101
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Recent advances in photoinduced catalysis for water splitting and environmental applications. J IND ENG CHEM 2019. [DOI: 10.1016/j.jiec.2019.01.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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102
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Mamun AA, Toda MJ, Kozlowski PM. Can photolysis of the Co C bond in coenzyme B12-dependent enzymes be used to mimic the native reaction? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 191:175-184. [DOI: 10.1016/j.jphotobiol.2018.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
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103
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Resa S, Millán A, Fuentes N, Crovetto L, Luisa Marcos M, Lezama L, Choquesillo-Lazarte D, Blanco V, Campaña AG, Cárdenas DJ, Cuerva JM. O–H and (CO)N–H bond weakening by coordination to Fe(ii). Dalton Trans 2019; 48:2179-2189. [DOI: 10.1039/c8dt04689a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coordination of hydroxyl/amide groups to Fe(ii) diminishes BDFEs of O–H and (CO)N–H bonds down to 76.0 and 80.5 kcal mol−1 respectively.
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104
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Dol C, Gerbaud G, Guigliarelli B, Bloch E, Gastaldi S, Besson E. Modulating lifetimes and relaxation times of phenoxyl radicals through their incorporation into different hybrid nanostructures. Phys Chem Chem Phys 2019; 21:16337-16344. [DOI: 10.1039/c9cp03052b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Playing with the structural features of various hybrid materials enables to adjust physical properties of phenoxyl radicals.
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Affiliation(s)
| | | | | | - Emily Bloch
- Aix Marseille Univ
- CNRS
- MADIREL
- Marseille
- France
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105
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Xia Q, Dong J, Song H, Wang Q. Visible‐Light Photocatalysis of the Ketyl Radical Coupling Reaction. Chemistry 2018; 25:2949-2961. [DOI: 10.1002/chem.201804873] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Qing Xia
- State Key Laboratory of Elemento-Organic ChemistryResearch Institute of, Elemento-Organic ChemistryCollege of ChemistryNankai University Tianjin 300071 P. R. China
| | - Jianyang Dong
- State Key Laboratory of Elemento-Organic ChemistryResearch Institute of, Elemento-Organic ChemistryCollege of ChemistryNankai University Tianjin 300071 P. R. China
| | - Hongjian Song
- State Key Laboratory of Elemento-Organic ChemistryResearch Institute of, Elemento-Organic ChemistryCollege of ChemistryNankai University Tianjin 300071 P. R. China
| | - Qingmin Wang
- State Key Laboratory of Elemento-Organic ChemistryResearch Institute of, Elemento-Organic ChemistryCollege of ChemistryNankai University Tianjin 300071 P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin 300071 P. R. China
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106
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Jana L, Maity PP, Perveen H, Dash M, Jana S, Dey A, De SK, Chattopadhyay S. Attenuation of utero-toxicity, metabolic dysfunction and inflammation by soy protein concentrate in rats exposed to fluoridated water: consequence of hyperlipidemia in parallel with hypohomocysteinemia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:36462-36473. [PMID: 30374712 DOI: 10.1007/s11356-018-3542-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/19/2018] [Indexed: 06/08/2023]
Abstract
Lipid peroxidation and ROS generation are the pathogenesis of chronic fluoride toxicity, and its detrimental effects on human reproduction are noted drastically. The aim of the present study was to elucidate the defensive effects of soy protein concentrate (SPC) against sodium fluoride (NaF)-induced uterine dysfunction at biochemical and histological level. Rats were randomly distributed into four groups as control, NaF-treated (200 ppm), and SPC co-administered groups (20 mg and 40 mg/ 100 g body weight) for 16 days. SPC reversed the toxic effects of NaF. SPC significantly ameliorated the NaF-induced alterations of the antioxidant system in the uterus by decreasing lipid peroxidation products and by increasing antioxidant activities. SPC significantly counteracted the adverse effects of NaF on serum level of lactate dehydrogenase (LDH) and inflammatory markers Interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α) and nuclear factor kappa-B (NF-κB). Our results also explored that lipid profile was meaningfully altered due to NaF and also focused a diminution of circulating homocysteine (Hcy) and altered lipid profiles along with a diminished quantity of serum B12 and B9. However, both the doses of SPC reverted back serum levels of B12, B9, and Hcy status in similar fashion along with its corrective action on lipid profile. NaF-treated group exhibited a marked degree of reduction in the weights of ovary and uterus with an alteration of normal tissue histology and significant diminution in serum estradiol (ES) levels without fluctuating uterine estradiol receptor-α (ER-α). However, SPC restored the normal tissue histoarchitecture and also increased the functional efficiency and expression of the ER-α receptor by overturning the ES levels in NaF-treated rats. Moreover, both the doses of SPC were effective against NaF-induced alterations, although 40 mg SPC/100 g body weight had better efficacy in ameliorating the NaF-induced adverse effects on the uterus and ovary.
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Affiliation(s)
- Lipirani Jana
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Pikash Pratim Maity
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Hasina Perveen
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Moumita Dash
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Suryashis Jana
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Arindam Dey
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Subrata Kumar De
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sandip Chattopadhyay
- Department of Biomedical Laboratory Science and Management, and Clinical Nutrition and Dietetics division (UGC Innovative Department), Vidyasagar University, Midnapore, West Bengal, 721102, India.
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107
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Marais A, Adams B, Ringsmuth AK, Ferretti M, Gruber JM, Hendrikx R, Schuld M, Smith SL, Sinayskiy I, Krüger TPJ, Petruccione F, van Grondelle R. The future of quantum biology. J R Soc Interface 2018; 15:20180640. [PMID: 30429265 PMCID: PMC6283985 DOI: 10.1098/rsif.2018.0640] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/12/2018] [Indexed: 01/17/2023] Open
Abstract
Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions.
