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Beyer L, Schäfer AB, Undabarrena A, Mattsby-Baltzer I, Tietze D, Svensson E, Stubelius A, Wenzel M, Cámara B, Tietze AA. Mimicking Nonribosomal Peptides from the Marine Actinomycete Streptomyces sp. H-KF8 Leads to Antimicrobial Peptides. ACS Infect Dis 2024; 10:79-92. [PMID: 38113038 PMCID: PMC10788856 DOI: 10.1021/acsinfecdis.3c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Microorganisms within the marine environment have been shown to be very effective sources of naturally produced antimicrobial peptides (AMPs). Several nonribosomal peptides were identified based on genome mining predictions of Streptomyces sp. H-KF8, a marine Actinomycetota isolated from a remote Northern Chilean Patagonian fjord. Based on these predictions, a series of eight peptides, including cyclic peptides, were designed and chemically synthesized. Six of these peptides showed antimicrobial activity. Mode of action studies suggest that two of these peptides potentially act on the cell membrane via a novel mechanism allowing the passage of small ions, resulting in the dissipation of the membrane potential. This study shows that though structurally similar peptides, determined by NMR spectroscopy, the incorporation of small sequence mutations results in a dramatic influence on their bioactivity including mode of action. The qualified hit sequence can serve as a basis for more potent AMPs in future studies.
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Affiliation(s)
- Luisa
I. Beyer
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Medicinaregatan
7B, Gothenburg 413 90, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Ann-Britt Schäfer
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Agustina Undabarrena
- Departamento
de Química & Centro de Biotecnología Daniel Alkalay
Lowitt, Laboratorio de Microbiología Molecular y Biotecnología
Ambiental, Universidad Técnica Federico
Santa María, Valparaíso 2340000, Chile
| | - Inger Mattsby-Baltzer
- Department
of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska
Academy at University of Gothenburg, University
of Gothenburg, Box 440, Göteborg 405 30, Sweden
| | - Daniel Tietze
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Medicinaregatan
7B, Gothenburg 413 90, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Elin Svensson
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
| | - Alexandra Stubelius
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
| | - Michaela Wenzel
- Department
of Life Sciences, Chalmers University of
Technology, Kemigården 4, Göteborg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
| | - Beatriz Cámara
- Departamento
de Química & Centro de Biotecnología Daniel Alkalay
Lowitt, Laboratorio de Microbiología Molecular y Biotecnología
Ambiental, Universidad Técnica Federico
Santa María, Valparaíso 2340000, Chile
| | - Alesia A. Tietze
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Medicinaregatan
7B, Gothenburg 413 90, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg, University of Gothenburg, Box 100, Göteborg 405 30, Sweden
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2
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Su L, Wang X, Wang J, Luh F, Yen Y. Impact of N221S missense mutation in human ribonucleotide reductase small subunit b on mitochondrial DNA depletion syndrome. Sci Rep 2023; 13:19899. [PMID: 37964013 PMCID: PMC10645729 DOI: 10.1038/s41598-023-47284-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/11/2023] [Indexed: 11/16/2023] Open
Abstract
The impact of N221S mutation in hRRM2B gene, which encodes the small subunit of human ribonucleotide reductase (RNR), on RNR activity and the pathogenesis of mitochondrial DNA depletion syndrome (MDDS) was investigated. Our results demonstrate that N221 mutations significantly reduce RNR activity, suggesting its role in the development of MDDS. We proposed an allosteric regulation pathway involving a chain of three phenylalanine residues on the αE helix of RNR small subunit β. This pathway connects the C-terminal loop of β2, transfers the activation signal from the large catalytic subunit α to β active site, and controls access of oxygen for radical generation. N221 is near this pathway and likely plays a role in regulating RNR activity. Mutagenesis studies on residues involved in the phenylalanine chain and the regulation pathway were conducted to confirm our proposed mechanism. We also performed molecular dynamic simulation and protein contact network analysis to support our findings. This study sheds new light on RNR small subunit regulation and provides insight on the pathogenesis of MDDS.
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Affiliation(s)
- Leila Su
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Xin Wang
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Jianghai Wang
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Frank Luh
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Yun Yen
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 110301, Taiwan.
- Center for Cancer Translational Research, Tzu Chi University, Hualien, 970374, Taiwan.
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3
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Griswold-Prenner I, Kashyap AK, Mazhar S, Hall ZW, Fazelinia H, Ischiropoulos H. Unveiling the human nitroproteome: Protein tyrosine nitration in cell signaling and cancer. J Biol Chem 2023; 299:105038. [PMID: 37442231 PMCID: PMC10413360 DOI: 10.1016/j.jbc.2023.105038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Covalent amino acid modification significantly expands protein functional capability in regulating biological processes. Tyrosine residues can undergo phosphorylation, sulfation, adenylation, halogenation, and nitration. These posttranslational modifications (PTMs) result from the actions of specific enzymes: tyrosine kinases, tyrosyl-protein sulfotransferase(s), adenylate transferase(s), oxidoreductases, peroxidases, and metal-heme containing proteins. Whereas phosphorylation, sulfation, and adenylation modify the hydroxyl group of tyrosine, tyrosine halogenation and nitration target the adjacent carbon residues. Because aberrant tyrosine nitration has been associated with human disorders and with animal models of disease, we have created an updated and curated database of 908 human nitrated proteins. We have also analyzed this new resource to provide insight into the role of tyrosine nitration in cancer biology, an area that has not previously been considered in detail. Unexpectedly, we have found that 879 of the 1971 known sites of tyrosine nitration are also sites of phosphorylation suggesting an extensive role for nitration in cell signaling. Overall, the review offers several forward-looking opportunities for future research and new perspectives for understanding the role of tyrosine nitration in cancer biology.
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Affiliation(s)
| | | | | | - Zach W Hall
- Nitrase Therapeutics, Brisbane, California, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Cui C, Song DY, Drennan CL, Stubbe J, Nocera DG. Radical Transport Facilitated by a Proton Transfer Network at the Subunit Interface of Ribonucleotide Reductase. J Am Chem Soc 2023; 145:5145-5154. [PMID: 36812162 PMCID: PMC10561588 DOI: 10.1021/jacs.2c11483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Ribonucleotide reductases (RNRs) play an essential role in the conversion of nucleotides to deoxynucleotides in all organisms. The Escherichia coli class Ia RNR requires two homodimeric subunits, α and β. The active form is an asymmetric αα'ββ' complex. The α subunit houses the site for nucleotide reduction initiated by a thiyl radical (C439•), and the β subunit houses the diferric-tyrosyl radical (Y122•) that is essential for C439• formation. The reactions require a highly regulated and reversible long-range proton-coupled electron transfer pathway involving Y122•[β] ↔ W48?[β] ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]. In a recent cryo-EM structure, Y356[β] was revealed for the first time and it, along with Y731[α], spans the asymmetric α/β interface. An E52[β] residue, which is essential for Y356 oxidation, allows access to the interface and resides at the head of a polar region comprising R331[α], E326[α], and E326[α'] residues. Mutagenesis studies with canonical and unnatural amino acid substitutions now suggest that these ionizable residues are important in enzyme activity. To gain further insights into the roles of these residues, Y356• was photochemically generated using a photosensitizer covalently attached adjacent to Y356[β]. Mutagenesis studies, transient absorption spectroscopy, and photochemical assays monitoring deoxynucleotide formation collectively indicate that the E52[β], R331[α], E326[α], and E326[α'] network plays the essential role of shuttling protons associated with Y356 oxidation from the interface to bulk solvent.
