1
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Sanfui S, Roychowdhury A, Usman M, Garribba E, Gómez-García CJ, Rath SP. Metal vs Ligand Oxidation: Coexistence of Both Metal-Centered and Ligand-Centered Oxidized Species. Inorg Chem 2024; 63:5423-5431. [PMID: 38483819 DOI: 10.1021/acs.inorgchem.3c04043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
A series of two-electron-oxidized cobalt porphyrin dimers have been synthesized upon controlled oxidations using halogens. Rather unexpectedly, X-ray structures of two of these complexes contain two structurally different low-spin molecules in the same asymmetric unit of their unit cells: one is the metal-centered oxidized diamagnetic entity of the type CoIII(por), while the other one is the ligand-centered oxidized paramagnetic entity of the type CoII(por•+). Spectroscopic, magnetic, and DFT investigations confirmed the coexistence of the two very different electronic structures both in the solid and solution phases and also revealed a ferromagnetic spin coupling between Co(II) and porphyrin π-cation radicals and a weak antiferromagnetic coupling between the π-cation radicals of two macrocycles via the bridge in the paramagnetic complex.
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Affiliation(s)
- Sarnali Sanfui
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Arya Roychowdhury
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Mohammad Usman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Eugenio Garribba
- Dipartimento di Medicina, Chirurgia e Farmacia, Viale San Pietro, Università di Sassari, Sassari I-07100, Italy
| | - Carlos J Gómez-García
- Departamento de Química Inorgánica, Universidad de Valencia, C/Dr. Moliner 50, Burjasot, Valencia 46100, Spain
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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2
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Fang J, Wang L, Zhang D, Liang Y, Li S, Tian J, He Q, Jin J, Zhu W. Integrative analysis of transcriptome and metabolome provide new insights into mechanisms of Capilliposide A against cisplatin-induced nephrotoxicity. J Pharm Biomed Anal 2024; 238:115814. [PMID: 37976990 DOI: 10.1016/j.jpba.2023.115814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
OBJECTIVE Cisplatin (CDDP) has been widely used for chemotherapy against tumours. However,the nephrotoxicity has limited its clinical use. Here, we reported a novel compound, Capilliposide A (CPS-A), to exhibit therapeutic effects on CDDP-induced acute kidney injury (AKI) and explored its potential mechanisms via transcriptome and metabolome. MATERIALS AND METHODS HK-2 cells were treated with CPS-A, after which cell viability, apoptosis and inflammation were investigated. A mouse model of AKI was constructed by single injection of CDDP in vivo. The renal function and morphology and mitochondrial function were assessed by pathological section and transmission electron microscope (TEM). Transcriptomics and metabolomics are used to explore possible mechanisms which was later verified in vitro. RESULTS CPS-A administration improved the survival rates of HK-2 cells with a significant decrease in the expression of KIM-1, NGAL, IL-6, IL-8 and IL-1β. In vivo results also suggested that CPS-A attenuates CDDP-induced kidney injury by reducing serum creatinine (Cr) and blood urea nitrogen (BUN) levels. Furthermore, TEM also showed the improvement of mitochondrial ultrastructure both in vivo and vitro. Transcriptomics analysis of the mice's renal cortex indicated the expression of ATF4 and CHOP were upregulated, which was further validated by qPCR and Western blotting in vitro. Integrative analysis of transcriptome and metabolome indicated that L-Leucine enriched in Valine, leucine and isoleucine degradation might be potential targets. CONCLUSIONS CPS-A can effectively regulate endogenous metabolites associated with amino acid metabolism and ameliorate apoptosis and oxidative stress in CDDP-induced AKI by reducing endoplasmic reticulum stress.
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Affiliation(s)
- Jiaxi Fang
- Urology & Nephrology Center, Department of Nephrology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, China; Department of Ultrasound, Taizhou Central Hospital (Taizhou University, Hospital), Taizhou, Zhejiang, China; Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University, (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, China
| | - Luping Wang
- College of Biomedicial Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Di Zhang
- Urology & Nephrology Center, Department of Nephrology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, China
| | - Yan Liang
- Urology & Nephrology Center, Department of Nephrology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, China
| | - Shouxin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
| | - Qiang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University, (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, China.
| | - Juan Jin
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University, (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, China.