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Affiliation(s)
- Adriana Marais
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Betony Adams
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Andrew K Ringsmuth
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
- ARC Centre of Excellence for Engineered Quantum Systems, The University of Queensland, St Lucia 4072, Australia
| | - Marco Ferretti
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - J Michael Gruber
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ruud Hendrikx
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Maria Schuld
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Samuel L Smith
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ilya Sinayskiy
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- National Institute for Theoretical Physics, KwaZulu-Natal, South Africa
| | - Tjaart P J Krüger
- Department of Physics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, South Africa
| | - Francesco Petruccione
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- National Institute for Theoretical Physics, KwaZulu-Natal, South Africa
| | - Rienk van Grondelle
- Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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108
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Greene BL, Stubbe J, Nocera DG. Photochemical Rescue of a Conformationally Inactivated Ribonucleotide Reductase. J Am Chem Soc 2018; 140:15744-15752. [PMID: 30347141 DOI: 10.1021/jacs.8b07902] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class Ia ribonucleotide reductase (RNR) of Escherichia coli contains an unusually stable tyrosyl radical cofactor in the β2 subunit (Y122•) necessary for nucleotide reductase activity. Upon binding the cognate α2 subunit, loaded with nucleoside diphosphate substrate and an allosteric/activity effector, a rate determining conformational change(s) enables rapid radical transfer (RT) within the active α2β2 complex from the Y122• site in β2 to the substrate activating cysteine residue (C439) in α2 via a pathway of redox active amino acids (Y122[β] ↔ W48[β]? ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]) spanning >35 Å. Ionizable residues at the α2β2 interface are essential in mediating RT, and therefore control activity. One of these mutations, E350X (where X = A, D, Q) in β2, obviates all RT, though the mechanism of control by which E350 mediates RT remains unclear. Herein, we utilize an E350Q-photoβ2 construct to photochemically rescue RNR activity from an otherwise inactive construct, wherein the initial RT event (Y122• → Y356) is replaced by direct photochemical radical generation of Y356•. These data present compelling evidence that E350 conveys allosteric information between the α2 and β2 subunits facilitating conformational gating of RT that specifically targets Y122• reduction, while the fidelity of the remainder of the RT pathway is retained.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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109
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Sayfutyarova ER, Goldsmith ZK, Hammes-Schiffer S. Theoretical Study of C-H Bond Cleavage via Concerted Proton-Coupled Electron Transfer in Fluorenyl-Benzoates. J Am Chem Soc 2018; 140:15641-15645. [PMID: 30383371 DOI: 10.1021/jacs.8b10461] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Developing new strategies to activate and cleave C-H bonds is important for a broad range of applications. Recently a new approach for C-H bond activation using multi-site concerted proton-coupled electron transfer (PCET) involving intermolecular electron transfer to an oxidant coupled to intramolecular proton transfer was reported. For a series of oxidants reacting with 2-(9 H-fluoren-9-yl)benzoate, experimental studies revealed an atypical Brønsted α, defined as the slope of the logarithm of the PCET rate constant versus the logarithm of the equilibrium constant or the scaled driving force. Herein this reaction is modeled with a vibronically nonadiabatic PCET theory. Hydrogen tunneling, thermal sampling of the proton donor-acceptor mode, solute and solvent reorganization, and contributions from excited vibronic states are found to play important roles. The calculations qualitatively reproduce the experimental observation of a Brønsted α significantly less than 0.5 and explain this shallow slope in terms of exoergic processes between pairs of electron-proton vibronic states. These fundamental mechanistic insights may guide the design of more effective strategies for C-H bond activation and cleavage.
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Affiliation(s)
- Elvira R Sayfutyarova
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Zachary K Goldsmith
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
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110
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Cinar ME, Lal M, Deiseroth HJ, Schlirf J, Schmittel M. Detection and follow-up reactions of distonic β
, β
-dimesityl enol radical cations containing nitrogen heterocyclic bases. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M. Emin Cinar
- Department Chemie-Biologie; Universität Siegen; Siegen Germany
| | - Mukul Lal
- Department Chemie-Biologie; Universität Siegen; Siegen Germany
| | | | - Jens Schlirf
- Department Chemie-Biologie; Universität Siegen; Siegen Germany
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111
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Srinivas V, Lebrette H, Lundin D, Kutin Y, Sahlin M, Lerche M, Eirich J, Branca RMM, Cox N, Sjöberg BM, Högbom M. Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens. Nature 2018; 563:416-420. [PMID: 30429545 PMCID: PMC6317698 DOI: 10.1038/s41586-018-0653-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductase (RNR) catalyses the only known de novo pathway for the production of all four deoxyribonucleotides that are required for DNA synthesis1,2. It is essential for all organisms that use DNA as their genetic material and is a current drug target3,4. Since the discovery that iron is required for function in the aerobic, class I RNR found in all eukaryotes and many bacteria, a dinuclear metal site has been viewed as necessary to generate and stabilize the catalytic radical that is essential for RNR activity5-7. Here we describe a group of RNR proteins in Mollicutes-including Mycoplasma pathogens-that possess a metal-independent stable radical residing on a modified tyrosyl residue. Structural, biochemical and spectroscopic characterization reveal a stable 3,4-dihydroxyphenylalanine (DOPA) radical species that directly supports ribonucleotide reduction in vitro and in vivo. This observation overturns the presumed requirement for a dinuclear metal site in aerobic ribonucleotide reductase. The metal-independent radical requires new mechanisms for radical generation and stabilization, processes that are targeted by RNR inhibitors. It is possible that this RNR variant provides an advantage under metal starvation induced by the immune system. Organisms that encode this type of RNR-some of which are developing resistance to antibiotics-are involved in diseases of the respiratory, urinary and genital tracts. Further characterization of this RNR family and its mechanism of cofactor generation will provide insight into new enzymatic chemistry and be of value in devising strategies to combat the pathogens that utilize it. We propose that this RNR subclass is denoted class Ie.
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Affiliation(s)
- Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Yuri Kutin
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Mülheim an der Ruhr, Germany
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Michael Lerche
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jürgen Eirich
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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112
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Mondal S, Bera S, Maity S, Ghosh P. Orthometalated N-(Benzophenoxazine)- o-aminophenol: Phenolato versus Phenoxyl States. ACS OMEGA 2018; 3:13323-13334. [PMID: 31458047 PMCID: PMC6645054 DOI: 10.1021/acsomega.8b01983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/03/2018] [Indexed: 06/10/2023]
Abstract
The molecular and electronic structures of the orthometalated ruthenium(III) and osmium(III) complexes of N-(benzophenoxazine)-o-aminophenol (OXLH2) that exhibits versatile redox activities are reported. The redox chemistry of OXLH2 is remarkably different from that of N-(aryl)-o-aminophenol (APLH2). The study established that OXLH2 is redox noninnocent and is a precursor of a phenoxyl radical. One of the C-H bonds of OXLH2 is activated by ions, and OXLH2 reveals three different redox states as dianionic phenolato (OXL2-), monoanionic phenoxyl radical (OXL•-), and zwitterionic phenoxium cation (OXL±) states. The reaction of OXLH2 with [RuII(PPh3)3Cl2] in boiling toluene in air affords an orthometalated OXL2- complex of ruthenium(III), trans-[(OXL2-)RuIII(PPh3)2(Cl)] (1), whereas the similar reaction with [OsII(PPh3)3Br2] yields an orthometalated OXL•- complex, cis-[(OXL•-)OsIII(PPh3)Br2] (2). 1 and 2 exhibit ligand-based reversible redox waves due to OXL•-/OXL2-, OXL±/OXL•-, and MIII/MII couples. The 1 + ion is a OXL•- complex of ruthenium(III). 2 - exhibits temperature-dependent valence tautomerism due to [OsII(OXL•-) ↔ OsIII(OXL2-)] equilibrium. 2 2- is a OXL2- complex of osmium(II), while 1 2+ and 2 + are OXL± complexes of metal(III). 2 is an oxidant and effective catalyst for oxidation of 3,5-di-tert-butylcatechol to the corresponding quinone, and the turnover number is 119.7 h-1. The UV-vis-NIR absorption spectrum of 1 displays an NIR band at 800 nm due to an intra-ligand-charge-transfer transition, which is absent in 2 incorporating a OXL•- radical. The molecular and electronic structures of 1 and 2 and their oxidized and reduced analogues were confirmed by single-crystal X-ray crystallography, variable-temperature electron paramagnetic resonance spectroscopy, spectroelectrochemical measurements, and density functional theory calculations.