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Affiliation(s)
- Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - David Y. Song
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Catherine L. Drennan
- Department of Chemistr, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - JoAnne Stubbe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Chemistr, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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5
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Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci 2023; 32:e4574. [PMID: 36691781 PMCID: PMC9926477 DOI: 10.1002/pro.4574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
14-3-3 proteins are central hub regulators of hundreds of phosphorylated "client" proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well-documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide-binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
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Affiliation(s)
- Phillip Zhu
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Kyle T. Nguyen
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Aidan B. Estelle
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of SciencesA.N. Bach Institute of BiochemistryMoscowRussia
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
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6
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Polyimide adhesive tapes as a versatile and disposable substrate to produce CO2 laser-induced carbon sensors for batch and microfluidic analysis. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Elgaabari A, Imatomi N, Kido H, Seki M, Tanaka S, Matsuyoshi Y, Nakashima T, Sawano S, Mizunoya W, Suzuki T, Nakamura M, Anderson JE, Tatsumi R. A pilot study on nitration/dysfunction of NK1 segment of myogenic stem cell activator HGF. Biochem Biophys Rep 2022; 31:101295. [PMID: 35721345 PMCID: PMC9198319 DOI: 10.1016/j.bbrep.2022.101295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Protein tyrosine residue (Y) nitration, a post-translational chemical-modification mode, has been associated with changes in protein activity and function; hence the accumulation of specific nitrated proteins in tissues may be used to monitor the onset and progression of pathological disorders. To verify the possible impact of nitration on postnatal muscle growth and regeneration, a pilot study was designed to examine the nitration/dysfunction of hepatocyte growth factor (HGF), a key ligand that is released from the extracellular tethering and activates myogenic stem satellite cells to enter the cell cycle upon muscle stretch and injury. Exposure of recombinant HGF (a hetero-dimer of α- and β-chains) to peroxynitrite induces Y nitration in HGF α-chain under physiological conditions. Physiological significance of this finding was emphasized by Western blotting that showed the NK1 segment of HGF (including a K1 domain critical for signaling-receptor c-met binding) undergoes nitration with a primary target of Y198. Peroxynitrite treatment abolished HGF-agonistic activity of the NK1 segment, as revealed by in vitro c-met binding and bromodeoxyuridine-incorporation assays. Importantly, direct-immunofluorescence microscopy of rat lower hind-limb muscles from two aged-groups (2-month-old “young” and 12-month-old “retired/adult”) provided in vivo evidence for age-related nitration of extracellular HGF (Y198). Overall, findings provide the insight that HGF/NK1 nitration/dysfunction perturbs myogenic stem cell dynamics and homeostasis; hence NK1 nitration may stimulate progression of muscular disorders and diseases including sarcopenia. NK1 segment of hepatocyte growth factor (HGF) undergoes tyrosine (Y) nitration. Y198 was identified as a primary target for nitration of NK1. NK1 nitration may abolish HGF-agonistic activity that activates myogenic stem cells. Nitration of extracellular HGF-Y198 was detected in vivo at early aging-phase of rat. Findings may provide a possible strategy to combat progressive muscle-atrophy.
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Affiliation(s)
- Alaa Elgaabari
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Department of Physiology, Faculty of Veterinary Medicine, Kafrelsheikh University, El-Geish Street, Kafrelsheikh 33516, Egypt
| | - Nana Imatomi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Hirochika Kido
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Miyumi Seki
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Sakiho Tanaka
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Matsuyoshi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Takashi Nakashima
- Department of Bioscience and Biotechnology, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Shoko Sawano
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Wataru Mizunoya
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Takahiro Suzuki
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Mako Nakamura
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Judy E. Anderson
- Department of Biological Sciences, Faculty of Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ryuichi Tatsumi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Corresponding author. Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture (West#5 bldg.), Kyushu University, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan.
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8
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Stieglitz JT, Lahiri P, Stout MI, Van Deventer JA. Exploration of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Activity in Yeast. ACS Synth Biol 2022; 11:1824-1834. [PMID: 35417129 PMCID: PMC10112046 DOI: 10.1021/acssynbio.2c00001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Archaeal pyrrolysyl-tRNA synthetases (PylRSs) have been used to genetically encode over 200 distinct noncanonical amino acids (ncAAs) in proteins in Escherichia coli and mammalian cells. This vastly expands the range of chemical functionality accessible within proteins produced in these organisms. Despite these clear successes, explorations of PylRS function in yeast remain limited. In this work, we demonstrate that the Methanomethylophilus alvus PylRS (MaPylRS) and its cognate tRNACUAMaPyl support the incorporation of ncAAs into proteins produced in Saccharomyces cerevisiae using stop codon suppression methodologies. Additionally, we prepared three MaPylRS mutants originally engineered in E. coli and determined that all three were active with one or more ncAAs, although with low efficiencies of ncAA incorporation in comparison to the parent MaPylRS. Alongside MaPylRS variants, we evaluated the activity of previously reported Methanosarcina mazei, Methanosarcina barkeri, and chimeric M. mazei and M. barkeri PylRSs. Using S. cerevisiae RJY100 and pairing these PylRSs with the M. mazei tRNACUA, we did not observe any detectable stop codon suppression activity under the same conditions that produced moderately efficient ncAA incorporation with MaPylRS. The addition of MaPylRS/tRNACUAMaPyl to the orthogonal translation machinery toolkit in S. cerevisiae potentially opens the door to hundreds of ncAAs that have not previously been genetically encodable using other aminoacyl-tRNA synthetase/tRNA pairs. Extending the scope of ncAA incorporation in yeast could powerfully advance chemical and biological research for applications ranging from basic biological discovery to enzyme engineering and therapeutic protein lead discovery.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Priyanka Lahiri
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Matthew I. Stout
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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9
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Schmidt S, Vogt Weisenhorn DM, Wurst W. Chapter 5 – “Parkinson's disease – A role of non-enzymatic posttranslational modifications in disease onset and progression?”. Mol Aspects Med 2022; 86:101096. [DOI: 10.1016/j.mam.2022.101096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 12/14/2022]
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10
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Meichsner SL, Kutin Y, Kasanmascheff M. In‐Cell Characterization of the Stable Tyrosyl Radical in
E. coli
Ribonucleotide Reductase Using Advanced EPR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shari L. Meichsner
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
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11
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Long T, Liu L, Tao Y, Zhang W, Quan J, Zheng J, Hegemann JD, Uesugi M, Yao W, Tian H, Wang H. Light‐Controlled Tyrosine Nitration of Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tengfang Long
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Lei Liu
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Youqi Tao
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Wanli Zhang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Jiale Quan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Jie Zheng
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Julian D. Hegemann
- Institute of Chemistry Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Uji Kyoto 611-0011 Japan
- School of Pharmacy Fudan University Shanghai 201203 China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center of Nanjing University Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University No. 163 Xianlin Ave Nanjing 210093 China
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12
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Meichsner SL, Kutin Y, Kasanmascheff M. In-Cell Characterization of the Stable Tyrosyl Radical in E. coli Ribonucleotide Reductase Using Advanced EPR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:19155-19161. [PMID: 33844392 PMCID: PMC8453577 DOI: 10.1002/anie.202102914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/11/2021] [Indexed: 12/21/2022]
Abstract
The E. coli ribonucleotide reductase (RNR), a paradigm for class Ia enzymes including human RNR, catalyzes the biosynthesis of DNA building blocks and requires a di‐iron tyrosyl radical (Y122.) cofactor for activity. The knowledge on the in vitro Y122. structure and its radical distribution within the β2 subunit has accumulated over the years; yet little information exists on the in vivo Y122.. Here, we characterize this essential radical in whole cells. Multi‐frequency EPR and electron‐nuclear double resonance (ENDOR) demonstrate that the structure and electrostatic environment of Y122. are identical under in vivo and in vitro conditions. Pulsed dipolar EPR experiments shed light on a distinct in vivo Y122. per β2 distribution, supporting the key role of Y. concentrations in regulating RNR activity. Additionally, we spectroscopically verify the generation of an unnatural amino acid radical, F3Y122., in whole cells, providing a crucial step towards unique insights into the RNR catalysis under physiological conditions.
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Affiliation(s)
- Shari L Meichsner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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13
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Hecker F, Stubbe J, Bennati M. Detection of Water Molecules on the Radical Transfer Pathway of Ribonucleotide Reductase by 17O Electron-Nuclear Double Resonance Spectroscopy. J Am Chem Soc 2021; 143:7237-7241. [PMID: 33957040 PMCID: PMC8154519 DOI: 10.1021/jacs.1c01359] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 12/19/2022]
Abstract
The role of water in biological proton-coupled electron transfer (PCET) is emerging as a key for understanding mechanistic details at atomic resolution. Here we demonstrate 17O high-frequency electron-nuclear double resonance (ENDOR) in conjunction with H217O-labeled protein buffer to establish the presence of ordered water molecules at three radical intermediates in an active enzyme complex, the α2β2 E. coli ribonucleotide reductase. Our data give unambiguous evidence that all three, individually trapped, intermediates are hyperfine coupled to one water molecule with Tyr-O···17O distances in the range 2.8-3.1 Å. The availability of this structural information will allow for quantitative models of PCET in this prototype enzyme. The results also provide a spectroscopic signature for water H-bonded to a tyrosyl radical.
