1
|
Bak DW, Weerapana E. Proteomic strategies to interrogate the Fe-S proteome. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119791. [PMID: 38925478 PMCID: PMC11365765 DOI: 10.1016/j.bbamcr.2024.119791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Iron‑sulfur (Fe-S) clusters, inorganic cofactors composed of iron and sulfide, participate in numerous essential redox, non-redox, structural, and regulatory biological processes within the cell. Though structurally and functionally diverse, the list of all proteins in an organism capable of binding one or more Fe-S clusters is referred to as its Fe-S proteome. Importantly, the Fe-S proteome is highly dynamic, with continuous cluster synthesis and delivery by complex Fe-S cluster biogenesis pathways. This cluster delivery is balanced out by processes that can result in loss of Fe-S cluster binding, such as redox state changes, iron availability, and oxygen sensitivity. Despite continued expansion of the Fe-S protein catalogue, it remains a challenge to reliably identify novel Fe-S proteins. As such, high-throughput techniques that can report on native Fe-S cluster binding are required to both identify new Fe-S proteins, as well as characterize the in vivo dynamics of Fe-S cluster binding. Due to the recent rapid growth in mass spectrometry, proteomics, and chemical biology, there has been a host of techniques developed that are applicable to the study of native Fe-S proteins. This review will detail both the current understanding of the Fe-S proteome and Fe-S cluster biology as well as describing state-of-the-art proteomic strategies for the study of Fe-S clusters within the context of a native proteome.
Collapse
Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States of America.
| |
Collapse
|
2
|
Lundahl MN, Greiner MB, Piquette MC, Gannon PM, Kaminsky W, Kovacs JA. Exploring the influence of H-bonding and ligand constraints on thiolate ligated non-heme iron mediated dioxygen activation. Chem Sci 2024; 15:12710-12720. [PMID: 39148773 PMCID: PMC11325341 DOI: 10.1039/d4sc02787f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/05/2024] [Indexed: 08/17/2024] Open
Abstract
Converting triplet dioxygen into a powerful oxidant is fundamentally important to life. The study reported herein quantitatively examines the formation of a well-characterized, reactive, O2-derived thiolate ligated FeIII-superoxo using low-temperature stopped-flow kinetics. Comparison of the kinetic barriers to the formation of this species via two routes, involving either the addition of (a) O2 to [FeII(S2 Me2N3(Pr,Pr))] (1) or (b) superoxide to [FeIII(S2 Me2N3(Pr,Pr))]+ (3) is shown to provide insight into the mechanism of O2 activation. Route (b) was shown to be significantly slower, and the kinetic barrier 14.9 kJ mol-1 higher than route (a), implying that dioxygen activation involves inner-sphere, as opposed to outer sphere, electron transfer from Fe(ii). H-bond donors and ligand constraints are shown to dramatically influence O2 binding kinetics and reversibility. Dioxygen binds irreversibly to [FeII(S2 Me2N3(Pr,Pr))] (1) in tetrahydrofuran, but reversibly in methanol. Hydrogen bonding decreases the ability of the thiolate sulfur to stabilize the transition state and the FeIII-superoxo, as shown by the 10 kJ mol-1 increase in the kinetic barrier to O2 binding in methanol vs. tetrahydrofuran. Dioxygen release from [FeIII(S2 Me2N3(Pr,Pr))O2] (2) is shown to be 24 kJ mol-1 higher relative to previously reported [FeIII(SMe2N4(tren))(O2)]+ (5), the latter of which contains a more flexible ligand. These kinetic results afford an experimentally determined reaction coordinate that illustrates the influence of H-bonding and ligand constraints on the kinetic barrier to dioxygen activation an essential step in biosynthetic pathways critical to life.