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Affiliation(s)
| | | | | | - Prasanta Ghosh
- E-mail: . Phone: +91-33-2428-7347. Fax: +91-33-2477-3597
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113
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Odella E, Mora SJ, Wadsworth BL, Huynh MT, Goings JJ, Liddell PA, Groy TL, Gervaldo M, Sereno LE, Gust D, Moore TA, Moore GF, Hammes-Schiffer S, Moore AL. Controlling Proton-Coupled Electron Transfer in Bioinspired Artificial Photosynthetic Relays. J Am Chem Soc 2018; 140:15450-15460. [DOI: 10.1021/jacs.8b09724] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emmanuel Odella
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - S. Jimena Mora
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Brian L. Wadsworth
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Mioy T. Huynh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joshua J. Goings
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Paul A. Liddell
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas L. Groy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Miguel Gervaldo
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal No. 3, 5800 Río Cuarto, Córdoba, Argentina
| | - Leónides E. Sereno
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal No. 3, 5800 Río Cuarto, Córdoba, Argentina
| | - Devens Gust
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas A. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Gary F. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana L. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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114
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Robbins JM, Geng J, Barry BA, Gadda G, Bommarius AS. Photoirradiation Generates an Ultrastable 8-Formyl FAD Semiquinone Radical with Unusual Properties in Formate Oxidase. Biochemistry 2018; 57:5818-5826. [PMID: 30226367 DOI: 10.1021/acs.biochem.8b00571] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate oxidase (FOX) was previously shown to contain a noncovalently bound 8-formyl FAD (8-fFAD) cofactor. However, both the absorption spectra and the kinetic parameters previously reported for FOX are inconsistent with more recent reports. The ultraviolet-visible (UV-vis) absorption spectrum reported in early studies closely resembles the spectra observed for protein-bound 8-formyl flavin semiquinone species, thus suggesting FOX may be photosensitive. Therefore, the properties of dark and light-exposed FOX were investigated using steady-state kinetics and site-directed mutagenesis analysis along with inductively coupled plasma optical emission spectroscopy, UV-vis absorption spectroscopy, circular dichroism spectroscopy, liquid chromatography and mass spectrometry, and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, these experimental results demonstrate that FOX is deactivated in the presence of light through generation of an oxygen stable, anionic (red) 8-fFAD semiquinone radical capable of persisting either in an aerobic environment for multiple weeks or in the presence of a strong reducing agent like sodium dithionite. Herein, we study the photoinduced formation of the 8-fFAD semiquinone radical in FOX and report the first EPR spectrum of this radical species. The stability of the 8-fFAD semiquinone radical suggests FOX to be a model enzyme for probing the structural and mechanistic features involved in stabilizing flavin semiquinone radicals. It is likely that the photoinduced formation of a stable 8-fFAD semiquinone radical is a defining characteristic of 8-formyl flavin-dependent enzymes. Additionally, a better understanding of the radical stabilization process may yield a FOX enzyme with more robust activity and broader industrial usefulness.
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Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States
| | - Jiafeng Geng
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Giovanni Gadda
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Biotechnology and Drug Design , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Department of Biology , Georgia State University , Atlanta , Georgia 30302-3965 , United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
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115
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Martinie RJ, Blaesi EJ, Bollinger JM, Krebs C, Finkelstein KD, Pollock CJ. Two-Color Valence-to-Core X-ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase. Angew Chem Int Ed Engl 2018; 57:12754-12758. [PMID: 30075052 PMCID: PMC6579043 DOI: 10.1002/anie.201807366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/20/2018] [Indexed: 12/20/2022]
Abstract
Proton transfer reactions are of central importance to a wide variety of biochemical processes, though determining proton location and monitoring proton transfers in biological systems is often extremely challenging. Herein, we use two-color valence-to-core X-ray emission spectroscopy (VtC XES) to identify protonation events across three oxidation states of the O2 -activating, radical-initiating manganese-iron heterodinuclear cofactor in a class I-c ribonucleotide reductase. This is the first application of VtC XES to an enzyme intermediate and the first simultaneous measurement of two-color VtC spectra. In contrast to more conventional methods of assessing protonation state, VtC XES is a more direct probe applicable to a wide range of metalloenzyme systems. These data, coupled to insight provided by DFT calculations, allow the inorganic cores of the MnIV FeIV and MnIV FeIII states of the enzyme to be assigned as MnIV (μ-O)2 FeIV and MnIV (μ-O)(μ-OH)FeIII , respectively.
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Affiliation(s)
- Ryan J Martinie
- Department of Chemistry, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - Elizabeth J Blaesi
- Department of Chemistry, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
| | - Kenneth D Finkelstein
- Cornell High Energy Synchrotron Source, Wilson Laboratory, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher J Pollock
- Department of Chemistry, The Pennsylvania State University, 318 Chemistry Building, University Park, PA, 16802, USA
- Present address: Cornell High Energy Synchrotron Source, Wilson Laboratory, Cornell University, Ithaca, NY, 14853, USA
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Martinie RJ, Blaesi EJ, Bollinger JM, Krebs C, Finkelstein KD, Pollock CJ. Two‐Color Valence‐to‐Core X‐ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ryan J. Martinie
- Department of Chemistry The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - Elizabeth J. Blaesi
- Department of Chemistry The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - J. Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
| | - Kenneth D. Finkelstein
- Cornell High Energy Synchrotron Source, Wilson Laboratory Cornell University Ithaca NY 14853 USA
| | - Christopher J. Pollock
- Department of Chemistry The Pennsylvania State University 318 Chemistry Building University Park PA 16802 USA
- Present address: Cornell High Energy Synchrotron Source Wilson Laboratory Cornell University Ithaca NY 14853 USA
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117
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Hammes-Schiffer S. Controlling Electrons and Protons through Theory: Molecular Electrocatalysts to Nanoparticles. Acc Chem Res 2018; 51:1975-1983. [PMID: 30110147 DOI: 10.1021/acs.accounts.8b00240] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The development of renewable energy sources that are environmentally friendly and economical is of critical importance. The effective utilization of such energy sources relies on catalysts to facilitate the interconversion between electrical and chemical energy through multielectron, multiproton reactions. The design of effective catalysts for these types of energy conversion processes requires the ability to control the localization and movement of electrons and protons, as well as the coupling between them. Theoretical calculations, in conjunction with experimental validation and feedback, are playing a key role in these catalyst design efforts. A general theory has been developed for describing proton-coupled electron transfer (PCET) reactions, which encompass all reactions involving the coupled transfer of electrons and protons, including sequential and concerted mechanisms for multielectron, multiproton processes. In addition, computational methods have been devised to compute the input quantities for the PCET rate constant expressions and to generate free energy pathways for molecular electrocatalysts. These methods have been extended to heterogeneous PCET reactions to enable the modeling of PCET processes at electrode and nanoparticle surfaces. Three distinct theoretical studies of PCET reactions relevant to catalyst design for energy conversion processes are discussed. In the first application, theoretical calculations of hydrogen production catalyzed by hangman metalloporphyrins predicted that the porphyrin ligand is reduced, leading to dearomatization and proton transfer from the carboxylic acid hanging group to the meso carbon of the porphyrin rather than the metal center, producing a phlorin intermediate. Subsequent experiments isolated and characterized the phlorin intermediate, validating this theoretical prediction. These molecular electrocatalysts exemplify the potential use of noninnocent ligands to localize electrons and protons on different parts of the catalyst and to direct their motions accordingly. In the second application, theoretical calculations on substituted benzimidazole phenol molecules predicted that certain substituents would lead to multiple intramolecular proton transfer reactions upon oxidation. Subsequent experiments verified these multiproton reactions, as well as the predicted shifts in the redox potentials and kinetic isotope effects. These bioinspired molecular systems demonstrate the potential use of multiproton relays to enable the transport of protons over longer distances along specified pathways, as well as the tuning of redox potentials through this movement of positive charge. In the third application, theoretical studies of heterogeneous PCET in photoreduced ZnO nanoparticles illustrated the significance of proton diffusion through the bulk of the nanoparticle as well as interfacial PCET to an organic radical in solution at its surface. These theoretical calculations were consistent with prior experimental studies of this system, although theoretical methods for heterogeneous PCET have not yet attained the level of predictive capability highlighted for the molecular electrocatalysts. These examples suggest that theory will play a significant role in the design of both molecular and heterogeneous catalysts to control the movement and coupling of electrons and protons. The resulting catalysts will be essential for the development of renewable energy sources to address current energy challenges.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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118
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Soudackov AV, Hammes-Schiffer S. Proton-coupled electron transfer reactions: analytical rate constants and case study of kinetic isotope effects in lipoxygenase. Faraday Discuss 2018; 195:171-189. [PMID: 27735009 DOI: 10.1039/c6fd00122j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general theory has been developed for proton-coupled electron transfer (PCET), which is vital to a wide range of chemical and biological processes. This theory describes PCET reactions in terms of nonadiabatic transitions between reactant and product electron-proton vibronic states and includes the effects of thermal fluctuations of the solvent or protein environment, as well as the proton donor-acceptor motion. Within the framework of this general PCET theory, a series of analytical rate constant expressions has been derived for PCET reactions in well-defined regimes. Herein, the application of this theory to PCET in the enzyme soybean lipoxygenase illustrates the regimes of validity for the various rate constant expressions and elucidates the fundamental physical principles dictating PCET reactions. Such theoretical studies provide significant physical insights that guide the interpretation of experimental data and lead to experimentally testable predictions. A combination of theoretical treatments with atomic-level simulations is essential to understanding PCET.
