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Zhang P, Lee WZ, Ye S. Insights into dioxygen binding on metal centers: an ab initio multireference electronic structure analysis. Phys Chem Chem Phys 2024. [PMID: 39301704 DOI: 10.1039/d4cp02915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Why does binding of dioxygen (O2) to metal centers, the initial step of O2 storage, transportation, and activation, almost inevitably induce metal-to-O2 single-electron transfer and generate superoxo (O2-˙) species, instead of genuine O02 adducts? To address this question, this study describes highly correlated wavefunction-based ab initio calculations using CASSCF/NEVPT2 (CASSCF = complete active space self-consistent field, and NEVPT2 = N-electron valence state second-order perturbation theory) approaches to explore the electronic-structure evolution of O2 association on Fe(II)(BDPP) (H2BDPP = 2,6-bis((2-(S)-diphenylhydroxylmethyl-1-pyrrolidinyl)methyl)pyridine) and Co(II)(BDPP) to produce S = 3 Fe(III)(BDPP)(O2-˙) (1) and Co(III)(BDPP)(O2-˙) (2). CASSCF/NEVPT2 calculations suggest that the processes furnishing 1 and 2 feature an avoided crossing resulting from interactions of two diabatic curves, of which one is characterized as Co(II) and Fe(II) centers interacting with a triplet O2 ligand and the other as Co(III) and Fe(III) centers bound to a superoxo ligand. In both cases, the avoided crossing induces a one-electron transfer from the divalent metal center to the incoming O2 ligand and leads to formation of trivalent metal-O2-˙ complexes. To facilitate the interpretation of complicated multireference wavefunctions, we formulated two-fragment spin eigenfunctions utilizing Clebsch-Gordan coefficients (CGCs) to rationalize computed spin populations on the metal centers and the O2 ligand and compared these results with usual valence bonding (VB) analyses. It turns out that both methods give the same results and are complementary to each other. Finally, the limitation of DFT approaches in describing complex electronic structures involving metal-ligand magnetic couplings is delineated.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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2
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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; 25:e202400303. [PMID: 38839574 DOI: 10.1002/cphc.202400303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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.
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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
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3
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Hota PK, Panda S, Phan H, Kim B, Siegler MA, Karlin KD. Dioxygenase Chemistry in Nucleophilic Aldehyde Deformylations Utilizing Dicopper O 2-Derived Peroxide Complexes. J Am Chem Soc 2024; 146:23854-23871. [PMID: 39141923 DOI: 10.1021/jacs.4c06243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The chemistry of copper-dioxygen complexes is relevant to copper enzymes in biology as well as in (ligand)Cu-O2 (or Cu2-O2) species utilized in oxidative transformations. For overall energy considerations, as applicable in chemical synthesis, it is beneficial to have an appropriate atom economy; both O-atoms of O2(g) are transferred to the product(s). However, examples of such dioxygenase-type chemistry are extremely rare or not well documented. Herein, we report on nucleophilic oxidative aldehyde deformylation reactivity by the peroxo-dicopper(II) species [Cu2II(BPMPO-)(O22-)]1+ {BPMPO-H = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} and [Cu2II(XYLO-)(O22-)]1+ (XYLO- = a BPMPO- analogue possessing bis(2-{2-pyridyl}ethyl)amine chelating arms). Their dicopper(I) precursors are dioxygenase catalysts. The O2(g)-derived peroxo-dicopper(II) intermediates react rapidly with aldehydes like 2-phenylpropionaldehyde (2-PPA) and cyclohexanecarboxaldehyde (CCA) in 2-methyltetrahydrofuran at -90 °C. Warming to room temperature (RT) followed by workup results in good yields of formate (HC(O)O-) along with ketones (acetophenone or cyclohexanone). Mechanistic investigation shows that [Cu2II(BPMPO-)(O22-)]1+ species initially reacts reversibly with the aldehydes to form detectable dicopper(II) peroxyhemiacetal intermediates, for which optical titrations provide the Keq (at -90 °C) of 73.6 × 102 M-1 (2-PPA) and 10.4 × 102 M-1 (CCA). In the reaction of [Cu2II(XYLO-)(O22-)]1+ with 2-PPA, product complexes characterized by single-crystal X-ray crystallography are the anticipated dicopper(I) complex, [Cu2I(XYLO-)]1+ plus a mixed-valent Cu(I)Cu(II)-formate species. Formate was further identified and confirmed by 1H NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) analysis. Using 18O2(g)-isotope labeling the reaction produced a high yield of 18-O incorporated acetophenone as well as formate. The overall results signify that true dioxygenase reactions have occurred, supported by a thorough mechanistic investigation.
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Affiliation(s)
- Pradip Kumar Hota
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hai Phan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Bohee Kim
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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4
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Su Y, Lai W. Unraveling the Mechanism of the Oxidative C-C Bond Coupling Reaction Catalyzed by Deoxypodophyllotoxin Synthase. Inorg Chem 2024; 63:13948-13958. [PMID: 39008659 DOI: 10.1021/acs.inorgchem.4c01263] [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: 07/17/2024]
Abstract
Deoxypodophyllotoxin synthase (DPS), a nonheme Fe(II)/2-oxoglutarate (2OG)-dependent oxygenase, is a key enzyme that is involved in the construction of the fused-ring system in (-)-podophyllotoxin biosynthesis by catalyzing the C-C coupling reaction. However, the mechanistic details of DPS-catalyzed ring formation remain unclear. Herein, our quantum mechanics/molecular mechanics (QM/MM) calculations reveal a novel mechanism that involves the recycling of CO2 (a product of decarboxylation of 2OG) to prevent the formation of hydroxylated byproducts. Our results show that CO2 can react with the FeIII-OH species to generate an unusual FeIII-bicarbonate species. In this way, hydroxylation is avoided by consuming the OH group. Then, the C-C coupling followed by desaturation yields the final product, deoxypodophyllotoxin. This work highlights the crucial role of the CO2 molecule, generated in the crevice between the iron active site and the substrate, in controlling the reaction selectivity.
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Affiliation(s)
- Yanzhuang Su
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Wenzhen Lai
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
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5
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Thomas M, Jaber Sathik Rifayee SB, Chaturvedi SS, Gorantla KR, White W, Wildey J, Schofield CJ, Christov CZ. The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A. Inorg Chem 2024; 63:10737-10755. [PMID: 38781256 PMCID: PMC11168414 DOI: 10.1021/acs.inorgchem.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.
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Affiliation(s)
- Midhun
George Thomas
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | | | - Shobhit S. Chaturvedi
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Koteswara Rao Gorantla
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Walter White
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Jon Wildey
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12, Mansfield Road, Oxford OX1 5JJ, U.K.
| | - Christo Z. Christov
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
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6
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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.