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
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3
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Paris JC, Hu S, Wen A, Weitz AC, Cheng R, Gee LB, Tang Y, Kim H, Vegas A, Chang WC, Elliott SJ, Liu P, Guo Y. An S=1 Iron(IV) Intermediate Revealed in a Non-Heme Iron Enzyme-Catalyzed Oxidative C-S Bond Formation. Angew Chem Int Ed Engl 2023; 62:e202309362. [PMID: 37640689 PMCID: PMC10592081 DOI: 10.1002/anie.202309362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/11/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol-histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O2 -dependent C-S bond formation catalyzed by non-heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competent S=1 iron(IV) intermediate supported by a four-histidine ligand environment (three from the protein residues and one from the substrate) in enabling C-S bond formation in OvoA from Methyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non-heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C-S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure-function relationship of high-valent iron intermediates supported by a histidine rich ligand environment.
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Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Sha Hu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Aiwen Wen
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Andrew C Weitz
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Ronghai Cheng
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Leland B Gee
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Hyomin Kim
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Arturo Vegas
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
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4
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Barreiro DS, Oliveira RN, Pauleta SR. Bacterial peroxidases – Multivalent enzymes that enable the use of hydrogen peroxide for microaerobic and anaerobic proliferation. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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5
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Manesis AC, Slater JW, Cantave K, Martin Bollinger J, Krebs C, Rosenzweig AC. Capturing a bis-Fe(IV) State in Methylosinus trichosporium OB3b MbnH. Biochemistry 2023; 62:1082-1092. [PMID: 36812111 PMCID: PMC10083075 DOI: 10.1021/acs.biochem.3c00021] [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] [Indexed: 02/24/2023]
Abstract
The diheme bacterial cytochrome c peroxidase (bCcP)/MauG superfamily is a diverse set of enzymes that remains largely uncharacterized. One recently discovered member, MbnH, converts a tryptophan residue in its substrate protein, MbnP, to kynurenine. Here we show that upon reaction with H2O2, MbnH forms a bis-Fe(IV) intermediate, a state previously detected in just two other enzymes, MauG and BthA. Using absorption, Mössbauer, and electron paramagnetic resonance (EPR) spectroscopies coupled with kinetic analysis, we characterized the bis-Fe(IV) state of MbnH and determined that this intermediate decays back to the diferric state in the absence of MbnP substrate. In the absence of MbnP substrate, MbnH can also detoxify H2O2 to prevent oxidative self damage, unlike MauG, which has long been viewed as the prototype for bis-Fe(IV) forming enzymes. MbnH performs a different reaction from MauG, while the role of BthA remains unclear. All three enzymes can form a bis-Fe(IV) intermediate but within distinct kinetic regimes. The study of MbnH significantly expands our knowledge of enzymes that form this species. Computational and structural analyses indicate that electron transfer between the two heme groups in MbnH and between MbnH and the target tryptophan in MbnP likely occurs via a hole-hopping mechanism involving intervening tryptophan residues. These findings set the stage for discovery of additional functional and mechanistic diversity within the bCcP/MauG superfamily.
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Affiliation(s)
- Anastasia C Manesis
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeffrey W Slater
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kenny Cantave
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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6
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Knox HL, Allen KN. Expanding the viewpoint: Leveraging sequence information in enzymology. Curr Opin Chem Biol 2023; 72:102246. [PMID: 36599282 PMCID: PMC10251232 DOI: 10.1016/j.cbpa.2022.102246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 01/04/2023]
Abstract
The use of protein sequence to inform enzymology in terms of structure, mechanism, and function has burgeoned over the past two decades. Referred to as genomic enzymology, the utilization of bioinformatic tools such as sequence similarity networks and phylogenetic analyses has allowed the identification of new substrates and metabolites, novel pathways, and unexpected reaction mechanisms. The holistic examination of superfamilies can yield insight into the origins and paths of evolution of enzymes and the range of their substrates and mechanisms. Herein, we highlight advances in the use of genomic enzymology to address problems which the in-depth analyses of a single enzyme alone could not enable.
