1
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Proximity Labeling Facilitates Defining the Proteome Neighborhood of Photosystem II Oxygen Evolution Complex in a Model Cyanobacterium. Mol Cell Proteomics 2022; 21:100440. [PMID: 36356940 PMCID: PMC9764255 DOI: 10.1016/j.mcpro.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Ascorbate peroxidase (APEX)-based proximity labeling coupled with mass spectrometry has a great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO. In total, 38 integral membrane proteins (IMPs) and 93 luminal proteins were identified as proximal to the OEC. A significant portion of these proteins are involved in PS II assembly, maturation, and repair, while the majority of the rest were not previously implicated with PS II. The IMPs include subunits of PS II and cytochrome b6/f, but not of photosystem I (except for PsaL) and ATP synthases, suggesting that the latter two complexes are spatially separated from the OEC with a distance longer than the APEX2 labeling radius. Besides, the topologies of six IMPs were successfully predicted because their lumen-facing regions exclusively contain potential APEX2 labeling sites. The luminal proteins include 66 proteins with a predicted signal peptide and 57 proteins localized also in periplasm, providing important targets to study the regulation and selectivity of protein translocation. Together, we not only developed a robust workflow for the application of APEX2-based proximity labeling in Synechocystis and showcased the feasibility to define the neighborhood proteome of an important protein complex with a short radius but also discovered a set of the proteins that potentially interact with and regulate PS II structure and function.
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2
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Liu X, Wang Y. Aha1 Is an Autonomous Chaperone for SULT1A1. Chem Res Toxicol 2022; 35:1418-1424. [PMID: 35926086 PMCID: PMC9378526 DOI: 10.1021/acs.chemrestox.2c00167] [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: 11/28/2022]
Abstract
The cochaperone Aha1 activates HSP90 ATPase to promote the folding of its client proteins; however, very few client proteins of Aha1 are known. With the use of an ascorbate peroxidase (APEX)-based proximity labeling method, we identified SULT1A1 as a proximity protein of HSP90 that is modulated by genetic depletion of Aha1. Immunoprecipitation followed by Western blot analysis showed the interaction of SULT1A1 with Aha1, but not HSP90. We also observed a reduced level of SULT1A1 protein upon genetic depletion of Aha1 but not upon pharmacological inhibition of HSP90, suggesting that the SULT1A1 protein level is regulated by Aha1 alone. Maturation-dependent interaction assay results showed that Aha1, but not HSP90, binds preferentially to newly synthesized SULT1A1. Reconstitution of Aha1-depleted cells with wild-type Aha1 and its E67K mutant, which is deficient in interacting with HSP90, restored SULT1A1 protein to the same level. Nonetheless, complementation of Aha1-depleted cells with an Aha1 mutant lacking the first 20 amino acids, which disrupts its autonomous chaperone function, was unable to rescue the SULT1A1 protein level. Together, our study revealed, for the first time, Aha1 as an autonomous chaperone in regulating SULT1A1. SULT1A1 is a phase-II metabolic enzyme, where it adds sulfate groups to hydroxyl functionalities in endogenous hormones and xenobiotic chemicals to improve their solubilities and promote their excretion. Thus, our work suggests the role of Aha1 cochaperone in modulating the detoxification of endogenous and environmental chemicals.
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Affiliation(s)
- Xiaochuan Liu
- Department of Chemistry, University of California, Riverside, Riverside, California 92502, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92502, United States
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3
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Fuentes-Lemus E, Hägglund P, López-Alarcón C, Davies MJ. Oxidative Crosslinking of Peptides and Proteins: Mechanisms of Formation, Detection, Characterization and Quantification. Molecules 2021; 27:15. [PMID: 35011250 PMCID: PMC8746199 DOI: 10.3390/molecules27010015] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/14/2022] Open
Abstract
Covalent crosslinks within or between proteins play a key role in determining the structure and function of proteins. Some of these are formed intentionally by either enzymatic or molecular reactions and are critical to normal physiological function. Others are generated as a consequence of exposure to oxidants (radicals, excited states or two-electron species) and other endogenous or external stimuli, or as a result of the actions of a number of enzymes (e.g., oxidases and peroxidases). Increasing evidence indicates that the accumulation of unwanted crosslinks, as is seen in ageing and multiple pathologies, has adverse effects on biological function. In this article, we review the spectrum of crosslinks, both reducible and non-reducible, currently known to be formed on proteins; the mechanisms of their formation; and experimental approaches to the detection, identification and characterization of these species.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark; (E.F.-L.); (P.H.)
| | - Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark; (E.F.-L.); (P.H.)
| | - Camilo López-Alarcón
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile;
| | - Michael J. Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark; (E.F.-L.); (P.H.)