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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
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7
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Burke EJ, Copeland RA, Dixit Y, Krebs C, Bollinger JM. Steric Perturbation of the Grob-like Final Step of Ethylene-Forming Enzyme Enables 3-Hydroxypropionate and Propylene Production. J Am Chem Soc 2024; 146:1977-1983. [PMID: 38226594 DOI: 10.1021/jacs.3c09733] [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: 01/17/2024]
Abstract
Ethylene-forming enzyme (EFE) is an iron(II)-dependent dioxygenase that fragments 2-oxoglutarate (2OG) to ethylene (from C3 and C4) and 3 equivs of carbon dioxide (from C1, C2, and C5). This major ethylene-forming pathway requires l-arginine as the effector and competes with a minor pathway that merely decarboxylates 2OG to succinate as it oxidatively fragments l-arginine. We previously proposed that ethylene forms in a polar-concerted (Grob-like) fragmentation of a (2-carboxyethyl)carbonatoiron(II) intermediate, formed by the coupling of a C3-C5-derived propion-3-yl radical to a C1-derived carbonate coordinated to the Fe(III) cofactor. Replacement of one or both C4 hydrogens of 2OG by fluorine, methyl, or hydroxyl favored the elimination products 2-(F1-2/Me/OH)-3-hydroxypropionate and CO2 over the expected olefin or carbonyl products, implying strict stereoelectronic requirements in the final step, as is known for Grob fragmentations. Here, we substituted active-site residues expected to interact sterically with the proposed Grob intermediate, aiming to disrupt or enable the antiperiplanar disposition of the carboxylate electrofuge and carbonate nucleofuge required for concerted fragmentation. The bulk-increasing A198L substitution barely affects the first partition between the major and minor pathways but then, as intended, markedly diminishes ethylene production in favor of 3-hydroxypropionate. Conversely, the bulk-diminishing L206V substitution enables propylene formation from (4R)-methyl-2OG, presumably by allowing the otherwise sterically disfavored antiperiplanar conformation of the Grob intermediate bearing the extra methyl group. The results provide additional evidence for a polar-concerted ethylene-yielding step and thus for the proposed radical-polar crossover via substrate-radical coupling to the Fe(III)-coordinated carbonate.
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Affiliation(s)
- Evan J Burke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Rachelle A Copeland
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yash Dixit
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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8
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Jaber Sathik Rifayee SB, Chaturvedi SS, Warner C, Wildey J, White W, Thompson M, Schofield CJ, Christov CZ. Catalysis by KDM6 Histone Demethylases - A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions. Chemistry 2023; 29:e202301305. [PMID: 37258457 PMCID: PMC10526731 DOI: 10.1002/chem.202301305] [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: 04/25/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/02/2023]
Abstract
KDM6A (UTX) and KDM6B (JMJD3) are human non-heme Fe(II) and 2-oxoglutarate (2OG) dependent JmjC oxygenases that catalyze the demethylation of trimethylated lysine 27 in the N-terminal tail of histone H3, a post-translational modification that regulates transcription. A Combined Quantum Mechanics/ Molecular Mechanics (QM/MM) and Molecular Dynamics (MD) study on the catalytic mechanism of KDM6A/B reveals that the transition state for the rate-limiting hydrogen atom transfer (HAT) reaction in KDM6A catalysis is stabilized by polar (Asn217) and aromatic (Trp369)/non-polar (Pro274) residues in contrast to KDM4, KDM6B and KDM7 demethylases where charged residues (Glu, Arg, Asp) are involved. KDM6A employs both σ- and π-electron transfer pathways for HAT, whereas KDM6B employs the σ-electron pathway. Differences in hydrogen bonding of the Fe-chelating Glu252(KDM6B) contribute to the lower energy barriers in KDM6B vs. KDM6A. The study reveals a dependence of the activation barrier of the rebound hydroxylation on the Fe-O-C angle in the transition state of KDM6A. Anti-correlation of the Zn-binding domain with the active site residues is a key factor distinguishing KDM6A/B from KDM7/4s. The results reveal the importance of communication between the Fe center, second coordination sphere, and long-range interactions in catalysis by KDMs and, by implication, other 2OG oxygenases.
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Affiliation(s)
| | | | - Cait Warner
- Department of Biological Sciences, Michigan Technological University, Houghton, MI-49931, USA
| | - Jon Wildey
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI-49931, USA
| | - Walter White
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Martin Thompson
- 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
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
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9
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Li L, Lai S, Lin H, Zhao X, Li X, Chen X, Liu J, Yang G, Zhan C. QM/MM study on the O2 activation reaction of 4-hydroxylphenyl pyruvate dioxygenase reveals a common mechanism for α-ketoglutarate dependent dioxygenase. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Weberg AB, Murphy RP, Tomson NC. Oriented internal electrostatic fields: an emerging design element in coordination chemistry and catalysis. Chem Sci 2022; 13:5432-5446. [PMID: 35694353 PMCID: PMC9116365 DOI: 10.1039/d2sc01715f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/21/2022] Open
Abstract
The power of oriented electrostatic fields (ESFs) to influence chemical bonding and reactivity is a phenomenon of rapidly growing interest. The presence of strong ESFs has recently been implicated as one of the most significant contributors to the activity of select enzymes, wherein alignment of a substrate's changing dipole moment with a strong, local electrostatic field has been shown to be responsible for the majority of the enzymatic rate enhancement. Outside of enzymology, researchers have studied the impacts of "internal" electrostatic fields via the addition of ionic salts to reactions and the incorporation of charged functional groups into organic molecules (both experimentally and computationally), and "externally" via the implementation of bulk fields between electrode plates. Incorporation of charged moieties into homogeneous inorganic complexes to generate internal ESFs represents an area of high potential for novel catalyst design. This field has only begun to materialize within the past 10 years but could be an area of significant impact moving forward, since it provides a means for tuning the properties of molecular complexes via a method that is orthogonal to traditional strategies, thereby providing possibilities for improved catalytic conditions and novel reactivity. In this perspective, we highlight recent developments in this area and offer insights, obtained from our own research, on the challenges and future directions of this emerging field of research.
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Affiliation(s)
- Alexander B Weberg
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| | - Ryan P Murphy
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| | - Neil C Tomson
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
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11
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Kelty ML, McNeece AJ, Kurutz JW, Filatov AS, Anderson JS. Electrostatic vs. inductive effects in phosphine ligand donor properties and reactivity. Chem Sci 2022; 13:4377-4387. [PMID: 35509471 PMCID: PMC9007067 DOI: 10.1039/d1sc04277g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/15/2022] [Indexed: 11/21/2022] Open
Abstract
Enhanced rates and selectivity in enzymes are enabled in part by precisely tuned electric fields within active sites. Analogously, the use of charged groups to leverage electrostatics in molecular systems is a promising strategy to tune reactivity. However, separation of the through space and through bond effects of charged functional groups is a long standing challenge that limits the rational application of electric fields in molecular systems. To address this challenge we developed a method using the phosphorus selenium coupling value (J P-Se) of anionic phosphine selenides to quantify the electrostatic contribution of the borate moiety to donor strength. In this analysis we report the synthesis of a novel anionic phosphine, PPh2CH2BF3K, the corresponding tetraphenyl phosphonium and tetraethyl ammonium selenides [PPh4][SePPh2CH2BF3] and [TEA][SePPh2CH2BF3], and the Rh carbonyl complex [PPh4][Rh(acac)(CO)(PPh2(CH2BF3))]. Solvent-dependent changes in J P-Se were fit using Coulomb's law and support up to an 80% electrostatic contribution to the increase in donor strength of [PPh4][SePPh2CH2BF3] relative to SePPh2Et, while controls with [TEA][SePPh2CH2BF3] exclude convoluting ion pairing effects. Calculations using explicit solvation or point charges effectively replicate the experimental data. This J P-Se method was extended to [PPh4][SePPh2(2-BF3Ph)] and likewise estimates up to a 70% electrostatic contribution to the increase in donor strength relative to SePPh3. The use of PPh2CH2BF3K also accelerates C-F oxidative addition reactivity with Ni(COD)2 by an order of magnitude in comparison to the comparatively donating neutral phosphines PEt3 and PCy3. This enhanced reactivity prompted the investigation of catalytic fluoroarene C-F borylation, with improved yields observed for less fluorinated arenes. These results demonstrate that covalently bound charged functionalities can exert a significant electrostatic influence under common solution phase reaction conditions and experimentally validate theoretical predictions regarding electrostatic effects in reactivity.