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Affiliation(s)
- Fabian Hecker
- Max
Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - JoAnne Stubbe
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 20139, United States
| | - Marina Bennati
- Max
Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department
of Chemistry, Georg-August-University, 37077 Göttingen, Germany
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14
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Long T, Liu L, Tao Y, Zhang W, Quan J, Zheng J, Hegemann JD, Uesugi M, Yao W, Tian H, Wang H. Light-Controlled Tyrosine Nitration of Proteins. Angew Chem Int Ed Engl 2021; 60:13414-13422. [PMID: 33847040 DOI: 10.1002/anie.202102287] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/31/2021] [Indexed: 12/30/2022]
Abstract
Tyrosine nitration of proteins is one of the most important oxidative post-translational modifications in vivo. A major obstacle for its biochemical and physiological studies is the lack of efficient and chemoselective protein tyrosine nitration reagents. Herein, we report a generalizable strategy for light-controlled protein tyrosine nitration by employing biocompatible dinitroimidazole reagents. Upon 390 nm irradiation, dinitroimidazoles efficiently convert tyrosine residues into 3-nitrotyrosine residues in peptides and proteins with fast kinetics and high chemoselectivity under neutral aqueous buffer conditions. The incorporation of 3-nitrotyrosine residues enhances the thermostability of lasso peptide natural products and endows murine tumor necrosis factor-α with strong immunogenicity to break self-tolerance. The light-controlled time resolution of this method allows the investigation of the impact of tyrosine nitration on the self-assembly behavior of α-synuclein.
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Affiliation(s)
- Tengfang Long
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Lei Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Youqi Tao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Wanli Zhang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiale Quan
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jie Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto, 611-0011, Japan.,School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, No. 163 Xianlin Ave, Nanjing, 210093, China
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15
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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16
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Computing Proton-Coupled Redox Potentials of Fluorotyrosines in a Protein Environment. J Phys Chem B 2020; 125:128-136. [PMID: 33378205 DOI: 10.1021/acs.jpcb.0c09974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation of tyrosine to form the neutral tyrosine radical via proton-coupled electron transfer is essential for a wide range of biological processes. The precise measurement of the proton-coupled redox potentials of tyrosine (Y) in complex protein environments is challenging mainly because of the highly oxidizing and reactive nature of the radical state. Herein, a computational strategy is presented for predicting proton-coupled redox potentials in a protein environment. In this strategy, both the reduced Y-OH and oxidized Y-O• forms of tyrosine are sampled with molecular dynamics using a molecular mechanical force field. For a large number of conformations, a quantum mechanical/molecular mechanical (QM/MM) electrostatic embedding scheme is used to compute the free-energy differences between the reduced and oxidized forms, including the zero-point energy and entropic contributions as well as the impact of the protein electrostatic environment. This strategy is applied to a series of fluorinated tyrosine derivatives embedded in a de novo α-helical protein denoted as α3Y. The force fields for both the reduced and oxidized forms of these noncanonical fluorinated tyrosine residues are parameterized for general use. The calculated relative proton-coupled redox potentials agree with experimentally measured values with a mean unsigned error of 24 mV. Analysis of the simulations illustrates that hydrogen-bonding interactions between tyrosine and water increase the redox potentials by ∼100-250 mV, with significant variations because of the fluctuating protein environment. This QM/MM approach enables the calculation of proton-coupled redox potentials of tyrosine and other residues such as tryptophan in a variety of protein systems.
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17
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3-Nitrotyrosine and related derivatives in proteins: precursors, radical intermediates and impact in function. Essays Biochem 2020; 64:111-133. [PMID: 32016371 DOI: 10.1042/ebc20190052] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/30/2019] [Accepted: 01/03/2020] [Indexed: 12/22/2022]
Abstract
Oxidative post-translational modification of proteins by molecular oxygen (O2)- and nitric oxide (•NO)-derived reactive species is a usual process that occurs in mammalian tissues under both physiological and pathological conditions and can exert either regulatory or cytotoxic effects. Although the side chain of several amino acids is prone to experience oxidative modifications, tyrosine residues are one of the preferred targets of one-electron oxidants, given the ability of their phenolic side chain to undergo reversible one-electron oxidation to the relatively stable tyrosyl radical. Naturally occurring as reversible catalytic intermediates at the active site of a variety of enzymes, tyrosyl radicals can also lead to the formation of several stable oxidative products through radical-radical reactions, as is the case of 3-nitrotyrosine (NO2Tyr). The formation of NO2Tyr mainly occurs through the fast reaction between the tyrosyl radical and nitrogen dioxide (•NO2). One of the key endogenous nitrating agents is peroxynitrite (ONOO-), the product of the reaction of superoxide radical (O2•-) with •NO, but ONOO--independent mechanisms of nitration have been also disclosed. This chemical modification notably affects the physicochemical properties of tyrosine residues and because of this, it can have a remarkable impact on protein structure and function, both in vitro and in vivo. Although low amounts of NO2Tyr are detected under basal conditions, significantly increased levels are found at pathological states related with an overproduction of reactive species, such as cardiovascular and neurodegenerative diseases, inflammation and aging. While NO2Tyr is a well-established stable oxidative stress biomarker and a good predictor of disease progression, its role as a pathogenic mediator has been laboriously defined for just a small number of nitrated proteins and awaits further studies.
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18
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Tinzl M, Hilvert D. Trapping Transient Protein Species by Genetic Code Expansion. Chembiochem 2020; 22:92-99. [PMID: 32810341 DOI: 10.1002/cbic.202000523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Nature employs a limited number of genetically encoded amino acids for the construction of functional proteins. By engineering components of the cellular translation machinery, however, it is now possible to genetically encode noncanonical building blocks with tailored electronic and structural properties. The ability to incorporate unique chemical functionality into proteins provides a powerful tool to probe mechanism and create novel function. In this minireview, we highlight several recent studies that illustrate how noncanonical amino acids have been used to capture and characterize reactive intermediates, fine-tune the catalytic properties of enzymes, and stabilize short-lived protein-protein complexes.
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Affiliation(s)
- Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
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19
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Reinhardt CR, Li P, Kang G, Stubbe J, Drennan CL, Hammes-Schiffer S. Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase. J Am Chem Soc 2020; 142:13768-13778. [PMID: 32631052 DOI: 10.1021/jacs.0c04325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven Connecticut 06520, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States
| | - Gyunghoon Kang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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20
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Ravichandran K, Olshansky L, Nocera DG, Stubbe J. Subunit Interaction Dynamics of Class Ia Ribonucleotide Reductases: In Search of a Robust Assay. Biochemistry 2020; 59:1442-1453. [PMID: 32186371 PMCID: PMC7160020 DOI: 10.1021/acs.biochem.0c00001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides (NDP) to deoxynucleotides (dNDP), in part, by controlling the ratios and quantities of dNTPs available for DNA replication and repair. The active form of Escherichia coli class Ia RNR is an asymmetric α2β2 complex in which α2 contains the active site and β2 contains the stable diferric-tyrosyl radical cofactor responsible for initiating the reduction chemistry. Each dNDP is accompanied by disulfide bond formation. We now report that, under in vitro conditions, β2 can initiate turnover in α2 catalytically under both "one" turnover (no external reductant, though producing two dCDPs) and multiple turnover (with an external reductant) assay conditions. In the absence of reductant, rapid chemical quench analysis of a reaction of α2, substrate, and effector with variable amounts of β2 (1-, 10-, and 100-fold less than α2) yields 3 dCDP/α2 at all ratios of α2:β2 with a rate constant of 8-9 s-1, associated with a rate-limiting conformational change. Stopped-flow fluorescence spectroscopy with a fluorophore-labeled β reveals that the rate constants for subunit association (163 ± 7 μM-1 s-1) and dissociation (75 ± 10 s-1) are fast relative to turnover, consistent with catalytic β2. When assaying in the presence of an external reducing system, the turnover number is dictated by the ratio of α2:β2, their concentrations, and the concentration and nature of the reducing system; the rate-limiting step can change from the conformational gating to a step or steps involving disulfide rereduction, dissociation of the inhibited α4β4 state, or both. The issues encountered with E. coli RNR are likely of importance in all class I RNRs and are central to understanding the development of screening assays for inhibitors of these enzymes.