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4
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Demasi M, Augusto O, Bechara EJH, Bicev RN, Cerqueira FM, da Cunha FM, Denicola A, Gomes F, Miyamoto S, Netto LES, Randall LM, Stevani CV, Thomson L. Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and Beyond. Antioxid Redox Signal 2021; 35:1016-1080. [PMID: 33726509 DOI: 10.1089/ars.2020.8176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The systematic investigation of oxidative modification of proteins by reactive oxygen species started in 1980. Later, it was shown that reactive nitrogen species could also modify proteins. Some protein oxidative modifications promote loss of protein function, cleavage or aggregation, and some result in proteo-toxicity and cellular homeostasis disruption. Recent Advances: Previously, protein oxidation was associated exclusively to damage. However, not all oxidative modifications are necessarily associated with damage, as with Met and Cys protein residue oxidation. In these cases, redox state changes can alter protein structure, catalytic function, and signaling processes in response to metabolic and/or environmental alterations. This review aims to integrate the present knowledge on redox modifications of proteins with their fate and role in redox signaling and human pathological conditions. Critical Issues: It is hypothesized that protein oxidation participates in the development and progression of many pathological conditions. However, no quantitative data have been correlated with specific oxidized proteins or the progression or severity of pathological conditions. Hence, the comprehension of the mechanisms underlying these modifications, their importance in human pathologies, and the fate of the modified proteins is of clinical relevance. Future Directions: We discuss new tools to cope with protein oxidation and suggest new approaches for integrating knowledge about protein oxidation and redox processes with human pathophysiological conditions. Antioxid. Redox Signal. 35, 1016-1080.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Etelvino J H Bechara
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Renata N Bicev
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda M Cerqueira
- CENTD, Centre of Excellence in New Target Discovery, Instituto Butantan, São Paulo, Brazil
| | - Fernanda M da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Denicola
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Fernando Gomes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lía M Randall
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Cassius V Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Leonor Thomson
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
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Kimmel J, Kehrer J, Frischknecht F, Spielmann T. Proximity-dependent biotinylation approaches to study apicomplexan biology. Mol Microbiol 2021; 117:553-568. [PMID: 34587292 DOI: 10.1111/mmi.14815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
In the last 10 years, proximity-dependent biotinylation (PDB) techniques greatly expanded the ability to study protein environments in the living cell that range from specific protein complexes to entire compartments. This is achieved by using enzymes such as BirA* and APEX that are fused to proteins of interest and biotinylate proteins in their proximity. PDB techniques are now also increasingly used in apicomplexan parasites. In this review, we first give an overview of the main PDB approaches and how they compare with other techniques that address similar questions. PDB is particularly valuable to detect weak or transient protein associations under physiological conditions and to study cellular structures that are difficult to purify or have a poorly understood protein composition. We also highlight new developments such as novel smaller or faster-acting enzyme variants and conditional PDB approaches, providing improvements in both temporal and spatial resolution which may offer broader application possibilities useful in apicomplexan research. In the second part, we review work using PDB techniques in apicomplexan parasites and how this expanded our knowledge about these medically important parasites.