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Affiliation(s)
- Hayley L Knox
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215-2521, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215-2521, USA.
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7
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Sarkar S, Sarkar P, Samanta D, Pati SK, Rath SP. Cooperativity in Diiron(III)porphyrin Dication Diradical-Catalyzed Oxa-Diels–Alder Reactions: Spectroscopic and Mechanistic Insights. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sabyasachi Sarkar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Pallavi Sarkar
- Theoretical Sciences Unit, School of Advanced Materials (SAMat), Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore 560064, India
| | - Deepannita Samanta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Swapan K Pati
- Theoretical Sciences Unit, School of Advanced Materials (SAMat), Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore 560064, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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8
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Sanfui S, Usman M, Sarkar S, Pramanik S, Garribba E, Rath SP. Highly Oxidized Cobalt Porphyrin Dimer: Control of Spin Coupling via a Bridge. Inorg Chem 2022; 61:8419-8430. [PMID: 35613476 DOI: 10.1021/acs.inorgchem.1c03807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A cobalt porphyrin dimer is constructed in which two Co(II)porphyrins are connected covalently through a redox-active diethylpyrrole moiety via a flexible but "nonconjugated" methylene bridge. Upon oxidation with even a mild oxidant such as iodine, each cobalt(II) center and porphyrin ring undergo 1e- oxidation, leading to the formation of a 4e--oxidized cobalt(III)porphyrin dication diradical complex. Other oxidants such as Cl2 and Br2 also produce similar results. To stabilize such highly oxidized dication diradicals, the "nonconjugated" methylene spacer undergoes a facile and spontaneous oxidation to form a methine group with a drastic structural change, thereby making the bridge fully π-conjugated and enabling through-bond communication. This results in a strong spin coupling between two π-cation radicals which stabilizes the singlet state. The experimental observations are also strongly supported by extensive density functional theory calculations. The present study highlights the crucial role played by the nature of the bridge in the long-range electronic communication.
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Affiliation(s)
- Sarnali Sanfui
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Mohammad Usman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sabyasachi Sarkar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Subhadip Pramanik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Eugenio Garribba
- Dipartimento di Scienze Mediche, Chirurgiche e Sperimentali, Università di Sassari, Viale San Pietro, Sassari I-07100, Italy
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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9
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Singh AK, Usman M, Sarkar S, Sciortino G, Kumar D, Garribba E, Rath SP. Ferromagnetic Coupling in Oxidovanadium(IV)-Porphyrin Radical Dimers. Inorg Chem 2021; 60:16492-16506. [PMID: 34664950 DOI: 10.1021/acs.inorgchem.1c02331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three different oxidovanadium(IV) porphyrin dimers with anti, cis, and trans arrangements of the two rings have been synthesized by changing the bridge between the porphyrin macrocycles. This provides a unique opportunity to investigate the role of the bridge and spatial arrangement between the two VIVO centers for their electronic communication and magnetic coupling. They were characterized by the combined application of XRD analysis, UV-vis and electron paramagnetic resonance (EPR) spectroscopy, cyclic voltammetry, magnetic susceptibility, and DFT calculations. One- and two-electron oxidations produce mono- and dication diradical species, respectively, which display an unusual ferromagnetic interaction between the unpaired spins of vanadium(IV) and porphyrin π-cation radical, in contrast to other metalloporphyrin dimers. The oxidized species show a dissimilar behavior between cis and trans isomers. The ferromagnetic coupling occurs between the porphyrin π-cation radical and the unpaired electron of the VIVO ion on the dxy orbital, orthogonal to the porphyrin-based molecular orbitals a1u and a2u.