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Affiliation(s)
- Kanchana Ravichandran
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Lisa Olshansky
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
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21
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Drienovská I, Roelfes G. Expanding the enzyme universe with genetically encoded unnatural amino acids. Nat Catal 2020. [DOI: 10.1038/s41929-019-0410-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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22
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Greene BL, Stubbe J, Nocera DG. Selenocysteine Substitution in a Class I Ribonucleotide Reductase. Biochemistry 2019; 58:5074-5084. [PMID: 31774661 DOI: 10.1021/acs.biochem.9b00973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ribonucleotide reductases (RNRs) employ a complex radical-based mechanism during nucleotide reduction involving multiple active site cysteines that both activate the substrate and reduce it. Using an engineered allo-tRNA, we substituted two active site cysteines with distinct function in the class Ia RNR of Escherichia coli for selenocysteine (U) via amber codon suppression, with efficiency and selectivity enabling biochemical and biophysical studies. Examination of the interactions of the C439U α2 mutant protein with nucleotide substrates and the cognate β2 subunit demonstrates that the endogenous Y122• of β2 is reduced under turnover conditions, presumably through radical transfer to form a transient U439• species. This putative U439• species is formed in a kinetically competent fashion but is incapable of initiating nucleotide reduction via 3'-H abstraction. An analogous C225U α2 protein is also capable of radical transfer from Y122•, but the radical-based substrate chemistry partitions between turnover and stalled reduction akin to the reactivity of mechanism-based inhibitors of RNR. The results collectively demonstrate the essential role of cysteine redox chemistry in the class I RNRs and establish a new tool for investigating thiyl radical reactivity in biology.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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23
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Gerding HR, Karreman C, Daiber A, Delp J, Hammler D, Mex M, Schildknecht S, Leist M. Reductive modification of genetically encoded 3-nitrotyrosine sites in alpha synuclein expressed in E.coli. Redox Biol 2019; 26:101251. [PMID: 31226647 PMCID: PMC6586993 DOI: 10.1016/j.redox.2019.101251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 11/26/2022] Open
Abstract
Tyrosine nitration is a post-translational protein modification relevant to various pathophysiological processes. Chemical nitration procedures have been used to generate and study nitrated proteins, but these methods regularly lead to modifications at other amino acid residues. A novel strategy employs a genetic code modification that allows incorporation of 3-nitrotyrosine (3-NT) during ribosomal protein synthesis to generate a recombinant protein with defined 3-NT-sites, in the absence of other post-translational modifications. This approach was applied to study the generation and stability of the 3-NT moiety in recombinant proteins produced in E.coli. Nitrated alpha-synuclein (ASYN) was selected as exemplary protein, relevant in Parkinson's disease (PD). A procedure was established to obtain pure tyrosine-modified ASYN in mg amounts. However, a rapid (t1/2 = 0.4 h) reduction of 3-NT to 3-aminotyrosine (3-AT) was observed. When screening for potential mechanisms, we found that 3-NT can be reduced enzymatically to 3-AT, whilst biologically relevant low molecular weight reductants, such as NADPH or GSH, did not affect 3-NT. A genetic screen for E.coli proteins, involved in the observed 3-NT reduction, revealed the contribution of several, possibly redundant pathways. Green fluorescent protein was studied as an alternative model protein. These data confirm 3-NT reduction as a broadly-relevant pathway in E.coli. In conclusion, incorporation of 3-NT as a genetically-encoded non-natural amino acid allows for generation of recombinant proteins with specific nitration sites. The potential reduction of the 3-NT moiety by E.coli, however, requires attention to the design of the purification strategy for obtaining pure nitrated protein. 3-nitrotyrosine in proteins is reduced to 3-aminotyrosine in E.coli. 3-aminotyrosine is stable in E.coli. 3-nitrotyrosine reduction is independent of the harboring protein but affected by protein structure.
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Affiliation(s)
- Hanne R Gerding
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Christiaan Karreman
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Andreas Daiber
- Zentrum für Kardiologie, Johannes Gutenberg Universität Mainz, 55131, Mainz, Germany
| | - Johannes Delp
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Daniel Hammler
- Research School Chemical Biology, Department of Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Martin Mex
- Research School Chemical Biology, Department of Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Stefan Schildknecht
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
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24
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Gillet N, Elstner M, Kubař T. Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer. J Chem Phys 2018; 149:072328. [PMID: 30134697 DOI: 10.1063/1.5027100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.
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Affiliation(s)
- Natacha Gillet
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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25
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Hasan MM, Khatun MS, Mollah MNH, Yong C, Dianjing G. NTyroSite: Computational Identification of Protein Nitrotyrosine Sites Using Sequence Evolutionary Features. Molecules 2018; 23:E1667. [PMID: 29987232 PMCID: PMC6099560 DOI: 10.3390/molecules23071667] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 02/06/2023] Open
Abstract
Nitrotyrosine is a product of tyrosine nitration mediated by reactive nitrogen species. As an indicator of cell damage and inflammation, protein nitrotyrosine serves to reveal biological change associated with various diseases or oxidative stress. Accurate identification of nitrotyrosine site provides the important foundation for further elucidating the mechanism of protein nitrotyrosination. However, experimental identification of nitrotyrosine sites through traditional methods are laborious and expensive. In silico prediction of nitrotyrosine sites based on protein sequence information are thus highly desired. Here, we report a novel predictor, NTyroSite, for accurate prediction of nitrotyrosine sites using sequence evolutionary information. The generated features were optimized using a Wilcoxon-rank sum test. A random forest classifier was then trained using these features to build the predictor. The final NTyroSite predictor achieved an area under a receiver operating characteristics curve (AUC) score of 0.904 in a 10-fold cross-validation test. It also significantly outperformed other existing implementations in an independent test. Meanwhile, for a better understanding of our prediction model, the predominant rules and informative features were extracted from the NTyroSite model to explain the prediction results. We expect that the NTyroSite predictor may serve as a useful computational resource for high-throughput nitrotyrosine site prediction. The online interface of the software is publicly available at https://biocomputer.bio.cuhk.edu.hk/NTyroSite/.
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Affiliation(s)
- Md Mehedi Hasan
- School of Life Sciences and the State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Mst Shamima Khatun
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh.
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh.
| | - Cao Yong
- Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen 518000, China.