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Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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6
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Zapatero-Belinchón FJ, Carriquí-Madroñal B, Gerold G. Proximity labeling approaches to study protein complexes during virus infection. Adv Virus Res 2021; 109:63-104. [PMID: 33934830 DOI: 10.1016/bs.aivir.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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7
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Paviani V, Junqueira de Melo P, Avakin A, Di Mascio P, Ronsein GE, Augusto O. Human cataractous lenses contain cross-links produced by crystallin-derived tryptophanyl and tyrosyl radicals. Free Radic Biol Med 2020; 160:356-367. [PMID: 32858158 DOI: 10.1016/j.freeradbiomed.2020.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/19/2020] [Indexed: 01/13/2023]
Abstract
Protein insolubilization, cross-linking and aggregation are considered critical to the development of lens opacity in cataract. However, the information about the presence of cross-links other than disulfides in cataractous lenses is limited. A potential role for cross-links produced from tryptophanyl radicals in cataract development is suggested by the abundance of the UV light-sensitive Trp residues in crystallin proteins. Here we developed a LC-MS/MS approach to examine the presence of Trp-Trp, Trp-Tyr and Tyr-Tyr cross-links and of peptides containing Trp-2H (-2.0156 Da) in the lens of three patients diagnosed with advanced nuclear cataract. In the proteins of two of the lenses, we characterized intermolecular cross-links between βB2-Tyr153-Tyr104-βA3 and βB2-Trp150-Tyr139-βS. An additional intermolecular cross-link (βB2-Tyr61-Trp200-βB3) was present in the lens of the oldest patient. In the proteins of all three lenses, we characterized two intramolecular Trp-Trp cross-links (Trp123-Trp126 in βB1 and Trp81-Trp84 in βB2) and six peptides containing Trp -2H residues, which indicate the presence of additional Trp-Trp cross-links. Relevantly, we showed that similar cross-links and peptides with modified Trp-2H residues are produced in a time-dependent manner in bovine β-crystallin irradiated with a solar simulator. Therefore, different crystallin proteins cross-linked by crystalline-derived tryptophanyl and tyrosyl radicals are present in advanced nuclear cataract lenses and similar protein modifications can be promoted by solar irradiation even in the absence of photosensitizers. Overall, the results indicate that a role for Trp-Tyr and Trp-Trp cross-links in the development of human cataract is possible and deserves further investigation.
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Affiliation(s)
- Verônica Paviani
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-000, São Paulo, Brazil
| | - Paulo Junqueira de Melo
- Hospital Das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 255, 05403-000, São Paulo, Brazil
| | - Amaryllis Avakin
- Hospital Das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 255, 05403-000, São Paulo, Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-000, São Paulo, Brazil
| | - Graziella Eliza Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-000, São Paulo, Brazil.
| | - Ohara Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-000, São Paulo, Brazil.
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8
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Fuentes-Lemus E, Mariotti M, Reyes J, Leinisch F, Hägglund P, Silva E, Davies MJ, López-Alarcón C. Photo-oxidation of lysozyme triggered by riboflavin is O 2-dependent, occurs via mixed type 1 and type 2 pathways, and results in inactivation, site-specific damage and intra- and inter-molecular crosslinks. Free Radic Biol Med 2020; 152:61-73. [PMID: 32142879 DOI: 10.1016/j.freeradbiomed.2020.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 12/21/2022]
Abstract
Photosensitized protein oxidation is a promising tool for medical procedures such as photochemical tissue bonding (PTB). We have recently reported that the binding of rose Bengal, a sensitizer employed in PTB, to lysozyme modulates the photooxidation and crosslinking of this protein. In this work we examined the photooxidation and crosslinking of lysozyme mediated by riboflavin (RF) an endogenous sensitizer also employed in PTB. We hypothesized that since RF does not bind strongly to proteins, the mechanism(s) and extent of enzymatic inactivation, amino acid modification and protein crosslinking would be dependent on the presence of O2, and differ to that induced by rose Bengal. This hypothesis was tested using UV-visible spectrophotometry, isothermal titration calorimetry (ITC), SDS-PAGE gels, quantification of amino acid consumption, and LC-MS analysis of sites of modification and crosslinks. Under N2, limited damage was detected arising from type 1 (radical) chemistry with formation of specific intra- (Tyr20-Tyr23) and inter- (Tyr23-Trp108) molecular crosslinks. In contrast, the presence of O2 triggered extensive protein damage through mixed type 1 and type 2 (1O2) mechanisms leading to Trp, Met, Tyr and His oxidation, loss of enzymatic activity and protein dimerization. LC-MS analysis provided evidence for crosslinking via radical-radical recombination reactions (Trp28-Tyr53), and secondary reactions involving nucleophilic attack of the side-chain amine of Lys116 on carbonyl groups. Overall, this behavior is in marked contrast to that detected with rose Bengal indicating that the mechanisms and sites of photo-oxidative damage, and consequences for protein function, can be modulated by the choice of sensitizing dye.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Pontificia Universidad Católica de Chile(,) Facultad de Química, Departamento de Química Física, Santiago, Chile
| | - Michele Mariotti
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Juan Reyes
- Pontificia Universidad Católica de Chile(,) Facultad de Química, Departamento de Química Física, Santiago, Chile
| | - Fabian Leinisch
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Per Hägglund
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Eduardo Silva
- Pontificia Universidad Católica de Chile(,) Facultad de Química, Departamento de Química Física, Santiago, Chile
| | - Michael J Davies
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark.
| | - Camilo López-Alarcón
- Pontificia Universidad Católica de Chile(,) Facultad de Química, Departamento de Química Física, Santiago, Chile.