Collapse
Affiliation(s)
- Maike N Lundahl
- Department of Chemistry, University of Washington Campus Box 351700 Seattle WA 98195 USA
| | - Maria B Greiner
- Department of Chemistry, University of Washington Campus Box 351700 Seattle WA 98195 USA
| | - Marc C Piquette
- Department of Chemistry, Tufts University 62 Talbot Avenue Medford Massachusetts 02155 USA
| | - Paige M Gannon
- Department of Chemistry, University of Washington Campus Box 351700 Seattle WA 98195 USA
| | - Werner Kaminsky
- Department of Chemistry, University of Washington Campus Box 351700 Seattle WA 98195 USA
| | - Julie A Kovacs
- Department of Chemistry, University of Washington Campus Box 351700 Seattle WA 98195 USA
| |
Collapse
|
3
|
Krishnan A, Waheed SO, Melayikandy S, LaRouche C, Paik M, Schofield CJ, Karabencheva-Christova TG. Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH. Chemphyschem 2024:e202400303. [PMID: 38839574 DOI: 10.1002/cphc.202400303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Aspartyl/asparaginyl hydroxylase (AspH) catalyzes the post-translational hydroxylations of vital human proteins, playing an essential role in maintaining their biological functions. Single-point mutations in the Second Coordination Sphere (SCS) and long-range (LR) residues of AspH have been linked to pathological conditions such as the ophthalmologic condition Traboulsi syndrome and chronic kidney disease (CKD). Although the clinical impacts of these mutations are established, there is a critical knowledge gap regarding their specific atomistic effects on the catalytic mechanism of AspH. In this study, we report integrated computational investigations on the potential mechanistic implications of four mutant forms of human AspH with clinical importance: R735W, R735Q, R688Q, and G434V. All the mutant forms exhibited altered binding interactions with the co-substrate 2-oxoglutarate (2OG) and the main substrate in the ferric-superoxo and ferryl complexes, which are critical for catalysis, compared to the wild-type (WT). Importantly, the mutations strongly influence the energetics of the frontier molecular orbitals (FMOs) and, thereby, the activation energies for the hydrogen atom transfer (HAT) step compared to the WT AspH. Insights from our study can contribute to enzyme engineering and the development of selective modulators for WT and mutants of AspH, ultimately aiding in treating cancers, Traboulsi syndrome and, CKD.
Collapse
Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Sreerag Melayikandy
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Techno, Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Meredith Paik
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | | |
Collapse
|
4
|
Vennelakanti V, Jeon M, Kulik HJ. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases? Inorg Chem 2024; 63:4997-5011. [PMID: 38428015 DOI: 10.1021/acs.inorgchem.3c04421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.
Collapse
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mugyeom Jeon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
5
|
Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
Collapse
Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
| | | |
Collapse
|
6
|
Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024; 45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.
Collapse
Affiliation(s)
- Freya Edholm
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
7
|
Tofoni A, Tavani F, Vandone M, Braglia L, Borfecchia E, Ghigna P, Stoian DC, Grell T, Stolfi S, Colombo V, D’Angelo P. Full Spectroscopic Characterization of the Molecular Oxygen-Based Methane to Methanol Conversion over Open Fe(II) Sites in a Metal-Organic Framework. J Am Chem Soc 2023; 145:21040-21052. [PMID: 37721732 PMCID: PMC10540213 DOI: 10.1021/jacs.3c07216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 09/19/2023]
Abstract
Iron-based enzymes efficiently activate molecular oxygen to perform the oxidation of methane to methanol (MTM), a reaction central to the contemporary chemical industry. Conversely, a very limited number of artificial catalysts have been devised to mimic this process. Herein, we employ the MIL-100(Fe) metal-organic framework (MOF), a material that exhibits isolated Fe sites, to accomplish the MTM conversion using O2 as the oxidant under mild conditions. We apply a diverse set of advanced operando X-ray techniques to unveil how MIL-100(Fe) can act as a catalyst for direct MTM conversion. Single-phase crystallinity and stability of the MOF under reaction conditions (200 or 100 °C, CH4 + O2) are confirmed by X-ray diffraction measurements. X-ray absorption, emission, and resonant inelastic scattering measurements show that thermal treatment above 200 °C generates Fe(II) sites that interact with O2 and CH4 to produce methanol. Experimental evidence-driven density functional theory (DFT) calculations illustrate that the MTM reaction involves the oxidation of the Fe(II) sites to Fe(III) via a high-spin Fe(IV)═O intermediate. Catalyst deactivation is proposed to be caused by the escape of CH3• radicals from the relatively large MOF pore cages, ultimately resulting in the formation of hydroxylated triiron units, as proven by valence-to-core X-ray emission spectroscopy. The O2-based MTM catalytic activity of MIL-100(Fe) in the investigated conditions is demonstrated for two consecutive reaction cycles, proving the MOF potential toward active site regeneration. These findings will desirably lay the groundwork for the design of improved MOF catalysts for the MTM conversion.