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Affiliation(s)
- Margaret L Kelty
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - Andrew J McNeece
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - Josh W Kurutz
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - Alexander S Filatov
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
| | - John S Anderson
- Department of Chemistry, University of Chicago 929 E 57th St Chicago IL 60637 USA
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12
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Tarrago M, Ye S, Neese F. Electronic structure analysis of electrochemical CO2 reduction by iron-porphyrins reveals basic requirements to design catalysts bearing non-innocent ligands. Chem Sci 2022; 13:10029-10047. [PMID: 36128248 PMCID: PMC9430493 DOI: 10.1039/d2sc01863b] [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: 03/31/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
Electrocatalytic CO2 reduction is a possible solution to the increasing CO2 concentration in the earth atmosphere, because it enables storage of energy while using the harmful CO2 feedstock as starting...
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Affiliation(s)
- Maxime Tarrago
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Shengfa Ye
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
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13
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Lin HY, Chen X, Dong J, Yang JF, Xiao H, Ye Y, Li LH, Zhan CG, Yang WC, Yang GF. Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study. J Am Chem Soc 2021; 143:15674-15687. [PMID: 34542283 DOI: 10.1021/jacs.1c06227] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing demands for efficient and versatile chemical reactions have prompted innovations in enzyme engineering. A major challenge in engineering α-ketoglutarate-dependent oxygenases is to develop a rational strategy which can be widely used for directly evolving the desired mutant to generate new products. Herein, we report a strategy for rational redesign of a model enzyme, 4-hydroxyphenylpyruvate dioxygenase (HPPD), based on quantum mechanics/molecular mechanics (QM/MM) calculation and molecular dynamic simulations. This strategy enriched our understanding of the HPPD catalytic reaction pathway and led to the discovery of a series of HPPD mutants producing hydroxyphenylacetate (HPA) as the alternative product other than the native product homogentisate. The predicted HPPD-Fe(IV)═O-HPA intermediate was further confirmed by the crystal structure of Arabidopsis thaliana HPPD/S267W complexed with HPA. These findings not only provide a good understanding of the structure-function relationship of HPPD but also demonstrate a generally applicable platform for the development of biocatalysts.
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Affiliation(s)
- Hong-Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Xi Chen
- College of Chemistry and Material Science, South-Central University for Nationalities, Wuhan 430074, P.R. China
| | - Jin Dong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Han Xiao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Ying Ye
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Lin-Hui Li
- College of Chemistry and Material Science, South-Central University for Nationalities, Wuhan 430074, P.R. China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
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14
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Winslow C, Lee HB, Field MJ, Teat SJ, Rittle J. Structure and Reactivity of a High-Spin, Nonheme Iron(III)- Superoxo Complex Supported by Phosphinimide Ligands. J Am Chem Soc 2021; 143:13686-13693. [PMID: 34424708 DOI: 10.1021/jacs.1c05276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonheme iron oxygenases utilize dioxygen to accomplish challenging chemical oxidations. A further understanding of the Fe-O2 intermediates implicated in these processes is challenged by their highly transient nature. To that end, we have developed a ligand platform featuring phosphinimide donors intended to stabilize oxidized, high-spin iron complexes. O2 exposure of single crystals of a three-coordinate Fe(II) complex of this framework allowed for in crystallo trapping of a terminally bound Fe-O2 complex suitable for XRD characterization. Spectroscopic and computational studies of this species support a high-spin Fe(III) center antiferromagnetically coupled to a superoxide ligand, similar to that proposed for numerous nonheme iron oxygenases. In addition to the apparent stability of this synthetic Fe-O2 complex, its ability to engage in a range of stoichiometric and catalytic oxidation processes demonstrates that this iron-phosphinimide system is primed for development in modeling oxidizing bioinorganic intermediates and green oxidation chemistry.
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Affiliation(s)
- Charles Winslow
- College of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Heui Beom Lee
- College of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Mackenzie J Field
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan Rittle
- College of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
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15
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Ramanan R, Waheed SO, Schofield CJ, Christov CZ. What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field? Chemistry 2021; 27:11827-11836. [PMID: 33989435 PMCID: PMC9212892 DOI: 10.1002/chem.202101174] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 11/11/2022]
Abstract
Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2-oxoglutarate dependent Jumonji-C (JmjC) Nϵ-methyl lysine histone demethylases also have N-methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N-methyl arginine demethylation by human KDM4E and compare the results with those reported for N-methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen-bond between the substrate Ser1 and Tyr178. The calculations imply that in either C-H or N-H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N-methyl arginine demethylation, electron transfer occurs via a σ-channel; the transition state for the N-H pathway is ∼10 kcal/mol higher than for the C-H pathway due to the higher bond dissociation energy of the N-H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier-lowering effect on the C-H pathway, by contrast, such EEFs inhibit the N-H activation rate. The overall results imply that KDM4 catalyzed N-methyl arginine demethylation and N-methyl lysine demethylation occur via similar C-H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates.
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Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
- Present address: Department of Chemistry, National Institute of Technology, Rourkela, Odisha 769001, India
| | - Sodiq O. Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Christopher J. Schofield
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, The Chemistry Research Laboratory, Mansfield Road, University of Oxford, OX1 5JJ, United Kingdom
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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16
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Singh W, Hui C, Li C, Huang M. Thebaine is Selectively Demethylated by Thebaine 6- O-Demethylase and Codeine-3- O-demethylase at Distinct Binding Sites: A Computational Study. Inorg Chem 2021; 60:10199-10214. [PMID: 34213893 DOI: 10.1021/acs.inorgchem.1c00468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Two homologous 2-oxoglutarate-dependent (ODD) nonheme enzymes thebaine 6-O-demethylase (T6ODM) and codeine-3-O-demethylase (CODM), are involved in the morphine biosynthesis pathway from thebaine, catalyzing the O-demethylation reaction with precise regioselectivity at C6 and C3 positions of thebaine respectively. We investigated the origin of the regioselectivity of these enzymes by combined molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations and found that Thebaine binds at the two distinct sites of T6ODM and CODM, which determines the regioselectivity of the enzymes. A remarkable oxo rotation is observed in the decarboxylation process. Starting from the closed pentacoordinate configuration, the C-terminal lid adopts an open conformation in the octahedral Fe(IV) = O complex to facilitate the subsequent demethylation. Phe241 and Phe311 stabilize the substrate in the binding pocket, while Arg219 acts as a gatekeeper residue to stabilize the substrate. Our results unravel the regioselectivity in 2-OG dependent nonheme enzymes and may shed light for exploring the substrate scope of these enzymes and developing novel biotechnology for morphine biosynthesis.
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Affiliation(s)
- Warispreet Singh
- Department of Chemistry & Chemical Engineering, Queen's University, Belfast BT9 5AG, United Kingdom
| | - Chenggong Hui
- Department of Chemistry & Chemical Engineering, Queen's University, Belfast BT9 5AG, United Kingdom
| | - Chun Li
- Key Lab of Industrial Biocatalysis Ministry of Education, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Meilan Huang
- Department of Chemistry & Chemical Engineering, Queen's University, Belfast BT9 5AG, United Kingdom
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17
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Ásgeirsson V, Birgisson BO, Bjornsson R, Becker U, Neese F, Riplinger C, Jónsson H. Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following. J Chem Theory Comput 2021; 17:4929-4945. [PMID: 34275279 DOI: 10.1021/acs.jctc.1c00462] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of reactions. It can make efficient use of parallel computing as the calculations of the discretization points, the so-called images, can be carried out simultaneously. In typical implementations, the images are distributed evenly along the path by connecting adjacent images with equally stiff springs. However, for systems with a high degree of flexibility, this can lead to poor resolution near the saddle point. By making the spring constants increase with energy, the resolution near the saddle point is improved. To assess the performance of this energy-weighted CI-NEB method, calculations are carried out for a benchmark set of 121 molecular reactions. The performance of the method is analyzed with respect to the input parameters. Energy-weighted springs are found to greatly improve performance and result in successful location of the saddle points in less than a thousand energy and force evaluations on average (about a hundred per image) using the same set of parameter values for all of the reactions. Even better performance is obtained by stopping the calculation before full convergence and complete the saddle point search using an eigenvector following method starting from the location of the climbing image. This combination of methods, referred to as NEB-TS, turns out to be robust and highly efficient as it reduces the average number of energy and force evaluations down to a third, to 305. An efficient and flexible implementation of these methods has been made available in the ORCA software.