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9
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Figueroa JD, Zárate AM, Fuentes-Lemus E, Davies MJ, López-Alarcón C. Formation and characterization of crosslinks, including Tyr–Trp species, on one electron oxidation of free Tyr and Trp residues by carbonate radical anion. RSC Adv 2020; 10:25786-25800. [PMID: 35518626 PMCID: PMC9055361 DOI: 10.1039/d0ra04051g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/28/2020] [Indexed: 01/04/2023] Open
Abstract
Dityrosine and ditryptophan bonds have been implied in protein crosslinking. This is associated with oxidative stress conditions including those involved in neurodegenerative pathologies and age-related processes. Formation of dityrosine and ditryptophan derives from radical–radical reactions involving Tyr˙ and Trp˙ radicals. However, cross reactions of Tyr˙ and Trp˙ leading to Tyr–Trp crosslinks and their biological consequences have been less explored. In the present work we hypothesized that exposure of free Tyr and Trp to a high concentration of carbonate anion radicals (CO3˙−), under anaerobic conditions, would result in the formation of Tyr–Trp species, as well as dityrosine and ditryptophan crosslinks. Here we report a simple experimental procedure, employing CO3˙− generated photochemically by illumination of a Co(iii) complex at 254 nm, that produces micromolar concentrations of Tyr–Trp crosslinks. Analysis by mass spectrometry of solutions containing only the individual amino acids, and the Co(iii) complex, provided evidence for the formation of o,o′-dityrosine and isodityrosine from Tyr, and three ditryptophan dimers from Trp. When mixtures of Tyr and Trp were illuminated in an identical manner, Tyr–Trp crosslinks were detected together with dityrosine and ditryptophan dimers. These results indicate that there is a balance between the formation of these three classes of crosslinks, which is dependent on the Tyr and Trp concentrations. The methods reported here allow the generation of significant yields of isolated Tyr–Trp adducts and their characterization. This technology should facilitate the detection, and examination of the biological consequences of Tyr–Trp crosslink formation in complex systems in future investigations. Exposure of free Tyr and Trp to a high concentration of carbonate anion radicals (CO3˙−), under anaerobic conditions, result in the formation of Tyr–Trp species, as well as dityrosine and ditryptophan crosslinks.![]()
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Affiliation(s)
- Juan David Figueroa
- Pontificia Universidad Católica de Chile, Facultad de Química y de Farmacia
- Departamento de Química Física
- Santiago
- Chile
| | - Ana María Zárate
- Pontificia Universidad Católica de Chile, Facultad de Química y de Farmacia
- Departamento de Química Física
- Santiago
- Chile
| | - Eduardo Fuentes-Lemus
- Pontificia Universidad Católica de Chile, Facultad de Química y de Farmacia
- Departamento de Química Física
- Santiago
- Chile
| | - Michael J. Davies
- University of Copenhagen
- Department of Biomedical Sciences
- Copenhagen
- Denmark
| | - Camilo López-Alarcón
- Pontificia Universidad Católica de Chile, Facultad de Química y de Farmacia
- Departamento de Química Física
- Santiago
- Chile
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10
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Hägglund P, Mariotti M, Davies MJ. Identification and characterization of protein cross-links induced by oxidative reactions. Expert Rev Proteomics 2018; 15:665-681. [DOI: 10.1080/14789450.2018.1509710] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
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11
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Mariotti M, Leinisch F, Leeming DJ, Svensson B, Davies MJ, Hägglund P. Mass-Spectrometry-Based Identification of Cross-Links in Proteins Exposed to Photo-Oxidation and Peroxyl Radicals Using 18O Labeling and Optimized Tandem Mass Spectrometry Fragmentation. J Proteome Res 2018; 17:2017-2027. [DOI: 10.1021/acs.jproteome.7b00881] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
| | - Fabian Leinisch
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
| | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
| | - Per Hägglund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
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12