Collapse
Affiliation(s)
- Alessandro Tofoni
- Dipartimento
di Chimica, Università degli Studi
di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Rome, Italy
| | - Francesco Tavani
- Dipartimento
di Chimica, Università degli Studi
di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Rome, Italy
| | - Marco Vandone
- Dipartimento
di Chimica & UdR INSTM di Milano, Università
degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Luca Braglia
- CNR-Istituto
Officina dei Materiali, TASC, 34149 Trieste, Italy
| | - Elisa Borfecchia
- Dipartimento
di Chimica & UdR INSTM di Torino, Università
di Torino, Via P. Giuria
7, 10125 Turin, Italy
| | - Paolo Ghigna
- Dipartimento
di Chimica, Università di Pavia, V.le Taramelli 13, I-27100 Pavia, Italy
| | - Dragos Costantin Stoian
- The Swiss-Norwegian
Beamlines (SNBL), European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Toni Grell
- Dipartimento
di Chimica & UdR INSTM di Milano, Università
degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Sara Stolfi
- CNR-Istituto
Officina dei Materiali, TASC, 34149 Trieste, Italy
| | - Valentina Colombo
- Dipartimento
di Chimica & UdR INSTM di Milano, Università
degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
- CNR
− SCITEC − Istituto di Scienze e Tecnologie Chimiche
“Giulio Natta”, Via Golgi 19, 20133 Milan, Italy
| | - Paola D’Angelo
- Dipartimento
di Chimica, Università degli Studi
di Roma “La Sapienza”, P.le A. Moro 5, I-00185 Rome, Italy
| |
Collapse
|
8
|
Braun A, Gee LB, Mara MW, Hill EA, Kroll T, Nordlund D, Sokaras D, Glatzel P, Hedman B, Hodgson KO, Borovik AS, Baker ML, Solomon EI. X-ray Spectroscopic Study of the Electronic Structure of a Trigonal High-Spin Fe(IV)═O Complex Modeling Non-Heme Enzyme Intermediates and Their Reactivity. J Am Chem Soc 2023; 145:18977-18991. [PMID: 37590931 PMCID: PMC10631461 DOI: 10.1021/jacs.3c06181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Fe K-edge X-ray absorption spectroscopy (XAS) has long been used for the study of high-valent iron intermediates in biological and artificial catalysts. 4p-mixing into the 3d orbitals complicates the pre-edge analysis but when correctly understood via 1s2p resonant inelastic X-ray scattering and Fe L-edge XAS, it enables deeper insight into the geometric structure and correlates with the electronic structure and reactivity. This study shows that in addition to the 4p-mixing into the 3dz2 orbital due to the short iron-oxo bond, the loss of inversion in the equatorial plane leads to 4p mixing into the 3dx2-y2,xy, providing structural insight and allowing the distinction of 6- vs 5-coordinate active sites as shown through application to the Fe(IV)═O intermediate of taurine dioxygenase. Combined with O K-edge XAS, this study gives an unprecedented experimental insight into the electronic structure of Fe(IV)═O active sites and their selectivity for reactivity enabled by the π-pathway involving the 3dxz/yz orbitals. Finally, the large effect of spin polarization is experimentally assigned in the pre-edge (i.e., the α/β splitting) and found to be better modeled by multiplet simulations rather than by commonly used time-dependent density functional theory.
Collapse
Affiliation(s)
- Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Leland B Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Michael W Mara
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Ethan A Hill
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dennis Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Pieter Glatzel
- ESRF-The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - A S Borovik
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Michael L Baker
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
- The University of Manchester at Harwell, Diamond Light Source, Harwell Campus, Didcot OX11 0DE, U.K
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| |
Collapse
|
9
|
Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
Collapse
Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
| |
Collapse
|
10
|
Smithwick ER, Wilson RH, Chatterjee S, Pu Y, Dalluge JJ, Damodaran AR, Bhagi-Damodaran A. Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542349. [PMID: 37292651 PMCID: PMC10245910 DOI: 10.1101/2023.05.25.542349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.