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Affiliation(s)
- Vilhjálmur Ásgeirsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Benedikt Orri Birgisson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Ragnar Bjornsson
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr 45470, Germany
| | - Ute Becker
- Max-Planck-Institute for Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institute for Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | | | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
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18
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Wang X, Lin H, Liu J, Zhao X, Chen X, Yang W, Yang G, Zhan CG. The structure of 4-hydroxylphenylpyruvate dioxygenase complexed with 4-hydroxylphenylpyruvic acid reveals an unexpected inhibition mechanism. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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19
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Direct coordination of pterin to Fe II enables neurotransmitter biosynthesis in the pterin-dependent hydroxylases. Proc Natl Acad Sci U S A 2021; 118:2022379118. [PMID: 33876764 PMCID: PMC8053929 DOI: 10.1073/pnas.2022379118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the FeII active site to form a highly reactive FeIV = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-FeIV = O intermediate and characterized its structure as a FeII-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate-bound ternary FeII active site before the O2 reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of FeIV = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the FeII site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the FeII site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes.
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20
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Copeland RA, Davis KM, Shoda TKC, Blaesi EJ, Boal AK, Krebs C, Bollinger JM. An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme. J Am Chem Soc 2021; 143:2293-2303. [PMID: 33522811 DOI: 10.1021/jacs.0c10923] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ethylene-forming enzyme (EFE) is an ambifunctional iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase. In its major (EF) reaction, it converts carbons 1, 2, and 5 of 2OG to CO2 and carbons 3 and 4 to ethylene, a four-electron oxidation drastically different from the simpler decarboxylation of 2OG to succinate mediated by all other Fe/2OG enzymes. EFE also catalyzes a minor reaction, in which the normal decarboxylation is coupled to oxidation of l-arginine (a required activator for the EF pathway), resulting in its conversion to l-glutamate semialdehyde and guanidine. Here we show that, consistent with precedent, the l-Arg-oxidation (RO) pathway proceeds via an iron(IV)-oxo (ferryl) intermediate. Use of 5,5-[2H2]-l-Arg slows decay of the ferryl complex by >16-fold, implying that RO is initiated by hydrogen-atom transfer (HAT) from C5. That this large substrate deuterium kinetic isotope effect has no impact on the EF:RO partition ratio implies that the same ferryl intermediate cannot be on the EF pathway; the pathways must diverge earlier. Consistent with this conclusion, the variant enzyme bearing the Asp191Glu ligand substitution accumulates ∼4 times as much of the ferryl complex as the wild-type enzyme and exhibits a ∼40-fold diminished EF:RO partition ratio. The selective detriment of this nearly conservative substitution to the EF pathway implies that it has unusually stringent stereoelectronic requirements. An active-site, like-charge guanidinium pair, which involves the l-Arg substrate/activator and is unique to EFE among four crystallographically characterized l-Arg-modifying Fe/2OG oxygenases, may serve to selectively stabilize the transition state leading to the unique EF branch.
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21
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Chaturvedi SS, Ramanan R, Hu J, Hausinger RP, Christov CZ. Atomic and Electronic Structure Determinants Distinguish between Ethylene Formation and l-Arginine Hydroxylation Reaction Mechanisms in the Ethylene-Forming Enzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.0c03349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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22
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Chen TY, Ho PH, Spyra CJ, Meyer F, Bill E, Ye S, Lee WZ. Ambiphilicity of a mononuclear cobalt(III) superoxo complex. Chem Commun (Camb) 2020; 56:14821-14824. [PMID: 33151205 DOI: 10.1039/d0cc05337f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Addition of HOTf to a mixture of CoIII(BDPP)(O2˙) (1, H2BDPP = 2,6-bis((2-(S)-diphenylhydroxylmethyl-1-pyrrolidinyl)methyl)pyridine) and Cp*2Fe produced H2O2 in high yield implying formation of CoIII(BDPP)(OOH) (3), and reaction of Sc(OTf)3 with the same mixture gave a peroxo-bridged CoIII/ScIII5. These findings demonstrate the ambiphilic property of CoIII-superoxo 1.
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Affiliation(s)
- Ting-Yi Chen
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan. and Universität Göttingen, Institut für Anorganische Chemie, D-37077 Göttingen, Germany.
| | - Po-Hsun Ho
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan.
| | - Can-Jerome Spyra
- Universität Göttingen, Institut für Anorganische Chemie, D-37077 Göttingen, Germany.
| | - Franc Meyer
- Universität Göttingen, Institut für Anorganische Chemie, D-37077 Göttingen, Germany.
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany.
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. and Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, D-45470, Germany.
| | - Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan. and Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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23
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Latifi R, Minnick JL, Quesne MG, de Visser SP, Tahsini L. Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways. Dalton Trans 2020; 49:4266-4276. [PMID: 32141456 DOI: 10.1039/d0dt00007h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Matthew G Quesne
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon, OX110FA, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, 131 Princess Street, Manchester M1 7DN, UK.
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
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24
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Li X, Zhu W, Liu Y. Mechanistic Insights into the Oxidative Rearrangement Catalyzed by the Unprecedented Dioxygenase ChaP Involved in Chartreusin Biosynthesis. Inorg Chem 2020; 59:13988-13999. [PMID: 32951427 DOI: 10.1021/acs.inorgchem.0c01706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ChaP is a non-heme iron-dependent dioxygenase belonging to the vicinal oxygen chelate (VOC) enzyme superfamily that catalyzes the final α-pyrone ring formation in the biosynthesis of chartreusin. In contrast to other common dioxygenases, for example, 2,3-catechol dioxygenase which uses the dioxygen molecule as the oxidant, ChaP requires the flavin-activated oxygen (O22-) as the equivalent. Previous experiments showed that the ChaP-catalyzed ring rearrangement contains two successive C-C bond cleavages and one lactonization; however, the detailed reaction mechanism is unknown. In this work, on the basis of the recently obtained crystal structure of ChaP, the computational model was constructed and the catalytic mechanism of ChaP was explored by performing quantum mechanical/molecular mechanical (QM/MM) calculations. Our calculation results reveal that ChaP uses the proximal oxygen in iron-coordinated HOO- to attack the carbonyl carbon of the substrate, whereas the previous proposal that Asp49 acts as a base to deprotonate the iron-coordinated HOO- to generate O22- is unlikely. In the first stage reaction, owing to the coordination of the substrate with iron, the substrate is activated by accepting an electron from iron and the resulting oxy-radical intermediate formed by O-O cleavage can easily trigger the ring rearrangement. In the final decarboxylation, the phenolic anion of the substrate cooperatively accepts the proton of iron-coordinated HOO- to facilitate the attack of the distal oxygen, and the proton-coupled electron transfer (PCET) from the substrate to the FeIV═O plays a key role for the decarboxylation. These findings may provide useful information for understanding the ChaP-catalyzed oxidative rearrangement and other flavin-dependent non-heme dioxygenases.