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Nicolussi A, Auer M, Sevcnikar B, Paumann-Page M, Pfanzagl V, Zámocký M, Hofbauer S, Furtmüller PG, Obinger C. Posttranslational modification of heme in peroxidases – Impact on structure and catalysis. Arch Biochem Biophys 2018; 643:14-23. [DOI: 10.1016/j.abb.2018.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/16/2022]
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13
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Leinisch F, Mariotti M, Rykaer M, Lopez-Alarcon C, Hägglund P, Davies MJ. Peroxyl radical- and photo-oxidation of glucose 6-phosphate dehydrogenase generates cross-links and functional changes via oxidation of tyrosine and tryptophan residues. Free Radic Biol Med 2017; 112:240-252. [PMID: 28756310 DOI: 10.1016/j.freeradbiomed.2017.07.025] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/11/2017] [Accepted: 07/25/2017] [Indexed: 02/05/2023]
Abstract
Protein oxidation is a frequent event as a result of the high abundance of proteins in biological samples and the multiple processes that generate oxidants. The reactions that occur are complex and poorly understood, but can generate major structural and functional changes on proteins. Current data indicate that pathophysiological processes and multiple human diseases are associated with the accumulation of damaged proteins. In this study we investigated the mechanisms and consequences of exposure of the key metabolic enzyme glucose-6-phosphate dehydrogenase (G6PDH) to peroxyl radicals (ROO•) and singlet oxygen (1O2), with particular emphasis on the role of Trp and Tyr residues in protein cross-linking and fragmentation. Cross-links and high molecular mass aggregates were detected by SDS-PAGE and Western blotting using specific antibodies. Amino acid analysis has provided evidence for Trp and Tyr consumption and formation of oxygenated products (diols, peroxides, N-formylkynurenine, kynurenine) from Trp, and di-tyrosine (from Tyr). Mass spectrometric data obtained after trypsin-digestion in the presence of H216O and H218O, has allowed the mapping of specific cross-linked residues and their locations. These data indicate that specific Tyr-Trp and di-Tyr cross-links are formed from residues that are proximal and surface-accessible, and that the extent of Trp oxidation varies markedly between sites. Limited modification at other residues is also detected. These data indicate that Trp and Tyr residues are readily modified by ROO• and 1O2 with this giving products that impact significantly on protein structure and function. The formation of such cross-links may help rationalize the accumulation of damaged proteins in vivo.
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Affiliation(s)
- Fabian Leinisch
- Dept. of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin Rykaer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Camilo Lopez-Alarcon
- Departamento de Química Física, Facultad de Química, Pontificia Universidad Catolica de Chile, Avda. Vicuña Mackenna 4860, Santiago, Chile
| | - Per Hägglund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael J Davies
- Dept. of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark.
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14
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Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nat Protoc 2016; 11:456-75. [PMID: 26866790 DOI: 10.1038/nprot.2016.018] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This protocol describes a method to obtain spatially resolved proteomic maps of specific compartments within living mammalian cells. An engineered peroxidase, APEX2, is genetically targeted to a cellular region of interest. Upon the addition of hydrogen peroxide for 1 min to cells preloaded with a biotin-phenol substrate, APEX2 generates biotin-phenoxyl radicals that covalently tag proximal endogenous proteins. Cells are then lysed, and biotinylated proteins are enriched with streptavidin beads and identified by mass spectrometry. We describe the generation of an appropriate APEX2 fusion construct, proteomic sample preparation, and mass spectrometric data acquisition and analysis. A two-state stable isotope labeling by amino acids in cell culture (SILAC) protocol is used for proteomic mapping of membrane-enclosed cellular compartments from which APEX2-generated biotin-phenoxyl radicals cannot escape. For mapping of open cellular regions, we instead use a 'ratiometric' three-state SILAC protocol for high spatial specificity. Isotopic labeling of proteins takes 5-7 cell doublings. Generation of the biotinylated proteomic sample takes 1 d, acquiring the mass spectrometric data takes 2-5 d and analysis of the data to obtain the final proteomic list takes 1 week.