Collapse
Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Yu Pu
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| |
Collapse
|
11
|
Xiong J, Liu Q, Lavina B, Hu MY, Zhao J, Alp EE, Deng L, Ye S, Guo Y. Spin polarization assisted facile C-H activation by an S = 1 iron(iv)-bisimido complex: a comprehensive spectroscopic and theoretical investigation. Chem Sci 2023; 14:2808-2820. [PMID: 36937578 PMCID: PMC10016330 DOI: 10.1039/d2sc06273a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
High valent iron terminal imido species (Fe[double bond, length as m-dash]NR) have been shown to be key reactive intermediates in C-H functionalization. However, the detailed structure-reactivity relationship in Fe[double bond, length as m-dash]NR species derived from studies of structurally well-characterized high-valent Fe[double bond, length as m-dash]NR complexes are still scarce, and the impact of imido N-substituents (electron-donating vs. electron-withdrawing) on their electronic structures and reactivities has not been thoroughly explored. In this study, we report spectroscopic and computational studies on a rare S = 1 iron(iv)-bisimido complex featuring trifluoromethyl groups on the imido N-substituents, [(IPr)Fe(NC(CF3)2Ph)2] (2), and two closely related S = 0 congeners bearing alkyl and aryl substituents, [(IPr)Fe(NC(CMe3)2Ph)2] (3) and [(IPr)Fe(NDipp)2] (1), respectively. Compared with 1 and 3, 2 exhibits a decreased Fe[double bond, length as m-dash]NR bond covalency due to the electron-withdrawing and the steric effect of the N-substituents, which further leads to a pseudo doubly degenerate ground electronic structure and spin polarization induced β spin density on the imido nitrogens. This unique electronic structure, which differs from those of the well-studied Fe(iv)-oxido complexes and many previously reported Fe(iv)-imido complexes, provides both kinetic and thermodynamic advantages for facile C-H activation, compared to the S = 0 counterparts.
Collapse
Affiliation(s)
- Jin Xiong
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania 15213 USA
| | - Qing Liu
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Barbara Lavina
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
- Center for Advanced Radiation Sources, University of Chicago Chicago Illinois 60439 USA
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Esen E Alp
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Liang Deng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University Pittsburgh Pennsylvania 15213 USA
| |
Collapse
|
12
|
Kastner DW, Nandy A, Mehmood R, Kulik HJ. Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- David W. Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
13
|
Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
Collapse
Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
14
|
Khamespanah F, Patel NM, Forney AK, Heitger DR, Amarasekarage CM, Springer LE, Belecki K, Lucas HR. Flavonol dioxygenase chemistry mediated by a synthetic nickel superoxide. J Inorg Biochem 2023; 238:112021. [PMID: 36395718 DOI: 10.1016/j.jinorgbio.2022.112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/01/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022]
Abstract
Nature exploits transition metal centers to enhance and tune the oxidizing power of natural oxidants such as O2 and H2O2. The design and interrogation of synthetic metallocomplexes with similar reactivity to metalloproteins provides one strategy for gaining insight into the mechanistic underpinnings of oxygen-activating enzymes such as oxidases, oxygenases, and dioxygenases like Ni-quercetinase (Ni-QueD). Ni-QueD catalyzes the oxidative ring opening of the polyphenol quercetin, a natural product with antioxidant properties. Herein, we report the synthesis and characterization of Ni(13-DOB), a Ni(II) species complexed by an N4-macrocycle that has been characterized by single crystal X-ray crystallography. Ni(13-DOB) forms a Ni-superoxide intermediate (Ni(13-DOB)O2•-) upon treatment with H2O2 and Et3N, as verified by resonance Raman spectroscopy. We demonstrate through UV/vis and LCMS that Ni(13-DOB)O2•- is capable of the 1-electron oxidation of flavonols, including both 3-hydroxyflavone (3-HF, the simplest flavonol) and quercetin itself. Incorporation of two O-atoms into the flavonol radical via superoxide from Ni(13-DOB)O2•- precedes oxidative cleavage of the flavonol scaffold in each case, consistent with quercetinase ring cleavage by Ni-QueD in Streptomyces sp. FLA. Conversion of 3-HF into 2-hydroxybenzoylbenzoic acid was accomplished with catalytic turnover of Ni(13-DOB) at ambient temperature, as confirmed by HPLC timecourses and GCMS analysis of isotopic labeling studies. The Ni(13-DOB)-mediated oxidative cleavage of quercetin to the corresponding biomimetic phenolic ester was also verified through 18O-isotopic labeling studies. Through the HPLC characterization of both on- and off-pathway products of flavonol dioxygenation by Ni(13-DOB)O2•-, the stringent reaction pathway control provided by enzyme active sites is highlighted.