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Affiliation(s)
- Xinyi Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering, Xuzhou Institute of Technology, Xuzhou, Jiangsu 221111, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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25
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Kumar A, Neese F, Valeev EF. Explicitly correlated coupled cluster method for accurate treatment of open-shell molecules with hundreds of atoms. J Chem Phys 2020; 153:094105. [PMID: 32891102 DOI: 10.1063/5.0012753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a near-linear scaling formulation of the explicitly correlated coupled-cluster singles and doubles with the perturbative triples method [CCSD(T)F12¯] for high-spin states of open-shell species. The approach is based on the conventional open-shell CCSD formalism [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] utilizing the domain local pair-natural orbitals (DLPNO) framework. The use of spin-independent set of pair-natural orbitals ensures exact agreement with the closed-shell formalism reported previously, with only marginally impact on the cost (e.g., the open-shell formalism is only 1.5 times slower than the closed-shell counterpart for the C160H322 n-alkane, with the measured size complexity of ≈1.2). Evaluation of coupled-cluster energies near the complete-basis-set (CBS) limit for open-shell systems with more than 550 atoms and 5000 basis functions is feasible on a single multi-core computer in less than 3 days. The aug-cc-pVTZ DLPNO-CCSD(T)F12¯ contribution to the heat of formation for the 50 largest molecules among the 348 core combustion species benchmark set [J. Klippenstein et al., J. Phys. Chem. A 121, 6580-6602 (2017)] had root-mean-square deviation (RMSD) from the extrapolated CBS CCSD(T) reference values of 0.3 kcal/mol. For a more challenging set of 50 reactions involving small closed- and open-shell molecules [G. Knizia et al., J. Chem. Phys. 130, 054104 (2009)], the aug-cc-pVQ(+d)Z DLPNO-CCSD(T)F12¯ yielded a RMSD of ∼0.4 kcal/mol with respect to the CBS CCSD(T) estimate.
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Affiliation(s)
- Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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26
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Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the JmjC histone demethylase KDM4A integrates substrate dynamics, correlated motions and molecular orbital control. Chem Sci 2020; 11:9950-9961. [PMID: 34094257 PMCID: PMC8162366 DOI: 10.1039/d0sc03713c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Nε-methyl lysine status of histones is important in the regulation of eukaryotic transcription. The Fe(ii) and 2-oxoglutarate (2OG) -dependent JmjC domain enzymes are the largest family of histone Nε-methyl lysine demethylases (KDMs). The human KDM4 subfamily of JmjC KDMs is linked with multiple cancers and some of its members are medicinal chemistry targets. We describe the use of combined molecular dynamics (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) methods to study the mechanism of KDM4A, which catalyzes demethylation of both tri- and di-methylated forms of histone H3 at K9 and K36. The results show that the oxygen activation at the active site of KDM4A is optimized towards the generation of the reactive Fe(iv)-oxo intermediate. Factors including the substrate binding mode, correlated motions of the protein and histone substrates, and molecular orbital control synergistically contribute to the reactivity of the Fe(iv)-oxo intermediate. In silico substitutions were performed to investigate the roles of residues (Lys241, Tyr177, and Asn290) in substrate orientation. The Lys241Ala substitution abolishes activity due to altered substrate orientation consistent with reported experimental studies. Calculations with a macrocyclic peptide substrate analogue reveal that induced conformational changes/correlated motions in KDM4A are sequence-specific in a manner that influences substrate binding affinity. Second sphere residues, such as Ser288 and Thr289, may contribute to KDM4A catalysis by correlated motions with active site residues. Residues that stabilize key intermediates, and which are predicted to be involved in correlated motions with other residues in the second sphere and beyond, are shown to be different in KDM4A compared to those in another JmjC KDM (PHF8), which acts on H3K9 di- and mono-methylated forms, suggesting that allosteric type inhibition is of interest from the perspective of developing selective JmjC KDM inhibitors. The second sphere residues and regions of the protein in histone demethylase enzymes that makes correlated motion with the active site contribute to efficient catalysis.![]()
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Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan Ann Arbor MI 48019 USA
| | | | | | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
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27
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Lin YH, Kutin Y, van Gastel M, Bill E, Schnegg A, Ye S, Lee WZ. A Manganese(IV)-Hydroperoxo Intermediate Generated by Protonation of the Corresponding Manganese(III)-Superoxo Complex. J Am Chem Soc 2020; 142:10255-10260. [PMID: 32412757 DOI: 10.1021/jacs.0c02756] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Earlier work revealed that metal-superoxo species primarily function as radicals and/or electrophiles. Herein, we present ambiphilicity of a MnIII-superoxo complex revealed by its proton- and metal-coupled electron-transfer processes. Specifically, a MnIV-hydroperoxo intermediate, [Mn(BDPBrP)(OOH)]+ (1, H2BDPBrP = 2,6-bis((2-(S)-di(4-bromo)phenylhydroxylmethyl-1-pyrrolidinyl)methyl)pyridine) was generated by treatment of a MnIII-superoxo complex, Mn(BDPBrP)(O2•) (2) with trifluoroacetic acid at -120 °C. Detailed insights into the electronic structure of 1 are obtained using resonance Raman and multi-frequency electron paramagnetic resonance spectroscopies coupled with density functional theory calculations. Similarly, the reaction of 2 with scandium(III) triflate was shown to give a Mn(IV)/Sc(III) bridging peroxo species, [Mn(BDPBrP)(OO)Sc(OTf)n](3-n)+ (4). Furthermore, it is found that deprotonation of 1 quantitatively regenerates 2, and that one-electron oxidation of the corresponding MnIII-hydroperoxo species, Mn(BDPBrP)(OOH) (3), also yields 1.
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Affiliation(s)
- Yen-Hao Lin
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yury Kutin
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr D-45470, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany
| | - Alexander Schnegg
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany
| | - Shengfa Ye
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr D-45470, Germany.,State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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28
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Roy L. Theoretical Identification of the Factors Governing the Reactivity of C-H Bond Activation by Non-Heme Iron(IV)-Oxo Complexes. Chempluschem 2020; 84:893-906. [PMID: 31943994 DOI: 10.1002/cplu.201900178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/30/2019] [Indexed: 11/06/2022]
Abstract
Selective functionalization of C-H bonds provides a straightforward approach to a large variety of well-defined derivatives. High-valent mononuclear iron(IV)-oxo complexes are proposed to carry out these C-H activation reactions in enzymes or in biomimetic syntheses. In this Minireview, we aim to highlight the features that delineate the distinct reactivity of non-heme oxo-iron(IV) motifs to cleave strong C-H bonds in hydrocarbons, primarily focusing on the hydrogen atom transfer (HAT) process. We describe how the structural and electronic properties of supporting ligands modulate the oxidative property of the iron(IV)-oxo complexes. Furthermore, we highlight the decisive role played by spin-state in these biomimetic reactions. We also discuss how tunneling and external perturbations like electric field influence the transfer of hydrogen atoms. Lastly, we emphasize how computations could work as a practical guide to sketch and develop synthetic models with greater efficacy.
