1
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Damle VG, Wu K, Arouri DJ, Schirhagl R. Detecting free radicals post viral infections. Free Radic Biol Med 2022; 191:8-23. [PMID: 36002131 DOI: 10.1016/j.freeradbiomed.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022]
Abstract
Free radical generation plays a key role in viral infections. While free radicals have an antimicrobial effect on bacteria or fungi, their interplay with viruses is complicated and varies greatly for different types of viruses as well as different radical species. In some cases, radical generation contributes to the defense against the viruses and thus reduces the viral load. In other cases, radical generation induces mutations or damages the host tissue and can increase the viral load. This has led to antioxidants being used to treat viral infections. Here we discuss the roles that radicals play in virus pathology. Furthermore, we critically review methods that facilitate the detection of free radicals in vivo or in vitro in viral infections.
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Affiliation(s)
- V G Damle
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - K Wu
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - D J Arouri
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - R Schirhagl
- Department of Biomedical Engineering, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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2
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Lyu C, Li WD, Peng JM, Cai XH. Identification of interaction domains in the pseudorabies virus ribonucleotide reductase large and small subunits. Vet Microbiol 2020; 246:108740. [PMID: 32605757 DOI: 10.1016/j.vetmic.2020.108740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/16/2020] [Accepted: 05/25/2020] [Indexed: 11/17/2022]
Abstract
Alphaherpesviral ribonucleotide reductase (RNR) is composed of large (pUL39, RR1) and small (pUL40, RR2) subunits. This enzyme can catalyze conversion of ribonucleotide to deoxynucleotide diphosphates that are further phosphorylated into deoxynucleotide triphosphate (dNTPs). The dNTPs are substrates for de novo viral DNA synthesis in infected host cells. The enzymatic activity of RNR depends on association between RR1 and RR2. However, the molecular basis underlying alphaherpesviral RNR complex formation is still largely unknown. In the current study, we investigated the pseudorabies virus (PRV) RNR interaction domains in pUL39 and pUL40. The interaction of pUL39 and pUL40 was identified by co-immunoprecipitation (co-IP) and colocalization analyses. Furthermore, the interaction amino acid (aa) domains in pUL39 and pUL40 were mapped using a series of truncated proteins. Consequently, the 90-210 aa in pUL39 was identified to be responsible for the interaction with pUL40. In turn, the 66-152, 218-258 and 280-303 aa in pUL40 could interact with pUL39, respectively. Deletion of 90-210 aa in pUL39 completely abrogated the interaction with pUL40. Deletion of 66-152, 218-258 and 280-303 aa in pUL40 remarkably weakened the interaction with pUL39, whereas a weak interaction could still be observed. Amino acid sequence alignments showed that the interaction domains identified in PRV pUL39/pUL40 were relatively non-conserved among the selected RNR subunits in alphaherpesviruses HSV1, HSV2, HHV3(VZV), BHV1, EHV1 and DEV. However, they were relatively conserved among PRV, HSV1 and HSV2. Collectively, our findings provided some molecular targets for inhibition of pUL39-pUL40 interaction to antagonize viral replication in PRV infected hosts.
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Affiliation(s)
- Chuang Lyu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Haping Road No.678, Harbin 150069, China
| | - Wei-Dong Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Haping Road No.678, Harbin 150069, China
| | - Jin-Mei Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Haping Road No.678, Harbin 150069, China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Haping Road No.678, Harbin 150069, China.
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3
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Proniewicz E, Tąta A, Wójcik A, Starowicz M, Pacek J, Molenda M. SERS activity and spectroscopic properties of Zn and ZnO nanostructures obtained by electrochemical and green chemistry methods for applications in biology and medicine. Phys Chem Chem Phys 2020; 22:28100-28114. [DOI: 10.1039/d0cp03517c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work evaluates the ability of homogeneous, stable, and pure zinc oxide nanoparticles (ZnONPs-GS) synthesized by “green chemistry” for the selective detection of four neurotransmitters present in body fluids and promotion of the SERS effect.