Collapse
Affiliation(s)
- F Khamespanah
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - N M Patel
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - A K Forney
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - D R Heitger
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - C M Amarasekarage
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - L E Springer
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America
| | - K Belecki
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America.
| | - H R Lucas
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, United States of America.
| |
Collapse
|
15
|
Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
Collapse
Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
16
|
Wilson RH, Chatterjee S, Smithwick ER, Dalluge JJ, Bhagi-Damodaran A. Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-heme Iron Enzymes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
17
|
Wang B, Wu P, Shaik S. Critical Roles of Exchange and Superexchange Interactions in Dictating Electron Transfer and Reactivity in Metalloenzymes. J Phys Chem Lett 2022; 13:2871-2877. [PMID: 35325545 DOI: 10.1021/acs.jpclett.2c00513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Electron transfer (ET) is a fundamental process in transition-metal-dependent metalloenzymes. In these enzymes, the spin-spin interactions within the same metal center and/or between different metal sites can play a pivotal role in the catalytic cycle and reactivity. This Perspective highlights that the exchange and/or superexchange interactions can intrinsically modulate the inner-sphere and long-range electron transfer, thus controlling the mechanism and activity of metalloenzymes. For mixed-valence diiron oxygenases, the spin-regulated inner-sphere ET can be dictated by exchange interactions, leading to efficient O-O bond activations. Likewise, the spin-regulated inner-sphere ET can be enhanced by both exchange and superexchange interactions in [Fe4S4]-dependent SAM enzymes, which enable the efficient cleavage of the S─C(γ) or S─C5' bond of SAM. In addition to inner-sphere ET, superexchange interactions may modulate the long-range ET between metalloenzymes. We anticipate that the exchange and superexchange enhanced reactivity could be applicable in other important metalloenzymes, such as Photosystem II and nitrogenases.
Collapse
Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
18
|
Rhoda HM, Heyer AJ, Snyder BER, Plessers D, Bols ML, Schoonheydt RA, Sels BF, Solomon EI. Second-Sphere Lattice Effects in Copper and Iron Zeolite Catalysis. Chem Rev 2022; 122:12207-12243. [PMID: 35077641 DOI: 10.1021/acs.chemrev.1c00915] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transition-metal-exchanged zeolites perform remarkable chemical reactions from low-temperature methane to methanol oxidation to selective reduction of NOx pollutants. As with metalloenzymes, metallozeolites have impressive reactivities that are controlled in part by interactions outside the immediate coordination sphere. These second-sphere effects include activating a metal site through enforcing an "entatic" state, controlling binding and access to the metal site with pockets and channels, and directing radical rebound vs cage escape. This review explores these effects with emphasis placed on but not limited to the selective oxidation of methane to methanol with a focus on copper and iron active sites, although other transition-metal-ion zeolite reactions are also explored. While the actual active-site geometric and electronic structures are different in the copper and iron metallozeolites compared to the metalloenzymes, their second-sphere interactions with the lattice or the protein environments are found to have strong parallels that contribute to their high activity and selectivity.