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Affiliation(s)
- Lisa Roy
- Institute of Chemical Technology Mumbai IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar, 751013, Odisha, India
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29
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Li J, Liao HJ, Tang Y, Huang JL, Cha L, Lin TS, Lee JL, Kurnikov IV, Kurnikova MG, Chang WC, Chan NL, Guo Y. Epoxidation Catalyzed by the Nonheme Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate. J Am Chem Soc 2020; 142:6268-6284. [PMID: 32131594 PMCID: PMC7343540 DOI: 10.1021/jacs.0c00484] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mechanisms of enzymatic epoxidation via oxygen atom transfer (OAT) to an olefin moiety is mainly derived from the studies on thiolate-heme containing epoxidases, such as cytochrome P450 epoxidases. The molecular basis of epoxidation catalyzed by nonheme-iron enzymes is much less explored. Herein, we present a detailed study on epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, AsqJ. The native substrate and analogues with different para substituents ranging from electron-donating groups (e.g., methoxy) to electron-withdrawing groups (e.g., trifluoromethyl) were used to probe the mechanism. The results derived from transient-state enzyme kinetics, Mössbauer spectroscopy, reaction product analysis, X-ray crystallography, density functional theory calculations, and molecular dynamic simulations collectively revealed the following mechanistic insights: (1) The rapid O2 addition to the AsqJ Fe(II) center occurs with the iron-bound 2OG adopting an online-binding mode in which the C1 carboxylate group of 2OG is trans to the proximal histidine (His134) of the 2-His-1-carboxylate facial triad, instead of assuming the offline-binding mode with the C1 carboxylate group trans to the distal histidine (His211); (2) The decay rate constant of the ferryl intermediate is not strongly affected by the nature of the para substituents of the substrate during the OAT step, a reactivity behavior that is drastically different from nonheme Fe(IV)-oxo synthetic model complexes; (3) The OAT step most likely proceeds through a stepwise process with the initial formation of a C(benzylic)-O bond to generate an Fe-alkoxide species, which is observed in the AsqJ crystal structure. The subsequent C3-O bond formation completes the epoxide installation.
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Affiliation(s)
- Jikun Li
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Hsuan-Jen Liao
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jhih-Liang Huang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Te-Sheng Lin
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Justin L. Lee
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Igor V. Kurnikov
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Maria G. Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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30
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Zima AM, Lyakin OY, Lubov DP, Bryliakov KP, Talsi EP. Aromatic C H oxidation by non-heme iron(V)-oxo intermediates bearing aminopyridine ligands. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2019.110708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Chaturvedi S, Ramanan R, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation. ACS Catal 2020; 10:1195-1209. [PMID: 31976154 PMCID: PMC6970271 DOI: 10.1021/acscatal.9b04907] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/10/2019] [Indexed: 02/07/2023]
Abstract
PHF8 (KDM7B) is a human non-heme 2-oxoglutarate (2OG) JmjC domain oxygenase that catalyzes the demethylation of the di/mono-Nε-methylated K9 residue of histone H3. Altered PHF8 activity is linked to genetic diseases and cancer; thus, it is an interesting target for epigenetic modulation. We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. A PHF8 crystal structure manifests the 2OG C-1 carboxylate bound to iron in a nonproductive orientation, i.e., trans to His247. A ferryl-oxo intermediate formed by activating dioxygen bound to the vacant site in this complex would be nonproductive, i.e., "off-line" with respect to reaction with Nε-methylated K9. We show rearrangement of the "off-line" ferryl-oxo intermediate to a productive "in-line" geometry via a solvent exchange reaction (called "ferryl-flip") is energetically unfavorable. The calculations imply that movement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis proceeds with a low barrier, suggesting that two possible 2OG C-1 carboxylate geometries can coexist at room temperature. We explored alternative mechanisms for hydrogen atom transfer and show that second sphere interactions orient the Nε-methylated lysine in a conformation where hydrogen abstraction from a methyl C-H bond is energetically more favorable than hydrogen abstraction from the N-H bond of the protonated Nε-methyl group. Using multiple HAT reaction path calculations, we demonstrate the crucial role of conformational flexibility in effective hydrogen transfer. Subsequent hydroxylation occurs through a rebound mechanism, which is energetically preferred compared to desaturation, due to second sphere interactions. The overall mechanistic insights reveal the crucial role of iron-center rearrangement, second sphere interactions, and conformational flexibility in PHF8 catalysis and provide knowledge useful for the design of mechanism-based PHF8 inhibitors.
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Affiliation(s)
- Shobhit
S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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32
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Zhang X, Wang Z, Gao J, Liu W. Chlorination versus hydroxylation selectivity mediated by the non-heme iron halogenase WelO5. Phys Chem Chem Phys 2020; 22:8699-8712. [DOI: 10.1039/d0cp00791a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O2 activation in WelO5 (an α-KG dependent halogenase) leads to a Fe(IV)O species with an equatorial conformation. After hydrogen abstraction, the hydroxyl ligand is far from the substrate radical which leads to the chlorination selectivity
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Affiliation(s)
- Xuan Zhang
- Beijing National Center for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Zikuan Wang
- Beijing National Center for Molecular Sciences
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics
- College of Informatics
- Huazhong Agricultural University
- Wuhan
- P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences
- Shandong University
- Qingdao 266237
- P. R. China
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33
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Singh W, Quinn D, Moody TS, Huang M. Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes. J Phys Chem B 2019; 123:7801-7811. [PMID: 31469562 DOI: 10.1021/acs.jpcb.9b06064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Histone demethylases (KDMs) catalyze histone lysine demethylation, an important epigenetic process that controls gene expression in eukaryotes, and represent important cancer drug targets for cancer treatment. Demethylation of histone is comprised of sequential reaction steps including oxygen activation, decarboxylation, and demethylation. The initial oxygen binding and activation steps have been studied. However, the information on the complete catalytic reaction cycle is limited, which has impeded the structure-based design of inhibitors targeting KDMs. Here we report the mechanism of the complete reaction steps catalyzed by a representative nonheme iron αKG-dependent KDM, PHF8 using QM/MM approaches. The atomic-level understanding on the complete reaction mechanism of PHF8 would shed light on the structure-based design of selective inhibitors targeting KDMs to intervene in cancer epigenetics.
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Affiliation(s)
- Warispreet Singh
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom.,Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Derek Quinn
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Thomas S Moody
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate , Athlone , Co. Roscommon , Ireland
| | - Meilan Huang
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom
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34
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Pan J, Wenger ES, Matthews ML, Pollock CJ, Bhardwaj M, Kim AJ, Allen BD, Grossman RB, Krebs C, Bollinger JM. Evidence for Modulation of Oxygen Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases. J Am Chem Soc 2019; 141:15153-15165. [PMID: 31475820 DOI: 10.1021/jacs.9b06689] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases generate iron(IV)-oxo (ferryl) intermediates that can abstract hydrogen from aliphatic carbons (R-H). Hydroxylation proceeds by coupling of the resultant substrate radical (R•) and oxygen of the Fe(III)-OH complex ("oxygen rebound"). Nonhydroxylation outcomes result from different fates of the Fe(III)-OH/R• state; for example, halogenation results from R• coupling to a halogen ligand cis to the hydroxide. We previously suggested that halogenases control substrate-cofactor disposition to disfavor oxygen rebound and permit halogen coupling to prevail. Here, we explored the general implication that, when a ferryl intermediate can ambiguously target two substrate carbons for different outcomes, rebound to the site capable of the alternative outcome should be slower than to the adjacent, solely hydroxylated site. We evaluated this prediction for (i) the halogenase SyrB2, which exclusively hydroxylates C5 of norvaline appended to its carrier protein but can either chlorinate or hydroxylate C4 and (ii) two bifunctional enzymes that normally hydroxylate one carbon before coupling that oxygen to a second carbon (producing an oxacycle) but can, upon encountering deuterium at the first site, hydroxylate the second site instead. In all three cases, substrate hydroxylation incorporates a greater fraction of solvent-derived oxygen at the site that can also undergo the alternative outcome than at the other site, most likely reflecting an increased exchange of the initially O2-derived oxygen ligand in the longer-lived Fe(III)-OH/R• states. Suppression of rebound may thus be generally important for nonhydroxylation outcomes by these enzymes.