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Affiliation(s)
- Akhil Kumar Singh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Mohammad Usman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sabyasachi Sarkar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Giuseppe Sciortino
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy.,Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), 43007 Tarragona, Spain
| | - Devesh Kumar
- Department of Physics, School for Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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10
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Kumar A, Usman M, Samanta D, Rath SP. Through Bridge Spin Coupling in Homo- and Heterobimetallic Porphyrin Dimers upon Stepwise Oxidations: A Spectroscopic and Theoretical Investigation. Chemistry 2021; 27:11428-11441. [PMID: 34061401 DOI: 10.1002/chem.202101384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 12/16/2022]
Abstract
We have described copper(II)-iron(III) and copper(II)-manganese(III) heterobimetallic porphyrin dimers and compared them with the corresponding homobimetallic analogs. UV-visible spectra are very distinct in the heterometallic species while electrochemical studies demonstrate that these species, as compared to the homobimetallic analog, are much easier to oxidize. Combined Mössbauer, EPR, NMR, magnetic and UV-visible spectroscopic studies show that upon 2e-oxidation of the heterobimetallic complexes only ring-centered oxidation occurs. The energy differences between HOMO and LUMO are linearly dependent with the low-energy NIR band obtained for the 2e-oxidized complexes. Also, strong electronic communication between two porphyrin rings through the bridge facilitates coupling between various unpaired spins present while the coupling model depends on the nature of metal ions used. While unpaired spins of Fe(III) and the porphyrin π-cation radical are strongly antiferromagnetically coupled, such coupling is rather weak between Mn(III) and a porphyrin π-cation radical. Moreover, the coupling between two π-cation radicals are much stronger in the 2e-oxidized complexes of dimanganese(III) and copper(II)-manganese(III) porphyrin dimers as compared to their diiron(III) and copper(II)-iron(III) analogs. Furthermore, coupling between the unpaired spins of a π-cation radical and copper(II) is much stronger in the 2e-oxidized complex of copper(II)-iron(III) porphyrin dimer as compared to its copper(II)-manganese(III) analog. The Mulliken spin density distributions in 2e-oxidized homo- and heterobimetallic complexes show symmetric and asymmetric spread between the two macrocycles, respectively. In both the 2e-oxidized heterobimetallic complexes, the Cu(II) porphyrin center acts as a charge donor while Fe(III)/Mn(III) porphyrin center act as a charge acceptor. The experimental observations are also strongly supported by DFT calculations.
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Affiliation(s)
- Amit Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Mohammad Usman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Deepannita Samanta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
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11
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Faure E, Ayata SD, Bittner L. Towards omics-based predictions of planktonic functional composition from environmental data. Nat Commun 2021; 12:4361. [PMID: 34272373 PMCID: PMC8285379 DOI: 10.1038/s41467-021-24547-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters' distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters' abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.
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Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
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12
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Zallot R, Oberg N, Gerlt JA. Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools. Curr Opin Biotechnol 2021; 69:77-90. [PMID: 33418450 DOI: 10.1016/j.copbio.2020.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/08/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022]
Abstract
The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be 'user-friendly' so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
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Affiliation(s)
- Remi Zallot
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Institute of Life Sciences, Swansea University Medical School, Swansea SA2 8PP, Wales, United Kingdom
| | - Nils Oberg
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - John A Gerlt
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
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Abstract
Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA.
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14
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Rizzolo K, Weitz AC, Cohen SE, Drennan CL, Hendrich MP, Elliott SJ. A Stable Ferryl Porphyrin at the Active Site of Y463M BthA. J Am Chem Soc 2020; 142:11978-11982. [PMID: 32564595 DOI: 10.1021/jacs.0c04023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BthA is a diheme enzyme that is a member of the bacterial cytochrome c peroxidase superfamily, capable of generating a highly unusual Fe(IV)Fe(IV)═O oxidation state, known to be responsible for long-range oxidative chemistry in the enzyme MauG. Here, we show that installing a canonical Met ligand in lieu of the Tyr found at the heme of MauG associated with electron transfer, results in a construct that yields an unusually stable Fe(IV)═O porphyrin at the peroxidatic heme. This state is spontaneously formed at ambient conditions using either molecular O2 or H2O2. The resulting data illustrate how a ferryl iron, with unforeseen stability, may be achieved in biology.