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Affiliation(s)
- Edyta Proniewicz
- Faculty of Foundry Engineering
- AGH University of Science and Technology
- 30-059 Krakow
- Poland
| | - Agnieszka Tąta
- Faculty of Foundry Engineering
- AGH University of Science and Technology
- 30-059 Krakow
- Poland
| | - Anna Wójcik
- Institute of Metallurgy and Materials Science of Polish Academy of Science
- 30-059 Krakow
- Poland
| | - Maria Starowicz
- Faculty of Foundry Engineering
- AGH University of Science and Technology
- 30-059 Krakow
- Poland
| | - Joanna Pacek
- Faculty of Chemistry
- Jagiellonian University
- 30-387 Krakow
- Poland
| | - Marcin Molenda
- Faculty of Chemistry
- Jagiellonian University
- 30-387 Krakow
- Poland
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4
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Singh RK, Blossom BM, Russo DA, Singh R, Weihe H, Andersen NH, Tiwari MK, Jensen PE, Felby C, Bjerrum MJ. Detection and Characterization of a Novel Copper-Dependent Intermediate in a Lytic Polysaccharide Monooxygenase. Chemistry 2019; 26:454-463. [PMID: 31603264 DOI: 10.1002/chem.201903562] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/08/2019] [Indexed: 01/27/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes capable of oxidizing crystalline cellulose which have large practical application in the process of refining biomass. The catalytic mechanism of LPMOs still remains debated despite several proposed reaction mechanisms. Here, we report a long-lived intermediate (t1/2 =6-8 minutes) observed in an LPMO from Thermoascus aurantiacus (TaLPMO9A). The intermediate with a strong absorption around 420 nm is formed when reduced LPMO-CuI reacts with sub-equimolar amounts of H2 O2 . UV/Vis absorption spectroscopy, electron paramagnetic resonance, resonance Raman and stopped-flow spectroscopy suggest that the observed long-lived intermediate involves the copper center and a nearby tyrosine (Tyr175). Additionally, activity assays in the presence of sub-equimolar amounts of H2 O2 showed an increase in the LPMO oxidation of phosphoric acid swollen cellulose. Accordingly, this suggests that the long-lived copper-dependent intermediate could be part of the catalytic mechanism for LPMOs. The observed intermediate offers a new perspective into the oxidative reaction mechanism of TaLPMO9A and hence for the biomass oxidation and the reactivity of copper in biological systems.
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Affiliation(s)
- Raushan K Singh
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Benedikt M Blossom
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - David A Russo
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
- Current address: Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ranjitha Singh
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Høgni Weihe
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Poul E Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - Claus Felby
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen, Denmark
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5
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Vázquez G, Caballero AB, Kokinda J, Hijano A, Sabaté R, Gamez P. Copper, dityrosine cross-links and amyloid-β aggregation. J Biol Inorg Chem 2019; 24:1217-1229. [PMID: 31667594 DOI: 10.1007/s00775-019-01734-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/08/2019] [Indexed: 12/31/2022]
Abstract
Copper is involved in Alzheimer's disease (AD) where it appears to affect the aggregation of amyloid-β (Aβ) and to catalyze the production of reactive oxygen species (ROS). Oxidative stress apparently produces Aβ dimers that are covalently linked through two tyrosine residues. Such dityrosine cross-links are considered as potential markers of the disease and seem to be implicated in the pathological disorder. In the present study, pure o,o'-dityrosine (diY) was prepared enzymatically (with horseradish peroxidase; HRP), which was subsequently used to construct calibration lines aimed at quantifying nanomolar amounts of diY in reaction mixtures by fluorescence spectroscopy. Hence, diY concentrations down to 67 nM could be determined, which allowed to find that ca. 3% of dityrosine-bridged dimers of Aβ(1-40) were produced after 3 days at 37 °C in the presence of copper and dihydrogen peroxide. These cross-linked dimers in the presence of copper(II) ions completely inhibit the typical aggregation of Aβ, since β sheets could not be detected applying the usual Thioflavin T (ThT) method. Furthermore, the use of a potent Cu(II) chelator, such as the ATCUN tripeptide, L-histidyl-L-alanyl-L-histidine (HAH), efficiently prevented the copper-mediated generation of ROS and the associated dityrosine-bridged Aβ dimers, suggesting that such metal chelators may find future applications in the field of anti-AD drug design.
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Affiliation(s)
- Guillem Vázquez
- Inorganic Chemistry Section, Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Ana B Caballero
- Inorganic Chemistry Section, Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain. .,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain.
| | - Jakub Kokinda
- Inorganic Chemistry Section, Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Ana Hijano
- Inorganic Chemistry Section, Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Raimon Sabaté
- Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain. .,Departament de Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Avda. Joan XXIII 27-31, 08028, Barcelona, Spain.