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Affiliation(s)
| | | | | | | | - Minakshi Bhardwaj
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40546-0312 , United States
| | | | | | - Robert B Grossman
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40546-0312 , United States
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35
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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36
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Mitchell AJ, Weng JK. Unleashing the Synthetic Power of Plant Oxygenases: From Mechanism to Application. PLANT PHYSIOLOGY 2019; 179:813-829. [PMID: 30670605 PMCID: PMC6393811 DOI: 10.1104/pp.18.01223] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/14/2019] [Indexed: 05/23/2023]
Abstract
The functions and biochemical mechanisms of major classes of plant oxygenases are discussed, and their potential utility for plant synthetic biology is explored.
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Affiliation(s)
- Andrew J Mitchell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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37
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Parker MJ, Weigele PR, Saleh L. Insights into the Biochemistry, Evolution, and Biotechnological Applications of the Ten-Eleven Translocation (TET) Enzymes. Biochemistry 2019; 58:450-467. [PMID: 30571101 DOI: 10.1021/acs.biochem.8b01185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A tight link exists between patterns of DNA methylation at carbon 5 of cytosine and differential gene expression in mammalian tissues. Indeed, aberrant DNA methylation results in various human diseases, including neurologic and immune disorders, and contributes to the initiation and progression of various cancers. Proper DNA methylation depends on the fidelity and control of the underlying mechanisms that write, maintain, and erase these epigenetic marks. In this Perspective, we address one of the key players in active demethylation: the ten-eleven translocation enzymes or TETs. These enzymes belong to the Fe2+/α-ketoglutarate-dependent dioxygenase superfamily and iteratively oxidize 5-methylcytosine (5mC) in DNA to produce 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine. The latter three bases may convey additional layers of epigenetic information in addition to being intermediates in active demethylation. Despite the intense interest in understanding the physiological roles TETs play in active demethylation and cell regulation, less has been done, in comparison, to illuminate details of the chemistry and factors involved in regulating the three-step oxidation mechanism. Herein, we focus on what is known about the biochemical features of TETs and explore questions whose answers will lead to a more detailed understanding of the in vivo modus operandi of these enzymes. We also summarize the membership and evolutionary history of the TET/JBP family and highlight the prokaryotic homologues as a reservoir of potentially diverse functionalities awaiting discovery. Finally, we spotlight sequencing methods that utilize TETs for mapping 5mC and its oxidation products in genomic DNA and comment on possible improvements in these approaches.
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Affiliation(s)
- Mackenzie J Parker
- Research Department , New England Biolabs, Inc. , 240 County Road , Ipswich , Massachusetts 01938 , United States
| | - Peter R Weigele
- Research Department , New England Biolabs, Inc. , 240 County Road , Ipswich , Massachusetts 01938 , United States
| | - Lana Saleh
- Research Department , New England Biolabs, Inc. , 240 County Road , Ipswich , Massachusetts 01938 , United States
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38
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Correia Cordeiro RS, Enoki J, Busch F, Mügge C, Kourist R. Cloning and characterization of a new delta-specific l-leucine dioxygenase from Anabaena variabilis. J Biotechnol 2018; 284:68-74. [DOI: 10.1016/j.jbiotec.2018.07.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 11/24/2022]
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39
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Chang WC, Liu P, Guo Y. Mechanistic Elucidation of Two Catalytically Versatile Iron(II)- and α-Ketoglutarate-Dependent Enzymes: Cases Beyond Hydroxylation. COMMENT INORG CHEM 2018. [DOI: 10.1080/02603594.2018.1509856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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40
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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41
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Mondal B, Neese F, Bill E, Ye S. Electronic Structure Contributions of Non-Heme Oxo-Iron(V) Complexes to the Reactivity. J Am Chem Soc 2018; 140:9531-9544. [PMID: 29984578 DOI: 10.1021/jacs.8b04275] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxo-iron(V) species have been implicated in the catalytic cycle of the Rieske dioxygenase. Their synthetic analog, [FeV(O)(OC(O)CH3)(PyNMe3)]2+ (1, PyNMe3 = 3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene-3,6,9-trimethyl), derived from the O-O bond cleavage of its acetylperoxo iron(III) precursor, has been shown experimentally to perform regio- and stereoselective C-H and C═C bond functionalization. However, its structure-activity relation is poorly understood. Herein we present a detailed electronic-structure and spectroscopic analysis of complex 1 along with well-characterized oxo-iron(V) complexes, [FeV(O)(TAML)]- (2, TAML = tetraamido macrocyclic ligand), [FeV(O)(TMC)(NC(O)CH3)]+ (4, TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), and [FeV(O)(TMC)(NC(OH)CH3)]2+ (4-H+), using wave function-based multireference complete active-space self-consistent field calculations. Our results reveal that the x/ y anisotropy of the 57Fe A-matrix is not a reliable spectroscopic marker to identify oxo-iron(V) species and that the drastically different A x and A y values determined for complexes 1, 4, and 4-H+ have distinctive origins compared to complex 2, a genuine oxo-iron(V) species. Complex 1, in fact, has a dominant character of [FeIV(O···OC(O)CH3)2-•]2+, i.e., an SFe = 1 iron(IV) center antiferromagnetically coupled to an O-O σ* radical, where the O-O bond has not been completely broken. Complex 4 is best described as a triplet ferryl unit that strongly interacts with the trans acetylimidyl radical in an antiferromagnetic fashion, [FeIV(O)(•N═C(O-)CH3)]+. Complex 4-H+ features a similar electronic structure, [FeIV(O)(•N═C(OH)CH3)]2+. Owing to the remaining approximate half σ-bond in the O-O moiety, complex 1 can arrange two electron-accepting orbitals (α σ*O-O and β Fe-d xz) in such a way that both orbitals can simultaneously interact with the doubly occupied electron-donating orbitals (σC-H or πC-C). Hence, complex 1 can promote a concerted yet asynchronous two-electron oxidation of the C-H and C═C bonds, which nicely explains the stereospecificity observed for complex 1 and the related species.
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Affiliation(s)
- Bhaskar Mondal
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim an der Ruhr , Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim an der Ruhr , Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim an der Ruhr , Germany
| | - Shengfa Ye
- Max-Planck-Institut für Chemische Energiekonversion , D-45470 Mülheim an der Ruhr , Germany
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42
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Dunham NP, Chang WC, Mitchell AJ, Martinie RJ, Zhang B, Bergman JA, Rajakovich LJ, Wang B, Silakov A, Krebs C, Boal AK, Bollinger JM. Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of α-Heteroatom Assistance. J Am Chem Soc 2018; 140:7116-7126. [PMID: 29708749 PMCID: PMC5999578 DOI: 10.1021/jacs.8b01933] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylation of aliphatic carbons by nonheme Fe(IV)-oxo (ferryl) complexes proceeds by hydrogen-atom (H•) transfer (HAT) to the ferryl and subsequent coupling between the carbon radical and Fe(III)-coordinated oxygen (termed rebound). Enzymes that use H•-abstracting ferryl complexes for other transformations must either suppress rebound or further process hydroxylated intermediates. For olefin-installing C-C desaturations, it has been proposed that a second HAT to the Fe(III)-OH complex from the carbon α to the radical preempts rebound. Deuterium (2H) at the second site should slow this step, potentially making rebound competitive. Desaturations mediated by two related l-arginine-modifying iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases behave oppositely in this key test, implicating different mechanisms. NapI, the l-Arg 4,5-desaturase from the naphthyridinomycin biosynthetic pathway, abstracts H• first from C5 but hydroxylates this site (leading to guanidine release) to the same modest extent whether C4 harbors 1H or 2H. By contrast, an unexpected 3,4-desaturation of l-homoarginine (l-hArg) by VioC, the l-Arg 3-hydroxylase from the viomycin biosynthetic pathway, is markedly disfavored relative to C4 hydroxylation when C3 (the second hydrogen donor) harbors 2H. Anchimeric assistance by N6 permits removal of the C4-H as a proton in the NapI reaction, but, with no such assistance possible in the VioC desaturation, a second HAT step (from C3) is required. The close proximity (≤3.5 Å) of both l-hArg carbons to the oxygen ligand in an X-ray crystal structure of VioC harboring a vanadium-based ferryl mimic supports and rationalizes the sequential-HAT mechanism. The results suggest that, although the sequential-HAT mechanism is feasible, its geometric requirements may make competing hydroxylation unavoidable, thus explaining the presence of α-heteroatoms in nearly all native substrates for Fe/2OG desaturases.
