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Jungen S, Chen P. Alkyl Radical Generation by an Intramolecular Homolytic Substitution Reaction between Iron(II) and Trialkylsulfonium Groups. Chemistry 2018; 24:11008-11020. [PMID: 29768681 DOI: 10.1002/chem.201801952] [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: 04/19/2018] [Revised: 05/15/2018] [Indexed: 11/08/2022]
Abstract
Intramolecular, homolytic substitution reactions between iron(II) species and various trialkylsulfonium groups were directly observed in the gas phase upon collision-induced dissociation. In spite of the notoriously low reduction potential of trialkylsulfonium species and the mismatched oxidation potential of iron(II), the reactions proceed at moderate collision energies, forming an alkyl radical as well as a thioether coordinated to the iron. In contrast to classical homolytic substitutions, the attacking radical is a "metalloradical", namely iron(II) that is oxidized to iron(III) during the reaction. With this process we demonstrate that the conceptually analogous, putative radical generation step in radical S-adenosyl methionine (SAM) enzymes is possible and plausible. Further, we show that this kind of reaction only occurs in constrained systems with a defined geometry. Combining experimental measurements with DFT studies and NBO analyses allowed us to gain insights into the reactivity and transition states of these systems. Based on our findings, we challenge the notion of a collinear transition state in the radical generation step of radical SAM enzymes and propose it to be bent instead.
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Affiliation(s)
- Stefan Jungen
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
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2
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Ruszczycky MW, Liu HW. Theory and Application of the Relationship Between Steady-State Isotope Effects on Enzyme Intermediate Concentrations and Net Rate Constants. Methods Enzymol 2017; 596:459-499. [PMID: 28911781 PMCID: PMC5837895 DOI: 10.1016/bs.mie.2017.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Steady-state kinetic isotope effects on enzyme-catalyzed reactions are often interpreted in terms of the microscopic rate constants associated with the elementary reactions of interest. Unfortunately, this approach can lead to confusion, especially when more than one elementary reaction is isotopically sensitive, because it forces one to consider the full catalytic cycle one step at a time rather than as a complete whole. Herein we argue that shifting focus from intrinsic effects to net rate constants and enzyme intermediate concentrations provides a more natural and holistic interpretation by which the effects of partial rate limitation are more easily understood. In doing so, we demonstrate how the experimental determination of isotope effects on enzyme intermediate concentrations allows a direct determination of isotope effects on net rate constants. The chapter is divided into three main sections. The first outlines the basic theory and its interpretation. The second discusses an application of the theory in the study of the radical SAM enzyme DesII. The final section then provides the complete mathematical treatment.
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Affiliation(s)
| | - Hung-Wen Liu
- University of Texas at Austin, Austin, TX, United States
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Abstract
DesII is a member of the radical SAM family of enzymes that catalyzes radical-mediated transformations of TDP-4-amino-4,6-didexoy-D-glucose as well as other sugar nucleotide diphosphates. Like nearly all radical SAM enzymes, the reactions begin with the reductive homolysis of SAM to produce a 5'-deoxyadenosyl radical which is followed by regiospecific hydrogen atom abstraction from the substrate. What happens next, however, depends on the nature of the substrate radical so produced. In the case of the biosynthetically relevant substrate, a radical-mediated deamination ensues; however, when this amino group is replaced with a hydroxyl, one instead observes dehydrogenation. The factors that govern the fate of the initially generated substrate radical as well as the mechanistic details underlying these transformations have been a key focus of research into the chemistry of DesII. This review will discuss recent discoveries pertaining to the enzymology of DesII, how it may relate to understanding other radical-mediated lyases and dehydrogenases and the working hypotheses currently being investigated regarding the mechanism of DesII catalysis.