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Affiliation(s)
- Kimberly Rizzolo
- Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States
| | - Andrew C Weitz
- Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States.,Carnegie Mellon University, Department of Chemistry, Pittsburgh, Pennsylvania 15213, United States
| | - Steven E Cohen
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts 02139, United States
| | - Catherine L Drennan
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts 02139, United States.,Massachusetts Institute of Technology, Department of Biology, Cambridge, Massachusetts 02139, United States.,Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
| | - Michael P Hendrich
- Carnegie Mellon University, Department of Chemistry, Pittsburgh, Pennsylvania 15213, United States
| | - Sean J Elliott
- Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States
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15
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Weitz AC, Biswas S, Rizzolo K, Elliott S, Bominaar EL, Hendrich MP. Electronic State of the His/Tyr-Ligated Heme of BthA by Mössbauer and DFT Analysis. Inorg Chem 2020; 59:10223-10233. [PMID: 32602712 DOI: 10.1021/acs.inorgchem.0c01349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The BthA protein from the microorganism Burkholderia thailandensis contains two hemes with axial His/OH2 and His/Tyr coordinations separated by the closest interheme distance of 14 Å. BthA has a similar structure and belongs to the same family of multiheme cytochrome c peroxidases as MauG, which performs long-range oxidation of the partner protein methylamine dehydrogenase. Magnetic Mössbauer spectroscopy of the diferric state of BthA corroborates previous structural work identifying a high-spin (His/OH2) peroxidatic heme and a low-spin (His/Tyr) electron transfer heme. Unlike MauG, addition of H2O2 fully converts the diferric form of BthA to a stable 2e- oxidized state, allowing a new assessment of this state. The peroxidatic heme is found to be oxidized to a canonical compound II, S = 1 oxoiron(IV) heme. In contrast, the electronic properties of the oxidized His/Tyr heme are puzzling. The isomer shift of the His/Tyr heme (0.17 mm/s) is close to that of the precursor S = 1/2 Fe3+ heme (0.21 mm/s) which suggests oxidation of the Tyr. However, the spin-dipolar hyperfine coupling constants are found here to be the same as those for the ferryl peroxidatic heme, indicating that the His/Tyr heme is also a compound II, S = 1 Fe4+ heme and ruling out oxidation of the Tyr. DFT calculations indicate that the unusually high isomer shift is not attributable to the rare axial His/Tyr heme coordination. The calculations are only compatible with spectroscopy for an unusually long Fe4+-OTyr distance, which is presumably under the influence of the protein environment of the His/Tyr heme moiety in the H2O2 oxidized state of the protein. The results offer new insights into how high valence intermediates can be tuned by the protein environment for performing long-range oxidation.