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Affiliation(s)
- Alexander V Soudackov
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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119
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Yan J, Yang Z, Chen Y, Chang Y, Lyu C, Luo C, Cheng M, Hsu H. Activation of O−H and C−O Bonds in Water and Methanol by a Vanadium‐Bound Thiyl Radical. Chemistry 2018; 24:15190-15194. [DOI: 10.1002/chem.201803431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/17/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Jyun‐An Yan
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Zi‐Kuan Yang
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Yu‐Sen Chen
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Ya‐Ho Chang
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Chiao‐Ling Lyu
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Chun‐Gang Luo
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Mu‐Jeng Cheng
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
| | - Hua‐Fen Hsu
- Department of ChemistryNational Cheng Kung University, No. 1 University Rd. 701 Tainan Taiwan
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120
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MacAleese L, Girod M, Nahon L, Giuliani A, Antoine R, Dugourd P. Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1826-1834. [PMID: 29949057 DOI: 10.1007/s13361-018-1989-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/27/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. Graphical Abstract.
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Affiliation(s)
- Luke MacAleese
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France.
| | - Marion Girod
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques UMR 5280, 69100, Villeurbanne, France
| | - Laurent Nahon
- Synchrotron SOLEIL, BP 48 St Aubin, 91192, Gif Sur Yvette, France
| | - Alexandre Giuliani
- Synchrotron SOLEIL, BP 48 St Aubin, 91192, Gif Sur Yvette, France
- UAR1008 CEPIA, INRA, BP 71627, 44316, Nantes, France
| | - Rodolphe Antoine
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France
| | - Philippe Dugourd
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, Institut Lumière Matière UMR 5306, 69622, Villeurbanne, France
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122
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Bowring MA, Bradshaw LR, Parada GA, Pollock TP, Fernández-Terán RJ, Kolmar SS, Mercado BQ, Schlenker CW, Gamelin DR, Mayer JM. Activationless Multiple-Site Concerted Proton-Electron Tunneling. J Am Chem Soc 2018; 140:7449-7452. [PMID: 29847111 PMCID: PMC6310214 DOI: 10.1021/jacs.8b04455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transfer of protons and electrons is key to energy conversion and storage, from photosynthesis to fuel cells. Increased understanding and control of these processes are needed. A new anthracene-phenol-pyridine molecular triad was designed to undergo fast photoinduced multiple-site concerted proton-electron transfer (MS-CPET), with the phenol moiety transferring an electron to the photoexcited anthracene and a proton to the pyridine. Fluorescence quenching and transient absorption experiments in solutions and glasses show rapid MS-CPET (3.2 × 1010 s-1 at 298 K). From 5.5 to 90 K, the reaction rate and kinetic isotope effect (KIE) are independent of temperature, with zero Arrhenius activation energy. From 145 to 350 K, there are only slight changes with temperature. This MS-CPET reaction thus occurs by tunneling of both the proton and electron, in different directions. Since the reaction proceeds without significant thermal activation energy, the rate constant indicates the magnitude of the electron/proton double tunneling probability.
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Affiliation(s)
- Miriam A. Bowring
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, Reed College, Portland, Oregon 97202, United States
| | - Liam R. Bradshaw
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Giovanny A. Parada
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Timothy P. Pollock
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Scott S. Kolmar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Cody W. Schlenker
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniel R. Gamelin
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - James M. Mayer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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123
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Yang JD, Ji P, Xue XS, Cheng JP. Recent Advances and Advisable Applications of Bond Energetics in Organic Chemistry. J Am Chem Soc 2018; 140:8611-8623. [DOI: 10.1021/jacs.8b04104] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jin-Dong Yang
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Pengju Ji
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiao-Song Xue
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Centre of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jin-Pei Cheng
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Centre of Chemical Science and Engineering, College of Chemistry, Nankai University, Tianjin 300071, China
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124
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Reguera G. Harnessing the power of microbial nanowires. Microb Biotechnol 2018; 11:979-994. [PMID: 29806247 PMCID: PMC6201914 DOI: 10.1111/1751-7915.13280] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/13/2018] [Accepted: 04/22/2018] [Indexed: 12/13/2022] Open
Abstract
The reduction of iron oxide minerals and uranium in model metal reducers in the genus Geobacter is mediated by conductive pili composed primarily of a structurally divergent pilin peptide that is otherwise recognized, processed and assembled in the inner membrane by a conserved Type IVa pilus apparatus. Electronic coupling among the peptides is promoted upon assembly, allowing the discharge of respiratory electrons at rates that greatly exceed the rates of cellular respiration. Harnessing the unique properties of these conductive appendages and their peptide building blocks in metal bioremediation will require understanding of how the pilins assemble to form a protein nanowire with specialized sites for metal immobilization. Also important are insights into how cells assemble the pili to make an electroactive matrix and grow on electrodes as biofilms that harvest electrical currents from the oxidation of waste organic substrates. Genetic engineering shows promise to modulate the properties of the peptide building blocks, protein nanowires and current‐harvesting biofilms for various applications. This minireview discusses what is known about the pilus material properties and reactions they catalyse and how this information can be harnessed in nanotechnology, bioremediation and bioenergy applications.