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Affiliation(s)
- Noah P. Dunham
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Andrew J. Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
| | - Ryan J. Martinie
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Jonathan A. Bergman
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
| | - Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
| | - Bo Wang
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802
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43
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Saitow M, Becker U, Riplinger C, Valeev EF, Neese F. A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory. J Chem Phys 2018; 146:164105. [PMID: 28456208 DOI: 10.1063/1.4981521] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N6) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approximately 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set.
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Affiliation(s)
- Masaaki Saitow
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Riplinger
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
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44
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Tian G, Su H, Liu Y. Mechanism of Sulfoxidation and C–S Bond Formation Involved in the Biosynthesis of Ergothioneine Catalyzed by Ergothioneine Synthase (EgtB). ACS Catal 2018. [DOI: 10.1021/acscatal.8b01473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ge Tian
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Hao Su
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
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45
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Lyakin OY, Zima AM, Tkachenko NV, Bryliakov KP, Talsi EP. Direct Evaluation of the Reactivity of Nonheme Iron(V)–Oxo Intermediates toward Arenes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00661] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oleg Y. Lyakin
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Alexandra M. Zima
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Nikolay V. Tkachenko
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Konstantin P. Bryliakov
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Evgenii P. Talsi
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
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46
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Song X, Lu J, Lai W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 2018; 19:20188-20197. [PMID: 28726913 DOI: 10.1039/c7cp02687k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an FeII/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated FeIV-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated FeIV-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated FeIV-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated FeIV-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive FeIV-oxo species.
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Affiliation(s)
- Xudan Song
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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47
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Acid-facilitated product release from a Mo(IV) center: relevance to oxygen atom transfer reactivity of molybdenum oxotransferases. J Biol Inorg Chem 2017; 23:193-207. [PMID: 29177705 DOI: 10.1007/s00775-017-1518-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/10/2017] [Indexed: 01/27/2023]
Abstract
We report that pyridinium ions (HPyr+) accelerate the conversion of [Tp*MoIVOCl(OPMe3)] (1) to [Tp*MoIVOCl(NCCH3)] (2) by 103-fold, affording 2 in near-quantitative yield; Tp* = hydrotris(3,5-dimethyl-1-pyrazolyl)borate. This novel reactivity and the mechanism of this reaction were investigated in detail. The formation of 2 followed pseudo-first-order kinetics, with the observed pseudo-first-order rate constant (k obs) linearly correlated with [HPyr+]. An Eyring plot revealed that this HPyr+-facilitated reaction has a small positive value of ∆S ‡ indicative of a dissociative interchange (Id) mechanism, different from the slower associative interchange (Ia) mechanism in the absence of HPyr+ marked with a negative ∆S ‡. Interestingly, log(k obs) was found to be linearly correlated to the acidity of substituted pyridinium ions. This novel reactivity is further investigated using combined DFT and ab initio coupled cluster methods. Different reaction pathways, including Id, Ia, and possible alternative routes in the absence or presence of HPyr+, were considered, and enthalpy and free energies were calculated for each pathway. Our computational results further underscored that the Id route is energetically favored in the presence of HPyr+, in contrast with the preferred Ia-NNO pathway in the absence of HPyr+. Our computational results also revealed molecular-level details for the HPyr+-facilitated Id route. Specifically, HPyr+ initially becomes hydrogen-bonded to the oxygen atom of the Mo(IV)-OPMe3 moiety, which lowers the activation barrier for the Mo-OPMe3 bond cleavage in a rate-limiting step to dissociate the OPMe3 product. The implications of our results were discussed in the context of molybdoenzymes, particularly the reductive half-reaction of sulfite oxidase.
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48
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Gani TZH, Kulik HJ. Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics. J Chem Theory Comput 2017; 13:5443-5457. [DOI: 10.1021/acs.jctc.7b00848] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Terry Z. H. Gani
- Department
of Chemical Engineering, 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
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49
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Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC, Silakov A, Bollinger JM, Krebs C, Boal AK. Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase. J Am Chem Soc 2017; 139:13830-13836. [PMID: 28823155 DOI: 10.1021/jacs.7b07374] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron(II)- and 2-(oxo)-glutarate-dependent oxygenases catalyze diverse oxidative transformations that are often initiated by abstraction of hydrogen from carbon by iron(IV)-oxo (ferryl) complexes. Control of the relative orientation of the substrate C-H and ferryl Fe-O bonds, primarily by direction of the oxo group into one of two cis-related coordination sites (termed inline and offline), may be generally important for control of the reaction outcome. Neither the ferryl complexes nor their fleeting precursors have been crystallographically characterized, hindering direct experimental validation of the offline hypothesis and elucidation of the means by which the protein might dictate an alternative oxo position. Comparison of high-resolution X-ray crystal structures of the substrate complex, an Fe(II)-peroxysuccinate ferryl precursor, and a vanadium(IV)-oxo mimic of the ferryl intermediate in the l-arginine 3-hydroxylase, VioC, reveals coordinated motions of active site residues that appear to control the intermediate geometries to determine reaction outcome.
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Affiliation(s)
- Andrew J Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Noah P Dunham
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Ryan J Martinie
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jonathan A Bergman
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher J Pollock
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Kai Hu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,The Huck Institutes for the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Benjamin D Allen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,The Huck Institutes for the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Wei-Chen Chang
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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50
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Castiñeira Reis M, Marín-Luna M, Silva López C, Faza ON. [MoO 2] 2+-Mediated Oxygen Atom Transfer via an Unusual Lewis Acid Mechanism. Inorg Chem 2017; 56:10570-10575. [PMID: 28829586 DOI: 10.1021/acs.inorgchem.7b01529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory is applied to the study of the oxygen atom transfer reaction from sulfoxide (DMSO) to phosphine (PMe3) catalyzed by the [MoO2]2+ active core. In this work, two fundamentally different roles are explored for this dioxometal complex in the first step of the catalytic cycle: as an oxidizing agent and as a Lewis acid. The latter turns out to be the favored pathway for the oxygen atom transfer. This finding may have more general implications for similar reactions catalyzed by the same [MoO2]2+ core.
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Affiliation(s)
- Marta Castiñeira Reis
- Departamento de Quı́mica Orgánica, Universidade de Vigo , Lagoas-Marcosende, 36310 Vigo, Spain
| | - Marta Marín-Luna
- Departamento de Quı́mica Orgánica, Universidade de Vigo , Lagoas-Marcosende, 36310 Vigo, Spain
| | - Carlos Silva López
- Departamento de Quı́mica Orgánica, Universidade de Vigo , Lagoas-Marcosende, 36310 Vigo, Spain
| | - Olalla Nieto Faza
- Departamento de Quı́mica Orgánica, Universidade de Vigo , Campus As Lagoas, 32004 Ourense, Spain
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