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Affiliation(s)
- Mark W. Ruszczycky
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 576] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Lee SC, Lo W, Holm RH. Developments in the biomimetic chemistry of cubane-type and higher nuclearity iron-sulfur clusters. Chem Rev 2014; 114:3579-600. [PMID: 24410527 PMCID: PMC3982595 DOI: 10.1021/cr4004067] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Wayne Lo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Corresponding Authors: S. C. Lee: . R. H. Holm:
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Gerlach DL, Coucouvanis D, Kampf J, Lehnert N. Isolation and Characterization of Single and Sulfide-Bridged Double [4Fe-4S] Cubane Clusters with 4-Pyridinethiolato Ligands. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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EPR-kinetic isotope effect study of the mechanism of radical-mediated dehydrogenation of an alcohol by the radical SAM enzyme DesII. Proc Natl Acad Sci U S A 2013; 110:2088-93. [PMID: 23329328 DOI: 10.1073/pnas.1209446110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The radical S-adenosyl-L-methionine enzyme DesII from Streptomyces venezuelae is able to oxidize the C3 hydroxyl group of TDP-D-quinovose to the corresponding ketone via an α-hydroxyalkyl radical intermediate. It is unknown whether electron transfer from the radical intermediate precedes or follows its deprotonation, and answering this question would offer considerable insight into the mechanism by which the small but important class of radical-mediated alcohol dehydrogenases operate. This question can be addressed by measuring steady-state kinetic isotope effects (KIEs); however, their interpretation is obfuscated by the degree to which the steps of interest limit catalysis. To circumvent this problem, we measured the solvent deuterium KIE on the saturating steady-state concentration of the radical intermediate using electron paramagnetic resonance spectroscopy. The resulting value, 0.22 ± 0.03, when combined with the solvent deuterium KIE on the maximum rate of turnover (V) of 1.8 ± 0.2, yielded a KIE of 8 ± 2 on the net rate constant specifically associated with the α-hydroxyalkyl radical intermediate. This result implies that electron transfer from the radical intermediate does not precede deprotonation. Further analysis of these isotope effects, along with the pH dependence of the steady-state kinetic parameters, likewise suggests that DesII must be in the correct protonation state for initial generation of the α-hydroxyalkyl radical. In addition to providing unique mechanistic insights, this work introduces a unique approach to investigating enzymatic reactions using KIEs.
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Ruszczycky MW, Ogasawara Y, Liu HW. Radical SAM enzymes in the biosynthesis of sugar-containing natural products. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1231-44. [PMID: 22172915 PMCID: PMC3438383 DOI: 10.1016/j.bbapap.2011.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
Abstract
Carbohydrates play a key role in the biological activity of numerous natural products. In many instances their biosynthesis requires radical mediated rearrangements, some of which are catalyzed by radical SAM enzymes. BtrN is one such enzyme responsible for the dehydrogenation of a secondary alcohol in the biosynthesis of 2-deoxystreptamine. DesII is another example that catalyzes a deamination reaction necessary for the net C4 deoxygenation of a glucose derivative en route to desosamine formation. BtrN and DesII represent the two most extensively characterized radical SAM enzymes involved in carbohydrate biosynthesis. In this review, we summarize the biosynthetic roles of these two enzymes, their mechanisms of catalysis, the questions that have arisen during these investigations and the insight they can offer for furthering our understanding of radical SAM enzymology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Mark W. Ruszczycky
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yasushi Ogasawara
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Vey JL, Drennan CL. Structural insights into radical generation by the radical SAM superfamily. Chem Rev 2011; 111:2487-506. [PMID: 21370834 PMCID: PMC5930932 DOI: 10.1021/cr9002616] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica L Vey
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Deng L, Majumdar A, Lo W, Holm RH. Stabilization of 3:1 site-differentiated cubane-type clusters in the [Fe(4)S(4)](1+) core oxidation state by tertiary phosphine ligation: synthesis, core structural diversity, and S = 1/2 ground states. Inorg Chem 2010; 49:11118-26. [PMID: 21038882 DOI: 10.1021/ic101702b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An extensive series of 3:1 site-differentiated cubane-type clusters [Fe(4)S(4)(PPr(i)(3))(3)L] (L = Cl(-), Br(-), I(-), RO(-), RS(-), RSe(-)) has been prepared in 40-80% yield by two methods: ligand substitution of [Fe(4)S(4)(PPr(i)(3))(4)](1+) in tetrahydrofuran (THF)/acetonitrile by reaction with monoanions, and reductive cleavage of ligand substrates (RSSR, RSeSeR, I(2)) by the all-ferrous clusters [Fe(8)S(8)(PPr(i)(3))(6)]/[Fe(16)S(16)(PPr(i)(3))(8)] in THF. These neutral clusters are stable and do not undergo ligand redistribution reactions involving charged species in benzene and THF solutions. X-ray structural studies confirm the cubane stereochemistry but with substantial and variable distortions of the [Fe(4)S(4)](1+) core from idealized cubic core geometry. Based on Fe-S bond lengths, seven clusters were found to have compressed tetragonal distortions (4 short and 8 long bonds), and the remaining seven display other types of distortions with different combinations of long, short, and intermediate bond lengths. These results further emphasize the facile deformabililty of this core oxidation state previously observed in [Fe(4)S(4)(SR)(4)](3-) clusters. The Fe(2.25+) mean oxidation state was demonstrated from (57)Fe isomer shifts, and the appearance of two quadrupole doublets arises from the spin-coupled |9/2,4,1/2> state. The S = 1/2 ground state was further supported by electron paramagnetic resonance spectra and magnetic susceptibility data.