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Affiliation(s)
- Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Rd., Rm. 6190, East Lansing, MI, 48824, USA
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125
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Chen PYT, Funk MA, Brignole EJ, Drennan CL. Disruption of an oligomeric interface prevents allosteric inhibition of Escherichia coli class Ia ribonucleotide reductase. J Biol Chem 2018; 293:10404-10412. [PMID: 29700111 DOI: 10.1074/jbc.ra118.002569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductases (RNRs) convert ribonucleotides to deoxynucleotides, a process essential for DNA biosynthesis and repair. Class Ia RNRs require two dimeric subunits for activity: an α2 subunit that houses the active site and allosteric regulatory sites and a β2 subunit that houses the diferric tyrosyl radical cofactor. Ribonucleotide reduction requires that both subunits form a compact α2β2 state allowing for radical transfer from β2 to α2 RNR activity is regulated allosterically by dATP, which inhibits RNR, and by ATP, which restores activity. For the well-studied Escherichia coli class Ia RNR, dATP binding to an allosteric site on α promotes formation of an α4β4 ring-like state. Here, we investigate whether the α4β4 formation causes or results from RNR inhibition. We demonstrate that substitutions at the α-β interface (S37D/S39A-α2, S39R-α2, S39F-α2, E42K-α2, or L43Q-α2) that disrupt the α4β4 oligomer abrogate dATP-mediated inhibition, consistent with the idea that α4β4 formation is required for dATP's allosteric inhibition of RNR. Our results further reveal that the α-β interface in the inhibited state is highly sensitive to manipulation, with a single substitution interfering with complex formation. We also discover that residues at the α-β interface whose substitution has previously been shown to cause a mutator phenotype in Escherichia coli (i.e. S39F-α2 or E42K-α2) are impaired only in their activity regulation, thus linking this phenotype with the inability to allosterically down-regulate RNR. Whereas the cytotoxicity of RNR inhibition is well-established, these data emphasize the importance of down-regulation of RNR activity.
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Affiliation(s)
| | | | - Edward J Brignole
- From the Departments of Chemistry and.,Biology and.,the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Catherine L Drennan
- From the Departments of Chemistry and .,Biology and.,the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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126
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Rose HR, Ghosh MK, Maggiolo AO, Pollock CJ, Blaesi EJ, Hajj V, Wei Y, Rajakovich LJ, Chang WC, Han Y, Hajj M, Krebs C, Silakov A, Pandelia ME, Bollinger JM, Boal AK. Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor. Biochemistry 2018; 57:2679-2693. [PMID: 29609464 DOI: 10.1021/acs.biochem.8b00247] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2-) for activation, but it does not require the O2--supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2- to the Mn2II/II cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.
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Affiliation(s)
| | | | | | | | | | | | - Yifeng Wei
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | | | | | | | | | | | | | - Maria-Eirini Pandelia
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
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Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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128
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Parent A, Benjdia A, Guillot A, Kubiak X, Balty C, Lefranc B, Leprince J, Berteau O. Mechanistic Investigations of PoyD, a Radical S-Adenosyl-l-methionine Enzyme Catalyzing Iterative and Directional Epimerizations in Polytheonamide A Biosynthesis. J Am Chem Soc 2018; 140:2469-2477. [PMID: 29253341 PMCID: PMC5824343 DOI: 10.1021/jacs.7b08402] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of bioactive peptides. Among RiPPs, the bacterial toxin polytheonamide A is characterized by a unique set of post-translational modifications catalyzed by novel radical S-adenosyl-l-methionine (SAM) enzymes. Here we show that the radical SAM enzyme PoyD catalyzes in vitro polytheonamide epimerization in a C-to-N directional manner. By combining mutagenesis experiments with labeling studies and investigating the enzyme substrate promiscuity, we deciphered in detail the mechanism of PoyD. We notably identified a critical cysteine residue as a likely key H atom donor and demonstrated that PoyD belongs to a distinct family of radical SAM peptidyl epimerases. In addition, our study shows that the core peptide directly influences the epimerization pattern allowing for production of peptides with unnatural epimerization patterns.
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Affiliation(s)
- Aubérie Parent
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Xavier Kubiak
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
| | - Benjamin Lefranc
- Inserm U1239, PRIMACEN, University of Rouen Normandy , 76000 Rouen, France
| | - Jérôme Leprince
- Inserm U1239, PRIMACEN, University of Rouen Normandy , 76000 Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay , 78350 Jouy-en-Josas, France
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129
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Streit BR, Celis AI, Moraski GC, Shisler KA, Shepard EM, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b. J Biol Chem 2018; 293:3989-3999. [PMID: 29414780 DOI: 10.1074/jbc.ra117.000830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/01/2018] [Indexed: 01/02/2023] Open
Abstract
The H2O2-dependent oxidative decarboxylation of coproheme III is the final step in the biosynthesis of heme b in many microbes. However, the coproheme decarboxylase reaction mechanism is unclear. The structure of the decarboxylase in complex with coproheme III suggested that the substrate iron, reactive propionates, and an active-site tyrosine convey a net 2e-/2H+ from each propionate to an activated form of H2O2 Time-resolved EPR spectroscopy revealed that Tyr-145 formed a radical species within 30 s of the reaction of the enzyme-coproheme complex with H2O2 This radical disappeared over the next 270 s, consistent with a catalytic intermediate. Use of the harderoheme III intermediate as substrate or substitutions of redox-active side chains (W198F, W157F, or Y113S) did not strongly affect the appearance or intensity of the radical spectrum measured 30 s after initiating the reaction with H2O2, nor did it change the ∼270 s required for the radical signal to recede to ≤10% of its initial intensity. These results suggested Tyr-145 as the site of a catalytic radical involved in decarboxylating both propionates. Tyr-145• was accompanied by partial loss of the initially present Fe(III) EPR signal intensity, consistent with the possible formation of Fe(IV)=O. Site-specifically deuterated coproheme gave rise to a kinetic isotope effect of ∼2 on the decarboxylation rate constant, indicating that cleavage of the propionate Cβ-H bond was partly rate-limiting. The inferred mechanism requires two consecutive hydrogen atom transfers, first from Tyr-145 to the substrate Fe/H2O2 intermediate and then from the propionate Cβ-H to Tyr-145•.
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Affiliation(s)
- Bennett R Streit
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Arianna I Celis
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Garrett C Moraski
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Krista A Shisler
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Eric M Shepard
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Kenton R Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Gudrun S Lukat-Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
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130
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Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
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Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
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131
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation. Chemphyschem 2018; 19:669-689. [DOI: 10.1002/cphc.201700339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/22/2017] [Indexed: 01/12/2023]
Affiliation(s)
- N. M. F. S. A. Cerqueira
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - P. A. Fernandes
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - M. J. Ramos
- REQUIMTE-UCIBIO; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
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132
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Davis I, Koto T, Liu A. Radical Trapping Study of the Relaxation of bis-Fe(IV) MauG. REACTIVE OXYGEN SPECIES (APEX, N.C.) 2018; 5:46-55. [PMID: 29479564 PMCID: PMC5822730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The di-heme enzyme, MauG, utilizes a high-valent, charge-resonance stabilized bis-Fe(IV) state to perform protein radical-based catalytic chemistry. Though the bis-Fe(IV) species is able to oxidize remote tryptophan residues on its substrate protein, it does not rapidly oxidize its own residues in the absence of substrate. The slow return of bis-Fe(IV) MauG to its resting di-ferric state occurs via up to two intermediates, one of which has been previously proposed by Ma et al. (Biochem J 2016; 473:1769) to be a methionine-based radical in a recent study. In this work, we pursue intermediates involved in the return of high-valent MauG to its resting state in the absence of the substrate by EPR spectroscopy and radical trapping. The bis-Fe(IV) MauG is shown by EPR, HPLC, UV-Vis, and high-resolution mass spectrometry to oxidize the trapping agent, 5,5-dimethyl-1-pyrroline N-oxide (DMPO) to a radical species directly. Nitrosobenzene was also employed as a trapping agent and was shown to form an adduct with high-valent MauG species. The effects of DMPO and nitrosobenzene on the kinetics of the return to di-ferric MauG were both investigated. This work eliminates the possibility that a MauG-based methionine radical species accumulates during the self-reduction of bis-Fe(IV) MauG.