| | - Patrick Gamez
- Inorganic Chemistry Section, Department of Inorganic and Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain. .,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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6
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Pagba CV, McCaslin TG, Veglia G, Porcelli F, Yohannan J, Guo Z, McDaniel M, Barry BA. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun 2015; 6:10010. [PMID: 26627888 PMCID: PMC4686667 DOI: 10.1038/ncomms10010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/23/2015] [Indexed: 01/29/2023] Open
Abstract
In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer. Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fernando Porcelli
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo 01100, Italy
| | - Jiby Yohannan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zhanjun Guo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miranda McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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7
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Meng Z, Yang X, Hu D, Wang K, Zhi F, Chen X, Gong G, Wu J, Hu Y. Replacing heme with paclitaxel to prepare drug-loaded globin nanoassembles for CD163 targeting. J Pharm Sci 2015; 104:1045-55. [PMID: 25640195 DOI: 10.1002/jps.24290] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 01/22/2023]
Abstract
Protein-based nanoparticles hold great promises in both preclinical and clinical practices, such as oncology diagnosis and treatment, because of their high biocompatibility and biodegradability. However, the complicated preparation and lack of targeting specific cells or tissues may limit their further uses. To overcome these limitations, we developed a novel replacing method for preparing dual-functional protein nanocarrier, such that one function is capable of encapsulating small molecule into protein, whereas the other function is cable of recognizing CD163 receptor [hemoglobin (Hb) scavenger receptor]. In this study, Hb was chosen as the targeting drug carrier. First, the heme group in the Hb was removed and replaced by paclitaxel (PTX) to form nanoparticles (Gb-NPs-PTX). The resulted Gb-NPs-PTX showed spherical shape and their diameter could be controlled in the range of 120-160 nm by altering the ratio of PTX to Hb. The binding activity of Gb-NPs-PTX to CD163 was confirmed by cell uptake in CD163(+) Chinese hamster ovary cells. Results in vivo also showed a CD163-dependent tissue accumulation of Gb-NPs-PTX in mice. In summary, by using the novel replacing method, PTX could be easily encapsulated into Hb nanoparticles and the targeting effects of Hb could also be kept.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Differentiation, Myelomonocytic/genetics
- Antigens, Differentiation, Myelomonocytic/metabolism
- Antineoplastic Agents, Phytogenic/administration & dosage
- Antineoplastic Agents, Phytogenic/chemistry
- Antineoplastic Agents, Phytogenic/pharmacokinetics
- Biological Transport
- CHO Cells
- Chemistry, Pharmaceutical
- Cricetulus
- Drug Carriers
- Globins/chemistry
- Globins/metabolism
- Heme/chemistry
- Heme/metabolism
- Mice, Inbred BALB C
- Nanoparticles
- Nanotechnology
- Paclitaxel/administration & dosage
- Paclitaxel/chemistry
- Paclitaxel/pharmacokinetics
- Particle Size
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Technology, Pharmaceutical/methods
- Tissue Distribution
- Transfection
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Affiliation(s)
- Zhengjie Meng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
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8
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The class Ib ribonucleotide reductase from Mycobacterium tuberculosis has two active R2F subunits. J Biol Inorg Chem 2014; 19:893-902. [PMID: 24585102 DOI: 10.1007/s00775-014-1121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to their corresponding deoxyribonucleotides, playing a crucial role in DNA repair and replication in all living organisms. Class Ib RNRs require either a diiron-tyrosyl radical (Y·) or a dimanganese-Y· cofactor in their R2F subunit to initiate ribonucleotide reduction in the R1 subunit. Mycobacterium tuberculosis, the causative agent of tuberculosis, contains two genes, nrdF1 and nrdF2, encoding the small subunits R2F-1 and R2F-2, respectively, where the latter has been thought to serve as the only active small subunit in the M. tuberculosis class Ib RNR. Here, we present evidence for the presence of an active Fe 2 (III) -Y· cofactor in the M. tuberculosis RNR R2F-1 small subunit, supported and characterized by UV-vis, X-band electron paramagnetic resonance, and resonance Raman spectroscopy, showing features similar to those for the M. tuberculosis R2F-2-Fe 2 (III) -Y· cofactor. We also report enzymatic activity of Fe 2 (III) -R2F-1 when assayed with R1, and suggest that the active M. tuberculosis class Ib RNR can use two different small subunits, R2F-1 and R2F-2, with similar activity.