| | - Guo Dianjing
- School of Life Sciences and the State Key Lab of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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26
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Olshansky L, Huerta-Lavorie R, Nguyen AI, Vallapurackal J, Furst A, Tilley TD, Borovik AS. Artificial Metalloproteins Containing Co 4O 4 Cubane Active Sites. J Am Chem Soc 2018; 140:2739-2742. [PMID: 29401385 PMCID: PMC5866047 DOI: 10.1021/jacs.7b13052] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Artificial metalloproteins (ArMs) containing Co4O4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial CoIII-OH2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e-/1H+ chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co4O4 active site provided a single H-bond to one of a set of cofacial CoIII-OH2 groups. With this variant, multi-e-/multi-H+ chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. With structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co4O4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e-/multi-H+ reactivity.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Raúl Huerta-Lavorie
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Andy I Nguyen
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Jaicy Vallapurackal
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
| | - Ariel Furst
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - T Don Tilley
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - A S Borovik
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
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27
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Ferrer-Sueta G, Campolo N, Trujillo M, Bartesaghi S, Carballal S, Romero N, Alvarez B, Radi R. Biochemistry of Peroxynitrite and Protein Tyrosine Nitration. Chem Rev 2018; 118:1338-1408. [DOI: 10.1021/acs.chemrev.7b00568] [Citation(s) in RCA: 292] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Gerardo Ferrer-Sueta
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Nicolás Campolo
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Madia Trujillo
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Silvina Bartesaghi
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sebastián Carballal
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Romero
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Laboratorio
de Fisicoquímica Biológica, Facultad de
Ciencias, ‡Center for Free Radical and Biomedical Research, §Departamento de Bioquímica,
Facultad de Medicina, ∥Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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28
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Topkaya SN, Ozyurt VH, Cetin AE, Otles S. Nitration of tyrosine and its effect on DNA hybridization. Biosens Bioelectron 2017; 102:464-469. [PMID: 29182929 DOI: 10.1016/j.bios.2017.11.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022]
Abstract
One major marker of nitrosative stress is the formation of 3-Nitrotyrosine (3-NT) from Tyrosine (Tyr) by adding a nitro group (-NO2) with nitrating agents. Nitration of Tyr often causes loss of protein activity and is linked with many diseases. In this article, we detect 3-NT and discriminate it from Tyr with Differential Pulse Voltammetry (DPV) as it is a very important biomarker. We first examined redox (oxidation/reduction) properties and stability of 3-NT in detail. Second, we provided the Tyr and 3-NT discrimination with DPV and compared with the chromatography. We then explored the interaction of 3-NT and DNA oligonucleotides. Our findings demonstrate that 3-NT can be used as a new electrochemical indicator, which is able to detect hybridization of probe (single stranded DNA-ssDNA) and hybrid (double stranded DNA-dsDNA) both via 3-NT reduction and guanine oxidation signal changes at the same time. The signal differences enabled us to distinguish ssDNA and dsDNA without using a label or a tag. Moreover, we achieved to detect hybridization of DNA by using the reduction signal of 3-NT obtained at -0.4V vs. Ag/AgCl. More importantly, we observed the changes of the reduction signals of 3-NT after the interaction of probe and hybrid sequences. We showed that 3-NT signal decreases more with hybrid than the probe. Our platform, for the first time, demonstrates the detection of hybridization both guanine oxidation and indicator reduction signal changes at the same time. Moreover, we, for the first time, demonstrated the interaction between 3-NT and DNA.
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Affiliation(s)
- Seda Nur Topkaya
- Department of Analytical Chemistry, Faculty of Pharmacy, İzmir Katip Celebi University, Izmir, Turkey.
| | - Vasfiye Hazal Ozyurt
- Department of Food Engineering, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Arif E Cetin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, USA
| | - Semih Otles
- Department of Food Engineering, Faculty of Engineering, Ege University, Izmir, Turkey
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29
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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: 11] [Impact Index Per Article: 1.6] [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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30
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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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31
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Batthyány C, Bartesaghi S, Mastrogiovanni M, Lima A, Demicheli V, Radi R. Tyrosine-Nitrated Proteins: Proteomic and Bioanalytical Aspects. Antioxid Redox Signal 2017; 26:313-328. [PMID: 27324931 PMCID: PMC5326983 DOI: 10.1089/ars.2016.6787] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
SIGNIFICANCE "Nitroproteomic" is under active development, as 3-nitrotyrosine in proteins constitutes a footprint left by the reactions of nitric oxide-derived oxidants that are usually associated to oxidative stress conditions. Moreover, protein tyrosine nitration can cause structural and functional changes, which may be of pathophysiological relevance for human disease conditions. Biological protein tyrosine nitration is a free radical process involving the intermediacy of tyrosyl radicals; in spite of being a nonenzymatic process, nitration is selectively directed toward a limited subset of tyrosine residues. Precise identification and quantitation of 3-nitrotyrosine in proteins has represented a "tour de force" for researchers. Recent Advances: A small number of proteins are preferential targets of nitration (usually less than 100 proteins per proteome), contrasting with the large number of proteins modified by other post-translational modifications such as phosphorylation, acetylation, and, notably, S-nitrosation. Proteomic approaches have revealed key features of tyrosine nitration both in vivo and in vitro, including selectivity, site specificity, and effects in protein structure and function. CRITICAL ISSUES Identification of 3-nitrotyrosine-containing proteins and mapping nitrated residues is challenging, due to low abundance of this oxidative modification in biological samples and its unfriendly behavior in mass spectrometry (MS)-based technologies, that is, MALDI, electrospray ionization, and collision-induced dissociation. FUTURE DIRECTIONS The use of (i) classical two-dimensional electrophoresis with immunochemical detection of nitrated proteins followed by protein ID by regular MS/MS in combination with (ii) immuno-enrichment of tyrosine-nitrated peptides and (iii) identification of nitrated peptides by a MIDAS™ experiment is arising as a potent methodology to unambiguously map and quantitate tyrosine-nitrated proteins in vivo. Antioxid. Redox Signal. 26, 313-328.
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Affiliation(s)
- Carlos Batthyány
- 1 Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Silvina Bartesaghi
- 3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay .,4 Departamento de Educación Médica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Analía Lima
- 1 Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Verónica Demicheli
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- 2 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,3 Facultad de Medicina, Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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32
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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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33
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Ravichandran K, Minnihan EC, Lin Q, Yokoyama K, Taguchi AT, Shao J, Nocera DG, Stubbe J. Glutamate 350 Plays an Essential Role in Conformational Gating of Long-Range Radical Transport in Escherichia coli Class Ia Ribonucleotide Reductase. Biochemistry 2017; 56:856-868. [PMID: 28103007 DOI: 10.1021/acs.biochem.6b01145] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli class Ia ribonucleotide reductase (RNR) is composed of two subunits that form an active α2β2 complex. The nucleoside diphosphate substrates (NDP) are reduced in α2, 35 Å from the essential diferric-tyrosyl radical (Y122•) cofactor in β2. The Y122•-mediated oxidation of C439 in α2 occurs by a pathway (Y122 ⇆ [W48] ⇆ Y356 in β2 to Y731 ⇆ Y730 ⇆ C439 in α2) across the α/β interface. The absence of an α2β2 structure precludes insight into the location of Y356 and Y731 at the subunit interface. The proximity in the primary sequence of the conserved E350 to Y356 in β2 suggested its importance in catalysis and/or conformational gating. To study its function, pH-rate profiles of wild-type β2/α2 and mutants in which 3,5-difluorotyrosine (F2Y) replaces residue 356, 731, or both are reported in the presence of E350 or E350X (X = A, D, or Q) mutants. With E350, activity is maintained at the pH extremes, suggesting that protonated and deprotonated states of F2Y356 and F2Y731 are active and that radical transport (RT) can occur across the interface by proton-coupled electron transfer at low pH or electron transfer at high pH. With E350X mutants, all RNRs were inactive, suggesting that E350 could be a proton acceptor during oxidation of the interface Ys. To determine if E350 plays a role in conformational gating, the strong oxidants, NO2Y122•-β2 and 2,3,5-F3Y122•-β2, were reacted with α2, CDP, and ATP in E350 and E350X backgrounds and the reactions were monitored for pathway radicals by rapid freeze-quench electron paramagnetic resonance spectroscopy. Pathway radicals are generated only when E350 is present, supporting its essential role in gating the conformational change(s) that initiates RT and masking its role as a proton acceptor.