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Affiliation(s)
- Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Teruaki Koto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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133
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Nakashige TG, Nolan EM. Human calprotectin affects the redox speciation of iron. Metallomics 2017; 9:1086-1095. [PMID: 28561859 DOI: 10.1039/c7mt00044h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report that the metal-sequestering human host-defense protein calprotectin (CP, S100A8/S100A9 oligomer) affects the redox speciation of iron (Fe) in bacterial growth media and buffered aqueous solution. Under aerobic conditions and in the absence of an exogenous reducing agent, CP-Ser (S100A8(C42S)/S100A9(C3S) oligomer) depletes Fe from three different bacterial growth media preparations over a 48 h timeframe (T = 30 °C). The presence of the reducing agent β-mercaptoethanol accelerates this process and allows CP-Ser to deplete Fe over a ≈1 h timeframe. Fe-depletion assays performed with metal-binding-site variants of CP-Ser show that the hexahistidine (His6) site, which coordinates Fe(ii) with high affinity, is required for Fe depletion. An analysis of Fe redox speciation in buffer containing Fe(iii) citrate performed under aerobic conditions demonstrates that CP-Ser causes a time-dependent increase in the [Fe(ii)]/[Fe(iii)] ratio. Taken together, these results indicate that the hexahistidine site of CP stabilizes Fe(ii) and thereby shifts the redox equilibrium of Fe to the reduced ferrous state under aerobic conditions. We also report that the presence of bacterial metabolites affects the Fe-depleting activity of CP-Ser. Supplementation of bacterial growth media with an Fe(iii)-scavenging siderophore (enterobactin, staphyloferrin B, or desferrioxamine B) attenuates the Fe-depleting activity of CP-Ser. This result indicates that formation of Fe(iii)-siderophore complexes blocks CP-mediated reduction of Fe(iii) and hence the ability of CP to coordinate Fe(ii). In contrast, the presence of pyocyanin (PYO), a redox-cycling phenazine produced by Pseudomonas aeruginosa that reduces Fe(iii) to Fe(ii), accelerates Fe depletion by CP-Ser under aerobic conditions. These findings indicate that the presence of microbial metabolites that contribute to metal homeostasis at the host/pathogen interface can affect the metal-sequestering function of CP.
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Affiliation(s)
- Toshiki G Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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134
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Shon JH, Teets TS. Potent Bis-Cyclometalated Iridium Photoreductants with β-Diketiminate Ancillary Ligands. Inorg Chem 2017; 56:15295-15303. [PMID: 29172506 DOI: 10.1021/acs.inorgchem.7b02859] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we outline a strategy to prepare a class of improved visible-light photosensitizers. Bis-cyclometalated iridium complexes with electron-rich β-diketiminate (NacNac) ancillary ligands are demonstrated to be potent excited-state electron donors. Evaluation of the photophysical and electrochemical properties establishes the excited-state redox potentials of the complexes, and Stern-Volmer quenching experiments inform on the kinetics of photoinduced electron transfer to the model substrates methyl viologen (MV2+) and benzophenone (BP). Compared to fac-Ir(ppy)3 (ppy = 2-phenylpyridine), widely regarded as a state-of-the-art photoreductant, the complexes we describe have excited-state redox potentials that are more potent by 300-400 mV and rates for photoinduced electron transfer that are accelerated by as much as a factor of 3. These complexes emerge as promising targets for application in photocatalytic reactions and other photochemical processes.
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Affiliation(s)
- Jong-Hwa Shon
- Department of Chemistry, University of Houston , 3585 Cullen Blvd., Room 112, Houston, Texas 77204-5003, United States
| | - Thomas S Teets
- Department of Chemistry, University of Houston , 3585 Cullen Blvd., Room 112, Houston, Texas 77204-5003, United States
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135
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Lennox JC, Dempsey JL. Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex. J Phys Chem B 2017; 121:10530-10542. [PMID: 29130684 DOI: 10.1021/acs.jpcb.7b06443] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pKa units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.
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Affiliation(s)
- J Christian Lennox
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
| | - Jillian L Dempsey
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States
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136
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Greene BL, Taguchi AT, Stubbe J, Nocera DG. Conformationally Dynamic Radical Transfer within Ribonucleotide Reductase. J Am Chem Soc 2017; 139:16657-16665. [PMID: 29037038 DOI: 10.1021/jacs.7b08192] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNR) catalyze the reduction of nucleotides to deoxynucleotides through a mechanism involving an essential cysteine based thiyl radical. In the E. coli class 1a RNR the thiyl radical (C439•) is a transient species generated by radical transfer (RT) from a stable diferric-tyrosyl radical cofactor located >35 Å away across the α2:β2 subunit interface. RT is facilitated by sequential proton-coupled electron transfer (PCET) steps along a pathway of redox active amino acids (Y122β ↔ [W48β?] ↔ Y356β ↔ Y731α ↔ Y730α ↔ C439α). The mutant R411A(α) disrupts the H-bonding environment and conformation of Y731, ostensibly breaking the RT pathway in α2. However, the R411A protein retains significant enzymatic activity, suggesting Y731 is conformationally dynamic on the time scale of turnover. Installation of the radical trap 3-amino tyrosine (NH2Y) by amber codon suppression at positions Y731 or Y730 and investigation of the NH2Y• trapped state in the active α2:β2 complex by HYSCORE spectroscopy validate that the perturbed conformation of Y731 in R411A-α2 is dynamic, reforming the H-bond between Y731 and Y730 to allow RT to propagate to Y730. Kinetic studies facilitated by photochemical radical generation reveal that Y731 changes conformation on the ns-μs time scale, significantly faster than the enzymatic kcat. Furthermore, the kinetics of RT across the subunit interface were directly assessed for the first time, demonstrating conformationally dependent RT rates that increase from 0.6 to 1.6 × 104 s-1 when comparing wild type to R411A-α2, respectively. These results illustrate the role of conformational flexibility in modulating RT kinetics by targeting the PCET pathway of radical transport.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Alexander T Taguchi
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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137
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Peptides as Bio-inspired Molecular Electronic Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 29081052 DOI: 10.1007/978-3-319-66095-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Understanding the electronic properties of single peptides is not only of fundamental importance to biology, but it is also pivotal to the realization of bio-inspired molecular electronic materials. Natural proteins have evolved to promote electron transfer in many crucial biological processes. However, their complex conformational nature inhibits a thorough investigation, so in order to study electron transfer in proteins, simple peptide models containing redox active moieties present as ideal candidates. Here we highlight the importance of secondary structure characteristic to proteins/peptides, and its relevance to electron transfer. The proposed mechanisms responsible for such transfer are discussed, as are details of the electrochemical techniques used to investigate their electronic properties. Several factors that have been shown to influence electron transfer in peptides are also considered. Finally, a comprehensive experimental and theoretical study demonstrates that the electron transfer kinetics of peptides can be successfully fine tuned through manipulation of chemical composition and backbone rigidity. The methods used to characterize the conformation of all peptides synthesized throughout the study are outlined, along with the various approaches used to further constrain the peptides into their geometric conformations. The aforementioned sheds light on the potential of peptides to one day play an important role in the fledgling field of molecular electronics.
