, van Berkel WJ, van Workum WA, Vervoort J. 19F-NMR study on the pH-dependent regioselectivity and rate of the ortho-hydroxylation of 3-fluorophenol by phenol hydroxylase from Trichosporon cutaneum. Implications for the reaction mechanism. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 218:345-53. [PMID: 8269923 DOI: 10.1111/j.1432-1033.1993.tb18383.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The regioselectivity and rate of the ortho-hydroxylation of 3-fluorophenol by phenol hydroxylase from Trichosporon cutaneum (EC 1.14.13.7) was studied using 19F-NMR. The regioselective hydroxylation as well as the rate of ortho-hydroxylation are pH dependent with a pKa of 6.5. At pH values below 6.5, 3-fluorophenol preferentially becomes hydroxylated at the C6 ortho position, resulting in a maximum C6/C2 hydroxylation ratio of 6.7. Upon increasing the pH, the total rate of conversion increases. Also, the C2 ortho-hydroxylation increases relatively to the C6 ortho-hydroxylation and yields a minimum C6/C2 hydroxylation ratio of 2.2 at pH values above 7.5. Based on data from 19F-NMR binding studies and molecular orbital calculations, a hypothesis is put forward which explains the pH-dependent effects observed. A mechanism is proposed involving an active-site amino acid residue acting as a base in the reduced form of the protein. Deprotonation of this residue results in hydrogen bond formation with the hydroxyl moiety of the phenolic substrate, leading to (partial) deprotonation of the substrate. Molecular orbital calculations demonstrate that such a (partial) deprotonation increases (a) the overall reactivity of 3-fluorophenol for an electrophilic attack and (b) the reactivity of C2 relative to the C6 position. The hypothesis may explain the decrease in the C6/C2 hydroxylation ratio. Furthermore the increased amount of ortho-hydroxylated products formed with increasing pH can also be explained by this hypothesis.
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Affiliation(s)
- S Peelen
- Department of Biochemistry, Agricultural University, The Netherlands
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On the reaction mechanism of phenol hydroxylase. New information obtained by correlation of fluorescence and absorbance stopped flow studies. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53590-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Vervoort J, Rietjens IM, van Berkel WJ, Veeger C. Frontier orbital study on the 4-hydroxybenzoate-3-hydroxylase-dependent activity with benzoate derivatives. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 206:479-84. [PMID: 1597186 DOI: 10.1111/j.1432-1033.1992.tb16950.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Based on molecular orbital computer calculations the present paper provides a new hypothesis for catalytic characteristics of 4-hydroxybenzoate-3-hydroxylase (EC 1.14.13.2). A clear correlation between in kcat for the conversion of a series of 4-hydroxylated substrates and their E(HOMO) leads to the hypothesis that Frontier orbital HOMO characteristics [E(HOMO) and HOMO density on C3] of the substrates are the predominant factor in regulating the fate of a benzoate derivative at the active site of the enzyme. The HOMO characteristics can be used to explain whether a compound will be converted by the enzyme or merely acts as an effector. Furthermore, the hypothesis provides quantitative theoretical support for a catalytic mechanism in which the substrate reacts in its dianionic form and for a mechanism in which the electrophilic attack of the C(4a)-peroxyflavin, or of the hydroxyl radical derived from it, on the benzoate dianion is the rate limiting step in catalysis at pH 8, 25 degrees C. Finally, it is demonstrated that the hypothesis can be used as a basis for the formulation of working hypotheses in future research, investigating the conversion and regioselective orientation of the various possible substrates in the active site of the wild-type 4-hydroxybenzoate-3-hydroxylase, its mutants as well as of various other flavin-dependent aromatic hydroxylases, such as for example 3-hydroxybenzoate-4-hydroxylase (EC 1.14.13.23), 3-hydroxybenzoate-6-hydroxylase (EC 1.14.13.24) and phenol hydroxylase (EC 1.14.13.7).
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Affiliation(s)
- J Vervoort
- Department of Biochemistry, Agricultural University, Wageningen, The Netherlands
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