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Affiliation(s)
| | | | - Qinghui Lin
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine , Hangzhou 310058, China
| | | | | | - Jimin Shao
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine , Hangzhou 310058, China
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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34
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Ravichandran KR, Taguchi AT, Wei Y, Tommos C, Nocera DG, Stubbe J. A >200 meV Uphill Thermodynamic Landscape for Radical Transport in Escherichia coli Ribonucleotide Reductase Determined Using Fluorotyrosine-Substituted Enzymes. J Am Chem Soc 2016; 138:13706-13716. [PMID: 28068088 PMCID: PMC5224885 DOI: 10.1021/jacs.6b08200] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Escherichia coli class Ia ribonucleotide reductase
(RNR) converts ribonucleotides to deoxynucleotides. A diferric-tyrosyl
radical (Y122•) in one subunit (β2) generates
a transient thiyl radical in another subunit (α2) via long-range
radical transport (RT) through aromatic amino acid residues (Y122 ⇆ [W48] ⇆ Y356 in β2
to Y731 ⇆ Y730 ⇆ C439 in α2). Equilibration of Y356•, Y731•, and Y730• was recently observed using
site specifically incorporated unnatural tyrosine analogs; however,
equilibration between Y122• and Y356•
has not been detected. Our recent report of Y356•
formation in a kinetically and chemically competent fashion in the
reaction of β2 containing 2,3,5-trifluorotyrosine at Y122 (F3Y122•-β2) with α2, CDP
(substrate), and ATP (effector) has now afforded the opportunity to
investigate equilibration of F3Y122•
and Y356•. Incubation of F3Y122•-β2, Y731F-α2 (or Y730F-α2),
CDP, and ATP at different temperatures (2–37 °C) provides
ΔE°′(F3Y122•–Y356•) of 20 ± 10 mV at 25
°C. The pH dependence of the F3Y122•
⇆ Y356• interconversion (pH 6.8–8.0)
reveals that the proton from Y356 is in rapid exchange
with solvent, in contrast to the proton from Y122. Insertion
of 3,5-difluorotyrosine (F2Y) at Y356 and rapid
freeze-quench EPR analysis of its reaction with Y731F-α2,
CDP, and ATP at pH 8.2 and 25 °C shows F2Y356• generation by the native Y122•. FnY-RNRs (n = 2 and 3) together
provide a model for the thermodynamic landscape of the RT pathway
in which the reaction between Y122 and C439 is
∼200 meV uphill.
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Affiliation(s)
| | | | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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35
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Xiao H, Schultz PG. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023945. [PMID: 27413101 DOI: 10.1101/cshperspect.a023945] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.
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Affiliation(s)
- Han Xiao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 California Institute for Biomedical Research, La Jolla, California 92037
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36
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Oyala PH, Ravichandran KR, Funk MA, Stucky PA, Stich TA, Drennan CL, Britt RD, Stubbe J. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example. J Am Chem Soc 2016; 138:7951-64. [PMID: 27276098 PMCID: PMC4929525 DOI: 10.1021/jacs.6b03605] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Fluorinated tyrosines
(FnY’s, n = 2
and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the
recently evolved M. jannaschii Y-tRNA synthetase/tRNA
pair. Class Ia RNRs require four redox active Y’s, a stable
Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y’s (356
in β and 731 and 730 in α) to initiate the radical-dependent
nucleotide reduction process. FnY (3,5;
2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β
and the X-ray structures of each resulting β with a diferric
cluster are reported and compared with wt-β2 crystallized under
the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe2+, and O2 to produce ∼1
Y·/β2 and ∼3 Fe3+/β2. The FnY· are stable and active in nucleotide
reduction with activities that vary from 5% to 85% that of wt-β2.
Each FnY·-β2 has been characterized
by 9 and 130 GHz electron paramagnetic resonance and high-field electron
nuclear double resonance spectroscopies. The hyperfine interactions
associated with the 19F nucleus provide unique signatures
of each FnY· that are readily distinguishable
from unlabeled Y·’s. The variability of the abiotic FnY pKa’s
(6.4 to 7.8) and reduction potentials (−30 to +130 mV relative
to Y at pH 7.5) provide probes of enzymatic reactions proposed to
involve Y·’s in catalysis and to investigate the importance
and identity of hopping Y·’s within redox active proteins
proposed to protect them from uncoupled radical chemistry.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | | | | | - Paul A Stucky
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Troy A Stich
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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37
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Demicheli V, Moreno DM, Jara GE, Lima A, Carballal S, Ríos N, Batthyany C, Ferrer-Sueta G, Quijano C, Estrı́n DA, Martí MA, Radi R. Mechanism of the Reaction of Human Manganese Superoxide Dismutase with Peroxynitrite: Nitration of Critical Tyrosine 34. Biochemistry 2016; 55:3403-17. [PMID: 27227512 DOI: 10.1021/acs.biochem.6b00045] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human Mn-containing superoxide dismutase (hMnSOD) is a mitochondrial enzyme that metabolizes superoxide radical (O2(•-)). O2(•-) reacts at diffusional rates with nitric oxide to yield a potent nitrating species, peroxynitrite anion (ONOO(-)). MnSOD is nitrated and inactivated in vivo, with active site Tyr34 as the key oxidatively modified residue. We previously reported a k of ∼1.0 × 10(5) M(-1) s(-1) for the reaction of hMnSOD with ONOO(-) by direct stopped-flow spectroscopy and the critical role of Mn in the nitration process. In this study, we further established the mechanism of the reaction of hMnSOD with ONOO(-), including the necessary re-examination of the second-order rate constant by an independent method and the delineation of the microscopic steps that lead to the regio-specific nitration of Tyr34. The redetermination of k was performed by competition kinetics utilizing coumarin boronic acid, which reacts with ONOO(-) at a rate of ∼1 × 10(6) M(-1) s(-1) to yield the fluorescence product, 7-hydroxycoumarin. Time-resolved fluorescence studies in the presence of increasing concentrations of hMnSOD provided a k of ∼1.0 × 10(5) M(-1) s(-1), fully consistent with the direct method. Proteomic analysis indicated that ONOO(-), but not other nitrating agents, mediates the selective modification of active site Tyr34. Hybrid quantum-classical (quantum mechanics/molecular mechanics) simulations supported a series of steps that involve the initial reaction of ONOO(-) with Mn(III) to yield Mn(IV) and intermediates that ultimately culminate in 3-nitroTyr34. The data reported herein provide a kinetic and mechanistic basis for rationalizing how MnSOD constitutes an intramitochondrial target for ONOO(-) and the microscopic events, with atomic level resolution, that lead to selective and efficient nitration of critical Tyr34.
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Affiliation(s)
- Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Diego M Moreno
- Instituto de Química de Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Suipacha 531, S2002LRK Rosario, Argentina
| | - Gabriel E Jara
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Analía Lima
- Unidad Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Sebastián Carballal
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Natalia Ríos
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Departamento de Química Orgánica, Facultad de Química, Universidad de la República , Avda. General Flores 2124, Montevideo, Uruguay
| | - Carlos Batthyany
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Unidad Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Gerardo Ferrer-Sueta
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la Repúbica , Igua 4225, Montevideo, Uruguay
| | - Celia Quijano
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Darío A Estrı́n
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
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38
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Kasanmascheff M, Lee W, Nick TU, Stubbe J, Bennati M. Radical transfer in E. coli ribonucleotide reductase: a NH 2Y 731/R 411A-α mutant unmasks a new conformation of the pathway residue 731. Chem Sci 2016; 7:2170-2178. [PMID: 29899944 PMCID: PMC5968753 DOI: 10.1039/c5sc03460d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/06/2015] [Indexed: 11/21/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all living organisms. The catalytic cycle of E. coli RNR involves a long-range proton-coupled electron transfer (PCET) from a tyrosyl radical (Y122˙) in subunit β2 to a cysteine (C439) in the active site of subunit α2, which subsequently initiates nucleotide reduction. This oxidation occurs over 35 Å and involves a specific pathway of redox active amino acids (Y122 ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2). The mechanisms of the PCET steps at the interface of the α2β2 complex remain puzzling due to a lack of structural information for this region. Recently, DFT calculations on the 3-aminotyrosyl radical (NH2Y731˙)-α2 trapped by incubation of NH2Y731-α2/β2/CDP(substrate)/ATP(allosteric effector) suggested that R411-α2, a residue close to the α2β2 interface, interacts with NH2Y731˙ and accounts in part for its perturbed EPR parameters. To examine its role, we further modified NH2Y731-α2 with a R411A substitution. NH2Y731˙/R411A generated upon incubation of NH2Y731/R411A-α2/β2/CDP/ATP was investigated using multi-frequency (34, 94 and 263 GHz) EPR, 34 GHz pulsed electron-electron double resonance (PELDOR) and electron-nuclear double resonance (ENDOR) spectroscopies. The data indicate a large conformational change in NH2Y731˙/R411A relative to the NH2Y731˙ single mutant. Particularly, the inter-spin distance from NH2Y731˙/R411A in one αβ pair to Y122˙ in a second αβ pair decreases by 3 Å in the presence of the R411A mutation. This is the first experimental evidence for the flexibility of pathway residue Y731-α2 in an α2β2 complex and suggests a role for R411 in the stacked Y731/Y730 conformation involved in collinear PCET. Furthermore, NH2Y731˙/R411A serves as a probe of the PCET process across the subunit interface.