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138
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Loderer C, Jonna VR, Crona M, Rozman Grinberg I, Sahlin M, Hofer A, Lundin D, Sjöberg BM. A unique cysteine-rich zinc finger domain present in a majority of class II ribonucleotide reductases mediates catalytic turnover. J Biol Chem 2017; 292:19044-19054. [PMID: 28972190 PMCID: PMC5704485 DOI: 10.1074/jbc.m117.806331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/28/2017] [Indexed: 12/04/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, used in DNA synthesis and repair. Two different mechanisms help deliver the required electrons to the RNR active site. Formate can be used as reductant directly in the active site, or glutaredoxins or thioredoxins reduce a C-terminal cysteine pair, which then delivers the electrons to the active site. Here, we characterized a novel cysteine-rich C-terminal domain (CRD), which is present in most class II RNRs found in microbes. The NrdJd-type RNR from the bacterium Stackebrandtia nassauensis was used as a model enzyme. We show that the CRD is involved in both higher oligomeric state formation and electron transfer to the active site. The CRD-dependent formation of high oligomers, such as tetramers and hexamers, was induced by addition of dATP or dGTP, but not of dTTP or dCTP. The electron transfer was mediated by an array of six cysteine residues at the very C-terminal end, which also coordinated a zinc atom. The electron transfer can also occur between subunits, depending on the enzyme's oligomeric state. An investigation of the native reductant of the system revealed no interaction with glutaredoxins or thioredoxins, indicating that this class II RNR uses a different electron source. Our results indicate that the CRD has a crucial role in catalytic turnover and a potentially new terminal reduction mechanism and suggest that the CRD is important for the activities of many class II RNRs.
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Affiliation(s)
- Christoph Loderer
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | | | - Mikael Crona
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Inna Rozman Grinberg
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Margareta Sahlin
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Anders Hofer
- the Department of Medical Biochemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Daniel Lundin
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Britt-Marie Sjöberg
- From the Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden and
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139
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O'Brien E, Holt ME, Thompson MK, Salay LE, Ehlinger AC, Chazin WJ, Barton JK. The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport. Science 2017; 355:355/6327/eaag1789. [PMID: 28232525 DOI: 10.1126/science.aag1789] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/23/2017] [Indexed: 01/05/2023]
Abstract
DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA charge transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication.
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Affiliation(s)
- Elizabeth O'Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marilyn E Holt
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew K Thompson
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Lauren E Salay
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Aaron C Ehlinger
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA.
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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140
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Zhang H, Wu W, Mo Y. Study of proton-coupled electron transfer (PCET) with four explicit diabatic states at the ab initio level. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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141
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Alcaide B, Almendros P, Aparicio B, Lázaro-Milla C, Luna A, Faza ON. Gold-Photoredox-Cocatalyzed Tandem Oxycyclization/Coupling Sequence of Allenols and Diazonium Salts with Visible Light Mediation. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700598] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Benito Alcaide
- Grupo de Lactamas y Heterociclos Bioactivos, Departamento de Química Orgánica I, Unidad Asociada al CSIC, Facultad de Química; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Pedro Almendros
- Instituto de Química Orgánica General, Consejo Superior de Investigaciones Científicas; IQOG-CSIC; Juan de la Cierva 3 28006 Madrid Spain
| | - Borja Aparicio
- Grupo de Lactamas y Heterociclos Bioactivos, Departamento de Química Orgánica I, Unidad Asociada al CSIC, Facultad de Química; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Carlos Lázaro-Milla
- Grupo de Lactamas y Heterociclos Bioactivos, Departamento de Química Orgánica I, Unidad Asociada al CSIC, Facultad de Química; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Amparo Luna
- Grupo de Lactamas y Heterociclos Bioactivos, Departamento de Química Orgánica I, Unidad Asociada al CSIC, Facultad de Química; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Olalla Nieto Faza
- Departamento de Química Orgánica, Facultade de Ciencias; Universidade de Vigo; Campus as Lagoas 32004 Ourense Spain
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142
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Zhang M, Wang L, Zhong D. Photolyase: Dynamics and electron-transfer mechanisms of DNA repair. Arch Biochem Biophys 2017; 632:158-174. [PMID: 28802828 DOI: 10.1016/j.abb.2017.08.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 11/16/2022]
Abstract
Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.
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Affiliation(s)
- Meng Zhang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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143
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Nick TU, Ravichandran KR, Stubbe J, Kasanmascheff M, Bennati M. Spectroscopic Evidence for a H Bond Network at Y 356 Located at the Subunit Interface of Active E. coli Ribonucleotide Reductase. Biochemistry 2017. [PMID: 28640584 DOI: 10.1021/acs.biochem.7b00462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction catalyzed by E. coli ribonucleotide reductase (RNR) composed of α and β subunits that form an active α2β2 complex is a paradigm for proton-coupled electron transfer (PCET) processes in biological transformations. β2 contains the diferric tyrosyl radical (Y122·) cofactor that initiates radical transfer (RT) over 35 Å via a specific pathway of amino acids (Y122· ⇆ [W48] ⇆ Y356 in β2 to Y731 ⇆ Y730 ⇆ C439 in α2). Experimental evidence exists for colinear and orthogonal PCET in α2 and β2, respectively. No mechanistic model yet exists for the PCET across the subunit (α/β) interface. Here, we report unique EPR spectroscopic features of Y356·-β, the pathway intermediate generated by the reaction of 2,3,5-F3Y122·-β2/CDP/ATP with wt-α2, Y731F-α2, or Y730F-α2. High field EPR (94 and 263 GHz) reveals a dramatically perturbed g tensor. [1H] and [2H]-ENDOR reveal two exchangeable H bonds to Y356·: a moderate one almost in-plane with the π-system and a weak one. DFT calculation on small models of Y· indicates that two in-plane, moderate H bonds (rO-H ∼1.8-1.9 Å) are required to reproduce the gx value of Y356· (wt-α2). The results are consistent with a model, in which a cluster of two, almost symmetrically oriented, water molecules provide the two moderate H bonds to Y356· that likely form a hydrogen bond network of water molecules involved in either the reversible PCET across the subunit interface or in H+ release to the solvent during Y356 oxidation.
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Affiliation(s)
- Thomas U Nick
- Research Group Electron-Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Kanchana R Ravichandran
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Müge Kasanmascheff
- Research Group Electron-Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany
| | - Marina Bennati
- Research Group Electron-Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany.,Department of Chemistry, University of Göttingen , 37077 Göttingen, Germany
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144
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Affiliation(s)
- Maeva Fincker
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
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145
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Long-range proton-coupled electron transfer in the Escherichia coli class Ia ribonucleotide reductase. Essays Biochem 2017; 61:281-292. [PMID: 28487404 DOI: 10.1042/ebc20160072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/17/2022]
Abstract
Escherichia coli class Ia ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to 2'-deoxynucleotides using a radical mechanism. Each turnover requires radical transfer from an assembled diferric tyrosyl radical (Y•) cofactor to the enzyme active site over 35 Å away. This unprecedented reaction occurs via an amino acid radical hopping pathway spanning two protein subunits. To study the mechanism of radical transport in RNR, a suite of biochemical approaches have been developed, such as site-directed incorporation of unnatural amino acids with altered electronic properties and photochemical generation of radical intermediates. The resulting variant RNRs have been investigated using a variety of time-resolved physical techniques, including transient absorption and stopped-flow UV-Vis spectroscopy, as well as rapid freeze-quench EPR, ENDOR, and PELDOR spectroscopic methods. The data suggest that radical transport occurs via proton-coupled electron transfer (PCET) and that the protein structure has evolved to manage the proton and electron transfer co-ordinates in order to prevent 'off-pathway' reactivity and build-up of oxidised intermediates. Thus, precise design and control over the factors that govern PCET is key to enabling reversible and long-range charge transport by amino acid radicals in RNR.