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Affiliation(s)
- Liang Deng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins. Proc Natl Acad Sci U S A 2009; 106:14867-71. [PMID: 19706452 DOI: 10.1073/pnas.0904385106] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Radical S-adenosine-L-methionine (SAM or AdoMet) proteins are involved in chemically difficult reactions including the synthesis of cofactors, the generation of protein radicals, and the maturation of complex organometallic catalytic sites. In the first and common step of the reaction, a conserved [Fe4S4] cluster donates an electron to perform the reductive cleavage of AdoMet into methionine and a reactive radical 5'-dA. species. The latter extracts a hydrogen atom from substrate eliciting one of the about 40 reactions so far characterized for this family of proteins. It has been suggested that the radical-generating mechanism differs depending on whether AdoMet is a cofactor or a substrate. It has also been speculated that electron transfer from the [Fe4S4] cluster to AdoMet is sulfur-based. Here we have used protein crystallography and theoretical calculations to show that regardless whether AdoMet serves as a cofactor or a substrate, the 5'-dA. generating mechanism should be common to the radical SAM proteins studied so far, and that electron transfer is mediated by a unique Fe from the conserved [Fe4S4] cluster. This unusual electron transfer is determined by the sulfonium ion in AdoMet.
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Control of radical chemistry in the AdoMet radical enzymes. Curr Opin Chem Biol 2009; 13:74-83. [PMID: 19269883 DOI: 10.1016/j.cbpa.2009.01.022] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 01/30/2009] [Indexed: 11/20/2022]
Abstract
The radical AdoMet superfamily comprises a diverse set of >2800 enzymes that utilize iron-sulfur clusters and S-adenosylmethionine (SAM or AdoMet) to initiate a diverse set of radical-mediated reactions. The intricate control these enzymes exercise over the radical transformations they catalyze is an amazing feat of elegance and sophistication in biochemistry. This review focuses on the accumulating evidence for how these enzymes control this remarkable chemistry, including controlling the reactivity between the iron-sulfur cluster and AdoMet, and controlling the subsequent radical transformations.
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van der Geer EPL, van Koten G, Klein Gebbink RJM, Hessen B. A [4Fe−4S] Cluster Dimer Bridged by Bis(2,2′:6′,2″-terpyridine-4′-thiolato)iron(II). Inorg Chem 2008; 47:2849-57. [DOI: 10.1021/ic702062q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erwin P. L. van der Geer
- Chemical Biology & Organic Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gerard van Koten
- Chemical Biology & Organic Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robertus J. M. Klein Gebbink
- Chemical Biology & Organic Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bart Hessen
- Chemical Biology & Organic Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Abstract
Persulfurated arenes have been known for about 50 years but they were underexploited in chemistry in spite of facile, mild, and high-yielding syntheses. Their properties (redox potentials, UV/Vis absorption, conductivity, nonlinear optical properties, etc.) are mainly due to the aromaticity of the ring with sp2-hybridized carbon atoms and to the electronic contribution from numerous divalent sulfur ligands, which also stabilize negative or positive charges. The characteristic conformational patterns of the sulfur ligands often facilitate preorganization in supramolecular assemblies, with or without thiophilic metal cations, for designing redox sensors, ion-selective membranes, clathrates, organic conductors, nonlinear optical materials, liquid crystals, coordination polymers, and bioinorganic systems. A new class of supramolecules with various molecular shapes such as asterisks, chains, wheels, and windmills were reported.
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Affiliation(s)
- Marc Gingras
- Chemistry Laboratory of Organic and Metallic Materials (CMOM), Faculty of Sciences, University of Nice-Sophia Antipolis, France.
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