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Affiliation(s)
- Müge Kasanmascheff
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- Department of Chemistry, University of Göttingen, 37077 Göttingen, Germany
| | - Wankyu Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Thomas U Nick
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
- Department of Chemistry, University of Göttingen, 37077 Göttingen, Germany
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39
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Olshansky L, Stubbe J, Nocera DG. Charge-Transfer Dynamics at the α/β Subunit Interface of a Photochemical Ribonucleotide Reductase. J Am Chem Soc 2016; 138:1196-205. [PMID: 26710997 PMCID: PMC4924928 DOI: 10.1021/jacs.5b09259] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides to provide the monomeric building blocks for DNA replication and repair. Nucleotide reduction occurs by way of multistep proton-coupled electron transfer (PCET) over a pathway of redox active amino acids spanning ∼35 Å and two subunits (α2 and β2). Despite the fact that PCET in RNR is rapid, slow conformational changes mask examination of the kinetics of these steps. As such, we have pioneered methodology in which site-specific incorporation of a [Re(I)] photooxidant on the surface of the β2 subunit (photoβ2) allows photochemical oxidation of the adjacent PCET pathway residue β-Y356 and time-resolved spectroscopic observation of the ensuing reactivity. A series of photoβ2s capable of performing photoinitiated substrate turnover have been prepared in which four different fluorotyrosines (FnYs) are incorporated in place of β-Y356. The FnYs are deprotonated under biological conditions, undergo oxidation by electron transfer (ET), and provide a means by which to vary the ET driving force (ΔG°) with minimal additional perturbations across the series. We have used these features to map the correlation between ΔG° and kET both with and without the fully assembled photoRNR complex. The photooxidation of FnY356 within the α/β subunit interface occurs within the Marcus inverted region with a reorganization energy of λ ≈ 1 eV. We also observe enhanced electronic coupling between donor and acceptor (HDA) in the presence of an intact PCET pathway. Additionally, we have investigated the dynamics of proton transfer (PT) by a variety of methods including dependencies on solvent isotopic composition, buffer concentration, and pH. We present evidence for the role of α2 in facilitating PT during β-Y356 photooxidation; PT occurs by way of readily exchangeable positions and within a relatively "tight" subunit interface. These findings show that RNR controls ET by lowering λ, raising HDA, and directing PT both within and between individual polypeptide subunits.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, 12 Oxford St., Harvard University, Cambridge, Massachusetts 02138, United States
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40
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Song DY, Pizano AA, Holder PG, Stubbe J, Nocera DG. Direct Interfacial Y 731 Oxidation in α 2 by a Photoβ 2 Subunit of E. coli Class Ia Ribonucleotide Reductase. Chem Sci 2015; 6:4519-4524. [PMID: 26504513 PMCID: PMC4618407 DOI: 10.1039/c5sc01125f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022] Open
Abstract
Proton-coupled electron transfer (PCET) is a fundamental mechanism important in a wide range of biological processes including the universal reaction catalysed by ribonucleotide reductases (RNRs) in making de novo, the building blocks required for DNA replication and repair. These enzymes catalyse the conversion of nucleoside diphosphates (NDPs) to deoxynucleoside diphosphates (dNDPs). In the class Ia RNRs, NDP reduction involves a tyrosyl radical mediated oxidation occurring over 35 Å across the interface of the two required subunits (β2 and α2) involving multiple PCET steps and the conserved tyrosine triad [Y356(β2)-Y731(α2)-Y730(α2)]. We report the synthesis of an active photochemical RNR (photoRNR) complex in which a Re(I)-tricarbonyl phenanthroline ([Re]) photooxidant is attached site-specifically to the Cys in the Y356C-(β2) subunit and an ionizable, 2,3,5-trifluorotyrosine (2,3,5-F3Y) is incorporated in place of Y731 in α2. This intersubunit PCET pathway is investigated by ns laser spectroscopy on [Re356]-β2:2,3,5-F3Y731-α2 in the presence of substrate, CDP, and effector, ATP. This experiment has allowed analysis of the photoinjection of a radical into α2 from β2 in the absence of the interfacial Y356 residue. The system is competent for light-dependent substrate turnover. Time-resolved emission experiments reveal an intimate dependence of the rate of radical injection on the protonation state at position Y731(α2), which in turn highlights the importance of a well-coordinated proton exit channel involving the key residues, Y356 and Y731, at the subunit interface.
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Affiliation(s)
- David Y. Song
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - Arturo A. Pizano
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - Patrick G. Holder
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - JoAnne Stubbe
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139-4307 , USA .
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
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41
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Extension of the fragment molecular orbital method to treat large open-shell systems in solution. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Larson BC, Pomponio JR, Shafaat HS, Kim RH, Leigh BS, Tauber MJ, Kim JE. Photogeneration and Quenching of Tryptophan Radical in Azurin. J Phys Chem B 2015; 119:9438-49. [PMID: 25625660 PMCID: PMC5092234 DOI: 10.1021/jp511523z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan and tyrosine can form radical intermediates that enable long-range, multistep electron transfer (ET) reactions in proteins. This report describes the mechanisms of formation and quenching of a neutral tryptophan radical in azurin, a blue-copper protein that contains native tyrosine (Y108 and Y72) and tryptophan (W48) residues. A long-lived neutral tryptophan radical W48• is formed upon UV-photoexcitation of a zinc(II)-substituted azurin mutant in the presence of an external electron acceptor. The quantum yield of W48• formation (Φ) depends upon the tyrosine residues in the protein. A tyrosine-deficient mutant, Zn(II)Az48W, exhibited a value of Φ = 0.080 with a Co(III) electron acceptor. A nearly identical quantum yield was observed when the electron acceptor was the analogous tyrosine-free, copper(II) mutant; this result for the Zn(II)Az48W:Cu(II)Az48W mixture suggests there is an interprotein ET path. A single tyrosine residue at one of the native positions reduced the quantum yield to 0.062 (Y108) or 0.067 (Y72). Wild-type azurin with two tyrosine residues exhibited a quantum yield of Φ = 0.045. These data indicate that tyrosine is able to quench the tryptophan radical in azurin.
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Affiliation(s)
- Bethany C. Larson
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jennifer R. Pomponio
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | - Rachel H. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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43
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Abstract
An enormous variety of biological redox reactions are accompanied by changes in proton content at enzyme active sites, in their associated cofactors, in substrates and/or products, and between protein interfaces. Understanding this breadth of reactivity is an ongoing chemical challenge. A great many workers have developed and investigated biomimetic model complexes to build new ways of thinking about the mechanistic underpinnings of such complex biological proton-coupled electron transfer (PCET) reactions. Of particular importance are those model reactions that involve transfer of one proton (H(+)) and one electron (e(-)), which is equivalent to transfer of a hydrogen atom (H(•)). In this Current Topic, we review key concepts in PCET reactivity and describe important advances in biomimetic PCET chemistry, with a special emphasis on research that has enhanced efforts to understand biological PCET reactions.
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Affiliation(s)
- Jeffrey J. Warren
- Simon Fraser University, Department of Chemistry, 8888 University Drive, Burnaby BC, Canada V5A 1S6
| | - James M. Mayer
- Yale University, Department of Chemistry, P.O. Box 208107, 225 Prospect Street, New Haven, CT 06520-8107
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44
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Nick T, Lee W, Koßmann S, Neese F, Stubbe J, Bennati M. Hydrogen bond network between amino acid radical intermediates on the proton-coupled electron transfer pathway of E. coli α2 ribonucleotide reductase. J Am Chem Soc 2015; 137:289-98. [PMID: 25516424 PMCID: PMC4304443 DOI: 10.1021/ja510513z] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 02/05/2023]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all organisms. In all Class Ia RNRs, initiation of nucleotide diphosphate (NDP) reduction requires a reversible oxidation over 35 Å by a tyrosyl radical (Y122•, Escherichia coli) in subunit β of a cysteine (C439) in the active site of subunit α. This radical transfer (RT) occurs by a specific pathway involving redox active tyrosines (Y122 ⇆ Y356 in β to Y731 ⇆ Y730 ⇆ C439 in α); each oxidation necessitates loss of a proton coupled to loss of an electron (PCET). To study these steps, 3-aminotyrosine was site-specifically incorporated in place of Y356-β, Y731- and Y730-α, and each protein was incubated with the appropriate second subunit β(α), CDP and effector ATP to trap an amino tyrosyl radical (NH2Y•) in the active α2β2 complex. High-frequency (263 GHz) pulse electron paramagnetic resonance (EPR) of the NH2Y•s reported the gx values with unprecedented resolution and revealed strong electrostatic effects caused by the protein environment. (2)H electron-nuclear double resonance (ENDOR) spectroscopy accompanied by quantum chemical calculations provided spectroscopic evidence for hydrogen bond interactions at the radical sites, i.e., two exchangeable H bonds to NH2Y730•, one to NH2Y731• and none to NH2Y356•. Similar experiments with double mutants α-NH2Y730/C439A and α-NH2Y731/Y730F allowed assignment of the H bonding partner(s) to a pathway residue(s) providing direct evidence for colinear PCET within α. The implications of these observations for the PCET process within α and at the interface are discussed.