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146
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Foskolou IP, Jorgensen C, Leszczynska KB, Olcina MM, Tarhonskaya H, Haisma B, D'Angiolella V, Myers WK, Domene C, Flashman E, Hammond EM. Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication. Mol Cell 2017; 66:206-220.e9. [PMID: 28416140 PMCID: PMC5405111 DOI: 10.1016/j.molcel.2017.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 02/13/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target. RRM2B is induced in response to hypoxia in both cell models and patient datasets RRM2B retains activity in hypoxic conditions and is the favored RNR subunit in hypoxia Loss of RRM2B has detrimental consequences for cell fate, specifically in hypoxia RRM2B depletion enhanced hypoxic-specific apoptosis and increased radiosensitivity
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Affiliation(s)
- Iosifina P Foskolou
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Christian Jorgensen
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Monica M Olcina
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Hanna Tarhonskaya
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Bauke Haisma
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - William K Myers
- Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Emily Flashman
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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147
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Lin Q, Parker MJ, Taguchi AT, Ravichandran K, Kim A, Kang G, Shao J, Drennan CL, Stubbe J. Glutamate 52-β at the α/β subunit interface of Escherichia coli class Ia ribonucleotide reductase is essential for conformational gating of radical transfer. J Biol Chem 2017; 292:9229-9239. [PMID: 28377505 DOI: 10.1074/jbc.m117.783092] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/02/2017] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleoside diphosphate substrates (S) to deoxynucleotides with allosteric effectors (e) controlling their relative ratios and amounts, crucial for fidelity of DNA replication and repair. Escherichia coli class Ia RNR is composed of α and β subunits that form a transient, active α2β2 complex. The E. coli RNR is rate-limited by S/e-dependent conformational change(s) that trigger the radical initiation step through a pathway of 35 Å across the subunit (α/β) interface. The weak subunit affinity and complex nucleotide-dependent quaternary structures have precluded a molecular understanding of the kinetic gating mechanism(s) of the RNR machinery. Using a docking model of α2β2 created from X-ray structures of α and β and conserved residues from a new subclassification of the E. coli Ia RNR (Iag), we identified and investigated four residues at the α/β interface (Glu350 and Glu52 in β2 and Arg329 and Arg639 in α2) of potential interest in kinetic gating. Mutation of each residue resulted in loss of activity and with the exception of E52Q-β2, weakened subunit affinity. An RNR mutant with 2,3,5-trifluorotyrosine radical (F3Y122•) replacing the stable Tyr122• in WT-β2, a mutation that partly overcomes conformational gating, was placed in the E52Q background. Incubation of this double mutant with His6-α2/S/e resulted in an RNR capable of catalyzing pathway-radical formation (Tyr356•-β2), 0.5 eq of dCDP/F3Y122•, and formation of an α2β2 complex that is isolable in pulldown assays over 2 h. Negative stain EM images with S/e (GDP/TTP) revealed the uniformity of the α2β2 complex formed.
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Affiliation(s)
- Qinghui Lin
- From the Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China and
| | | | | | | | | | | | - Jimin Shao
- From the Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China and
| | - Catherine L Drennan
- the Departments of Chemistry and .,Biology, and.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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148
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Gong ZL, Deng LY, Zhong YW, Yao J. Anion-regulated electronic communication in a cyclometalated diruthenium complex with a urea bridge. Phys Chem Chem Phys 2017; 19:8902-8907. [PMID: 28294210 DOI: 10.1039/c6cp08019g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined study of electrochemical measurements, intervalence charge transfer analysis, and DFT calculations suggests that the degree of urea-mediated electronic coupling between two cyclometalated ruthenium sites is enhanced by the coordination of urea with Br- or Cl-via hydrogen bonding. In contrast, the redox waves of the diruthenium complex become highly irreversible in the presence of relatively strong basic anions such as H2PO4-, F-, or OAc-. This work demonstrates that the anion-urea interaction can be employed to regulate the electronic coupling and electron transfer between redox-active sites, suggesting the potential applications of the urea-functionalized diruthenium complex in anion sensing and stimuli-responsive molecular electronics.
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Affiliation(s)
- Zhong-Liang Gong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Li-Ye Deng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yu-Wu Zhong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiannian Yao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. and University of Chinese Academy of Sciences, Beijing 100049, China
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149
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Ravichandran KR, Zong AB, Taguchi AT, Nocera DG, Stubbe J, Tommos C. Formal Reduction Potentials of Difluorotyrosine and Trifluorotyrosine Protein Residues: Defining the Thermodynamics of Multistep Radical Transfer. J Am Chem Soc 2017; 139:2994-3004. [PMID: 28171730 DOI: 10.1021/jacs.6b11011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox-active tyrosines (Ys) play essential roles in enzymes involved in primary metabolism including energy transduction and deoxynucleotide production catalyzed by ribonucleotide reductases (RNRs). Thermodynamic characterization of Ys in solution and in proteins remains a challenge due to the high reduction potentials involved and the reactive nature of the radical state. The structurally characterized α3Y model protein has allowed the first determination of formal reduction potentials (E°') for a Y residing within a protein (Berry, B. W.; Martı́nez-Rivera, M. C.; Tommos, C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9739-9743). Using Schultz's technology, a series of fluorotyrosines (FnY, n = 2 or 3) was site-specifically incorporated into α3Y. The global protein properties of the resulting α3(3,5)F2Y, α3(2,3,5)F3Y, α3(2,3)F2Y and α3(2,3,6)F3Y variants are essentially identical to those of α3Y. A protein film square-wave voltammetry approach was developed to successfully obtain reversible voltammograms and E°'s of the very high-potential α3FnY proteins. E°'(pH 5.5; α3FnY(O•/OH)) spans a range of 1040 ± 3 mV to 1200 ± 3 mV versus the normal hydrogen electrode. This is comparable to the potentials of the most oxidizing redox cofactors in nature. The FnY analogues, and the ability to site-specifically incorporate them into any protein of interest, provide new tools for mechanistic studies on redox-active Ys in proteins and on functional and aberrant hole-transfer reactions in metallo-enzymes. The former application is illustrated here by using the determined α3FnY ΔE°'s to model the thermodynamics of radical-transfer reactions in FnY-RNRs and to experimentally test and support the key prediction made.
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Affiliation(s)
| | - Allan B Zong
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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150
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Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL. Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J Am Chem Soc 2017; 139:1900-1911. [PMID: 27936663 PMCID: PMC5348300 DOI: 10.1021/jacs.6b11324] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.
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Affiliation(s)
- Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - George H. Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Bennett R. Streit
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Garrett C. Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
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