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9
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Hammerstad M, Hersleth HP, Tomter AB, Røhr ÅK, Andersson KK. Crystal structure of Bacillus cereus class Ib ribonucleotide reductase di-iron NrdF in complex with NrdI. ACS Chem Biol 2014; 9:526-37. [PMID: 24295378 DOI: 10.1021/cb400757h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y•) cofactor in their NrdF (β2) subunit to initiate ribonucleotide reduction in the NrdE (α2) subunit. Contrary to the diferric tyrosyl radical (Fe(III)2-Y•) cofactor, which can self-assemble from Fe(II)2-NrdF and O2, generation of the Mn(III)2-Y• cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 Å resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-Mn(II)2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus Mn(II)2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the dimetal site and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF dimetal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y• cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested α2β2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Ane B. Tomter
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Åsmund K. Røhr
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - K. Kristoffer Andersson
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
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10
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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11
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Penzkofer A, Tanwar M, Veetil S, Kateriya S, Stierl M, Hegemann P. Photo-dynamics of the lyophilized photo-activated adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Offenbacher AR, Burns LA, Sherrill CD, Barry BA. Redox-linked conformational control of proton-coupled electron transfer: Y122 in the ribonucleotide reductase β2 subunit. J Phys Chem B 2013; 117:8457-68. [PMID: 23822111 DOI: 10.1021/jp404757r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.
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Affiliation(s)
- Adam R Offenbacher
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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13
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Penzkofer A, Tanwar M, Veetil S, Kateriya S, Stierl M, Hegemann P. Photo-dynamics and thermal behavior of the BLUF domain containing adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bikas R, Hosseini-Monfared H, Zoppellaro G, Herchel R, Tucek J, Owczarzak AM, Kubicki M, Zboril R. Synthesis, structure, magnetic properties and theoretical calculations of methoxy bridged dinuclear iron(iii) complex with hydrazone based O,N,N-donor ligand. Dalton Trans 2013; 42:2803-12. [DOI: 10.1039/c2dt31751f] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Tomter AB, Zoppellaro G, Andersen NH, Hersleth HP, Hammerstad M, Røhr ÅK, Sandvik GK, Strand KR, Nilsson GE, Bell CB, Barra AL, Blasco E, Le Pape L, Solomon EI, Andersson KK. Ribonucleotide reductase class I with different radical generating clusters. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sandvik GK, Tomter AB, Bergan J, Zoppellaro G, Barra AL, Røhr AK, Kolberg M, Ellefsen S, Andersson KK, Nilsson GE. Studies of ribonucleotide reductase in crucian carp-an oxygen dependent enzyme in an anoxia tolerant vertebrate. PLoS One 2012; 7:e42784. [PMID: 22916159 PMCID: PMC3419237 DOI: 10.1371/journal.pone.0042784] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/11/2012] [Indexed: 11/19/2022] Open
Abstract
The enzyme ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides, the precursors for DNA. RNR requires a thiyl radical to activate the substrate. In RNR of eukaryotes (class Ia RNR), this radical originates from a tyrosyl radical formed in reaction with oxygen (O(2)) and a ferrous di-iron center in RNR. The crucian carp (Carassius carassius) is one of very few vertebrates that can tolerate several months completely without oxygen (anoxia), a trait that enables this fish to survive under the ice in small ponds that become anoxic during the winter. Previous studies have found indications of cell division in this fish after 7 days of anoxia. This appears nearly impossible, as DNA synthesis requires the production of new deoxyribonucleotides and therefore active RNR. We have here characterized RNR in crucian carp, to search for adaptations to anoxia. We report the full-length sequences of two paralogs of each of the RNR subunits (R1i, R1ii, R2i, R2ii, p53R2i and p53R2ii), obtained by cloning and sequencing. The mRNA levels of these subunits were measured with quantitative PCR and were generally well maintained in hypoxia and anoxia in heart and brain. We also report maintained or increased mRNA levels of the cell division markers proliferating cell nuclear antigen (PCNA), brain derived neurotrophic factor (BDNF) and Ki67 in anoxic hearts and brains. Electron paramagnetic resonance (EPR) measurements on in vitro expressed crucian carp R2 and p53R2 proteins gave spectra similar to mammalian RNRs, including previously unpublished human and mouse p53R2 EPR spectra. However, the radicals in crucian carp RNR small subunits, especially in the p53R2ii subunit, were very stable at 0°C. A long half-life of the tyrosyl radical during wintertime anoxia could allow for continued cell division in crucian carp.
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Affiliation(s)
- Guro K Sandvik
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway.
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Spectroscopic studies of the iron and manganese reconstituted tyrosyl radical in Bacillus cereus ribonucleotide reductase R2 protein. PLoS One 2012; 7:e33436. [PMID: 22432022 PMCID: PMC3303829 DOI: 10.1371/journal.pone.0033436] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/08/2012] [Indexed: 11/24/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g1-value of 2.0090 for the tyrosyl radical was extracted. This g1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity.
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