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Affiliation(s)
- Thomas
U. Nick
- Max
Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wankyu Lee
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Simone Koßmann
- Max
Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max
Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - JoAnne Stubbe
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Marina Bennati
- Max
Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department
of Chemistry, University of Göttingen, 37077 Göttingen, Germany
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45
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Gamiz-Hernandez AP, Magomedov A, Hummer G, Kaila VRI. Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer. J Phys Chem B 2015; 119:2611-9. [DOI: 10.1021/jp508790n] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ana P. Gamiz-Hernandez
- Department
Chemie, Technische Universität München (TUM) Lichtenbergstraße
4, D-85747 Garching, Germany
| | - Artiom Magomedov
- Department
Chemie, Technische Universität München (TUM) Lichtenbergstraße
4, D-85747 Garching, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
| | - Ville R. I. Kaila
- Department
Chemie, Technische Universität München (TUM) Lichtenbergstraße
4, D-85747 Garching, Germany
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46
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Olshansky L, Pizano AA, Wei Y, Stubbe J, Nocera DG. Kinetics of hydrogen atom abstraction from substrate by an active site thiyl radical in ribonucleotide reductase. J Am Chem Soc 2014; 136:16210-6. [PMID: 25353063 PMCID: PMC4244835 DOI: 10.1021/ja507313w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Ribonucleotide
reductases (RNRs) catalyze the conversion of nucleotides
to deoxynucleotides in all organisms. Active E. coli class Ia RNR is an α2β2 complex
that undergoes reversible, long-range proton-coupled electron transfer
(PCET) over a pathway of redox active amino acids (β-Y122 → [β-W48] → β-Y356 → α-Y731 → α-Y730 → α-C439) that spans ∼35 Å.
To unmask PCET kinetics from rate-limiting conformational changes,
we prepared a photochemical RNR containing a [ReI] photooxidant
site-specifically incorporated at position 355 ([Re]-β2), adjacent to PCET pathway residue Y356 in β. [Re]-β2 was further modified by replacing Y356 with 2,3,5-trifluorotyrosine
to enable photochemical generation and spectroscopic observation of
chemically competent tyrosyl radical(s). Using transient absorption
spectroscopy, we compare the kinetics of Y· decay in the presence
of substrate and wt-α2, Y731F-α2 ,or C439S-α2, as well as with
3′-[2H]-substrate and wt-α2. We
find that only in the presence of wt-α2 and the unlabeled
substrate do we observe an enhanced rate of radical decay indicative
of forward radical propagation. This observation reveals that cleavage
of the 3′-C–H bond of substrate by the transiently formed
C439· thiyl radical is rate-limiting in forward PCET
through α and has allowed calculation of a lower bound for the
rate constant associated with this step of (1.4 ± 0.4) ×
104 s–1. Prompting radical propagation
with light has enabled observation of PCET events heretofore inaccessible,
revealing active site chemistry at the heart of RNR catalysis.
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Affiliation(s)
- Lisa Olshansky
- Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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47
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Barry BA. Reaction dynamics and proton coupled electron transfer: studies of tyrosine-based charge transfer in natural and biomimetic systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:46-54. [PMID: 25260243 DOI: 10.1016/j.bbabio.2014.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/27/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
Abstract
In bioenergetic reactions, electrons are transferred long distances via a hopping mechanism. In photosynthesis and DNA synthesis, the aromatic amino acid residue, tyrosine, functions as an intermediate that is transiently oxidized and reduced during long distance electron transfer. At physiological pH values, oxidation of tyrosine is associated with a deprotonation of the phenolic oxygen, giving rise to a proton coupled electron transfer (PCET) reaction. Tyrosine-based PCET reactions are important in photosystem II, which carries out the light-induced oxidation of water, and in ribonucleotide reductase, which reduces ribonucleotides to form deoxynucleotides. Photosystem II contains two redox-active tyrosines, YD (Y160 in the D2 polypeptide) and YZ (Y161 in the D1 polypeptide). YD forms a light-induced stable radical, while YZ functions as an essential charge relay, oxidizing the catalytic Mn₄CaO₅ cluster on each of four photo-oxidation reactions. In Escherichia coli class 1a RNR, the β2 subunit contains the radical initiator, Y122O•, which is reversibly reduced and oxidized in long range electron transfer with the α2 subunit. In the isolated E. coli β2 subunit, Y122O• is a stable radical, but Y122O• is activated for rapid PCET in an α2β2 substrate/effector complex. Recent results concerning the structure and function of YD, YZ, and Y122 are reviewed here. Comparison is made to recent results derived from bioengineered proteins and biomimetic compounds, in which tyrosine-based charge transfer mechanisms have been investigated. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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48
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Chemistry and biology of biomolecule nitration. ACTA ACUST UNITED AC 2014; 19:1086-92. [PMID: 22999877 DOI: 10.1016/j.chembiol.2012.07.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 07/25/2012] [Accepted: 07/27/2012] [Indexed: 12/27/2022]
Abstract
Posttranslational modifications of proteins play key roles in the regulation of biological processes and lead to various physiological responses. In recent years, a number of analytical technologies have been developed to help understand the diversity and disease relevance of these modifications. The main areas of focus have included phosphorylation, cysteine redox chemistry, and transformations mediated directly by oxidative stress. However, the nitration of biomolecules is an exciting and relatively understudied area of research. Reactive nitrogen species generated in various disease states can create nitrated biomolecules, and we are only beginning to understand the potential implications of these species. This review explores some of the recent advances in current knowledge concerning the chemistry and biology of nitrated biomolecules.
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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Sandhiya L, Kolandaivel P, Senthilkumar K. Oxidation and nitration of tyrosine by ozone and nitrogen dioxide: reaction mechanisms and biological and atmospheric implications. J Phys Chem B 2014; 118:3479-90. [PMID: 24611937 DOI: 10.1021/jp4106037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The nitration of tyrosine by atmospheric oxidants, O3 and NO2, is an important cause for the spread of allergenic diseases. In the present study, the mechanism and pathways for the reaction of tyrosine with the atmospheric oxidants O3 and NO2 are studied using DFT-M06-2X, B3LYP, and B3LYP-D methods with the 6-311+G(d,p) basis set. The energy barrier for the initial oxidation reactions is also calculated at the CCSD(T)/6-31+G(d,p) level of theory. The reaction is studied in gas, aqueous, and lipid media. The initial oxidation of tyrosine by O3 proceeds by H atom abstraction and addition reactions and leads to the formation of six different intermediates. The subsequent nitration reaction is studied for all the intermediates, and the results show that the nitration affects both the side chain and the aromatic ring of tyrosine. The rate constant of the favorable oxidation and nitration reaction is calculated using variational transition state theory over the temperature range of 278-350 K. The spectral properties of the oxidation and nitration products are calculated at the TD-M06-2X/6-311+G(d,p) level of theory. The fate of the tyrosine radical intermediate is studied by its reaction with glutathione antioxidant. This study provides an enhanced understanding of the oxidation and nitration of tyrosine by O3 and NO2 in the context of improving the air quality and reducing the allergic diseases.
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Affiliation(s)
- L Sandhiya
- Department of Physics, Bharathiar University , Coimbatore 641 046, India
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