Collapse
Affiliation(s)
- Hannah M Rhoda
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander J Heyer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Benjamin E R Snyder
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dieter Plessers
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Max L Bols
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Robert A Schoonheydt
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Bert F Sels
- Department of Microbial and Molecular Systems, Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Photon Science, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| |
Collapse
|
19
|
Song X, Liu J, Wang B. Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitong Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| |
Collapse
|
20
|
Davydov R, Herzog AE, Jodts RJ, Karlin KD, Hoffman BM. End-On Copper(I) Superoxo and Cu(II) Peroxo and Hydroperoxo Complexes Generated by Cryoreduction/Annealing and Characterized by EPR/ENDOR Spectroscopy. J Am Chem Soc 2022; 144:377-389. [PMID: 34981938 PMCID: PMC8785356 DOI: 10.1021/jacs.1c10252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this report, we investigate the physical and chemical properties of monocopper Cu(I) superoxo and Cu(II) peroxo and hydroperoxo complexes. These are prepared by cryoreduction/annealing of the parent [LCuI(O2)]+ Cu(I) dioxygen adducts with the tripodal, N4-coordinating, tetradentate ligands L = PVtmpa, DMMtmpa, TMG3tren and are best described as [LCuII(O2•-)]+ Cu(II) complexes that possess end-on (η1-O2•-) superoxo coordination. Cryogenic γ-irradiation (77 K) of the EPR-silent parent complexes generates mobile electrons from the solvent that reduce the [LCuII(O2•-)]+ within the frozen matrix, trapping the reduced form fixed in the structure of the parent complex. Cryoannealing, namely progressively raising the temperature of a frozen sample in stages and then cooling back to low temperature at each stage for examination, tracks the reduced product as it relaxes its structure and undergoes chemical transformations. We employ EPR and ENDOR (electron-nuclear double resonance) as powerful spectroscopic tools for examining the properties of the states that form. Surprisingly, the primary products of reduction of the Cu(II) superoxo species are metastable cuprous superoxo [LCuI(O2•-)]+ complexes. During annealing to higher temperatures this state first undergoes internal electron transfer (IET) to form the end-on Cu(II) peroxo state, which is then protonated to form Cu(II)-OOH species. This is the first time these methods, which have been used to determine key details of metalloenzyme catalytic cycles and are a powerful tools for tracking PCET reactions, have been applied to copper coordination compounds.
Collapse
Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
| | - Austin E Herzog
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Richard J Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201, United States
| |
Collapse
|
21
|
Ma S, Mandalapu D, Wang S, Zhang Q. Biosynthesis of cyclopropane in natural products. Nat Prod Rep 2021; 39:926-945. [PMID: 34860231 DOI: 10.1039/d1np00065a] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2021Cyclopropane attracts wide interests in the fields of synthetic and pharmaceutical chemistry, and chemical biology because of its unique structural and chemical properties. This structural motif is widespread in natural products, and is usually essential for biological activities. Nature has evolved diverse strategies to access this structural motif, and increasing knowledge of the enzymes forming cyclopropane (i.e., cyclopropanases) has been revealed over the last two decades. Here, the scientific literature from the last two decades relating to cyclopropane biosynthesis is summarized, and the enzymatic cyclopropanations, according to reaction mechanism, which can be grouped into two major pathways according to whether the reaction involves an exogenous C1 unit from S-adenosylmethionine (SAM) or not, is discussed. The reactions can further be classified based on the key intermediates required prior to cyclopropane formation, which can be carbocations, carbanions, or carbon radicals. Besides the general biosynthetic pathways of the cyclopropane-containing natural products, particular emphasis is placed on the mechanism and engineering of the enzymes required for forming this unique structure motif.
Collapse
Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | | | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
22
|
Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Phys Chem Chem Phys 2021; 23:22227-22240. [PMID: 34586107 PMCID: PMC8516722 DOI: 10.1039/d1cp03800a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA alkylation is used as the key epigenetic mark in eukaryotes, however, most alkylation in DNA can result in deleterious effects. Therefore, this process needs to be tightly regulated. The enzymes of the AlkB and Ten-Eleven Translocation (TET) families are members of the Fe and alpha-ketoglutarate-dependent superfamily of enzymes that are tasked with dealkylating DNA and RNA in cells. Members of these families span all species and are an integral part of transcriptional regulation. While both families catalyze oxidative dealkylation of various bases, each has specific preference for alkylated base type as well as distinct catalytic mechanisms. This perspective aims to provide an overview of computational work carried out to investigate several members of these enzyme families including AlkB, ALKB Homolog 2, ALKB Homolog 3 and Ten-Eleven Translocate 2. Insights into structural details, mutagenesis studies, reaction path analysis, electronic structure features in the active site, and substrate preferences are presented and discussed.
Collapse
Affiliation(s)
- Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, USA
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas, 76201, USA.
| |
Collapse
|