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Affiliation(s)
- Andrew C Weitz
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kim Rizzolo
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sean Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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16
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Liew FN, Brandys MA, Biswas S, Nguyen JN, Rahmawati M, Nevala M, Elmore BO, Hendrich MP, Kim HJ. Cytochrome c' β-Met Is a Variant in the P460 Superfamily Lacking the Heme-Lysyl Cross-Link: A Peroxidase Mimic Generating a Ferryl Intermediate. Biochemistry 2020; 59:704-716. [PMID: 31887031 DOI: 10.1021/acs.biochem.9b00810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A defining characteristic of bacterial cytochromes (cyt's) in the P460 family is an unusual cross-link connecting the heme porphyrin to the side chain of a lysyl residue in the protein backbone. Here, via proteomics of the periplasmic fraction of the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea, we report the identification of a variant member of the P460 family that contains a methionyl residue in place of the cross-linking lysine. We formally designate this protein cytochrome "c'β-Met" to distinguish it from other members bearing different residues at this position (e.g., cyt c'β-Phe from the methane-oxidizing Methylococcus capsulatus Bath). As isolated, the monoheme cyt c'β-Met is high-spin (S = 5/2). Optical spectroscopy suggests that a cross-link is absent. Hydroxylamine, the substrate for the cross-linked cyt P460 from N. europaea, did not appreciably alter the optical spectrum of cyt c'β with up to 1000-fold excess at pH 7.5. Cyt c'β-Met did however bind 1 equiv of H2O2, and with a slight excess, Mössbauer spectroscopy indicated the formation of a semistable ferryl (FeIV═O) Compound II-like species. The corresponding electron paramagnetic resonance showed a very low intensity signal indicative of a radical at g = 2.0. Furthermore, cyt c'β-Met exhibited guaiacol-dependent peroxidase activity (kcat = 20.0 ± 1.2 s-1; KM = 2.6 ± 0.4 mM). Unlike cyt c'β-Met, cyt P460 showed evidence of heme inactivation in the presence of 2 equiv of H2O2 with no appreciable guaiacol-dependent peroxidase activity. Mutagenesis of the cross-linking lysyl residue to an alanine in cyt P460, however, reversed this lack of activity.
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Affiliation(s)
- Fong Ning Liew
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Marisa A Brandys
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Saborni Biswas
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Mustika Rahmawati
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
| | - Michael Nevala
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States.,Veolia Nuclear Solutions Federal Solutions , Richland , Washington 99354 , United States
| | - Bradley O Elmore
- Newport Laboratories , Worthington , Minnesota 56187 , United States
| | - Michael P Hendrich
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry , University of Washington Bothell , Bothell , Washington 98012 , United States
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17
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Kenney GE, Dassama LMK, Manesis AC, Ross MO, Chen S, Hoffman BM, Rosenzweig AC. MbnH is a diheme MauG-like protein associated with microbial copper homeostasis. J Biol Chem 2019; 294:16141-16151. [PMID: 31511324 PMCID: PMC6827288 DOI: 10.1074/jbc.ra119.010202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/06/2019] [Indexed: 01/09/2023] Open
Abstract
Methanobactins (Mbns) are ribosomally-produced, post-translationally modified peptidic copper-binding natural products produced under conditions of copper limitation. Genes encoding Mbn biosynthetic and transport proteins have been identified in a wide variety of bacteria, indicating a broader role for Mbns in bacterial metal homeostasis. Many of the genes in the Mbn operons have been assigned functions, but two genes usually present, mbnP and mbnH, encode uncharacterized proteins predicted to reside in the periplasm. MbnH belongs to the bacterial diheme cytochrome c peroxidase (bCcP)/MauG protein family, and MbnP contains no domains of known function. Here, we performed a detailed bioinformatic analysis of both proteins and have biochemically characterized MbnH from Methylosinus (Ms.) trichosporium OB3b. We note that the mbnH and mbnP genes typically co-occur and are located proximal to genes associated with microbial copper homeostasis. Our bioinformatics analysis also revealed that the bCcP/MauG family is significantly more diverse than originally appreciated, and that MbnH is most closely related to the MauG subfamily. A 2.6 Å resolution structure of Ms. trichosporium OB3b MbnH combined with spectroscopic data and peroxidase activity assays provided evidence that MbnH indeed more closely resembles MauG than bCcPs, although its redox properties are significantly different from those of MauG. The overall similarity of MbnH to MauG suggests that MbnH could post-translationally modify a macromolecule, such as internalized CuMbn or its uncharacterized partner protein, MbnP. Our results indicate that MbnH is a MauG-like diheme protein that is likely involved in microbial copper homeostasis and represents a new family within the bCcP/MauG superfamily.
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Affiliation(s)
- Grace E. Kenney
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Laura M. K. Dassama
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Anastasia C. Manesis
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Matthew O. Ross
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Siyu Chen
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brian M. Hoffman
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and Chemistry, Northwestern University, Evanston, Illinois 60208, To whom correspondence should be addressed. Tel.:
847-467-5301; Fax:
847-467-6489; E-mail:
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