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15
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Kruft BI, Magliozzo RS, Jarzęcki AA. Density Functional Theory Insights into the Role of the Methionine–Tyrosine–Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate. J Phys Chem A 2015; 119:6850-66. [DOI: 10.1021/jp511358p] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bonnie I. Kruft
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Andrzej A. Jarzęcki
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
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16
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Chreifi G, Hollingsworth SA, Li H, Tripathi S, Arce AP, Magaña-Garcia HI, Poulos TL. Enzymatic Mechanism of Leishmania major Peroxidase and the Critical Role of Specific Ionic Interactions. Biochemistry 2015; 54:3328-36. [PMID: 25941976 DOI: 10.1021/acs.biochem.5b00338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leishmania major peroxidase (LmP) is very similar to the well-known yeast cytochrome c peroxidase (CcP). Both enzymes catalyze the peroxidation of cytochrome c. Like CcP, LmP reacts with H2O2 to form Compound I, which consists of a ferryl heme and a Trp radical, Fe(IV)═O;Trp(•+). Cytochrome c (Cytc) reduces the Trp radical to give Compound II, Fe(IV)═O;Trp, which is followed by an intramolecular electron transfer to give Fe(III)-OH;Trp(•+), and in the last step, Cytc reduces the Trp radical. In this study, we have used steady-state and single-turnover kinetics to improve our understanding of the overall mechanism of LmP catalysis. While the activity of CcP greatly increases with ionic strength, the kcat for LmP remains relatively constant at all ionic strengths tested. Therefore, unlike CcP, where dissociation of oxidized Cytc is limiting at low ionic strengths, association/dissociation reactions are not limiting at any ionic strength in LmP. We conclude that in LmP, the intramolecular electron transfer reaction, Fe(IV)═O;Trp to Fe(III)-OH;Trp(•+), is limiting at all ionic strengths. Unlike CcP, LmP depends on key intermolecular ion pairs to form the electron transfer competent complex. Mutating these sites causes the initial rate of association to decrease by 2 orders of magnitude and a substantial decrease in kcat. The drop in kcat is due to a switch in the rate-limiting step of the mutants from intramolecular electron transfer to the rate of association in forming the LmP-LmCytc complex. These studies show that while LmP and CcP form very similar complexes and exhibit similar activities, they substantially differ in how their activity changes as a function of ionic strength. This difference is primarily due to the heavy reliance of LmP on highly specific intermolecular ion pairs, while CcP relies mainly on nonpolar interactions.
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Affiliation(s)
- Georges Chreifi
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Scott A Hollingsworth
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Huiying Li
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Sarvind Tripathi
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Anton P Arce
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Hugo I Magaña-Garcia
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- †Department of Molecular Biology and Biochemistry, ‡Department of Chemistry, and §Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
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17
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Miner KD, Pfister TD, Hosseinzadeh P, Karaduman N, Donald LJ, Loewen PC, Lu Y, Ivancich A. Identifying the elusive sites of tyrosyl radicals in cytochrome c peroxidase: implications for oxidation of substrates bound at a site remote from the heme. Biochemistry 2014; 53:3781-9. [PMID: 24901481 PMCID: PMC4063442 DOI: 10.1021/bi500353p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The location of the Trp radical and the catalytic function of the [Fe(IV)═O Trp₁₉₁(•+)] intermediate in cytochrome c peroxidase (CcP) are well-established; however, the unambiguous identification of the site(s) for the formation of tyrosyl radical(s) and their possible biological roles remain elusive. We have now performed a systematic investigation of the location and reactivity of the Tyr radical(s) using multifrequency Electron Paramagnetic Resonance (EPR) spectroscopy combined with multiple-site Trp/Tyr mutations in CcP. Two tyrosines, Tyr71 and Tyr236, were identified as those contributing primarily to the EPR spectrum of the tyrosyl radical, recorded at 9 and 285 GHz. The EPR characterization also showed that the heme distal-side Trp51 is involved in the intramolecular electron transfer between Tyr71 and the heme and that formation of Tyr₇₁(•) and Tyr₂₃₆(•) is independent of the [Fe(IV)═O Trp₁₉₁(•+)] intermediate. Tyr71 is located in an optimal position to mediate the oxidation of substrates binding at a site, more than 20 Å from the heme, which has been reported recently in the crystal structures of CcP with bound guaicol and phenol [Murphy, E. J., et al. (2012) FEBS J. 279, 1632-1639]. The possibility of discriminating the radical intermediates by their EPR spectra allowed us to identify Tyr₇₁(•) as the reactive species with the guaiacol substrate. Our assignment of the surface-exposed Tyr236 as the other radical site agrees well with previous studies based on MNP labeling and protein cross-linking [Tsaprailis, G., and English, A. M. (2003) JBIC, J. Biol. Inorg. Chem. 8, 248-255] and on its covalent modification upon reaction of W191G CcP with 2-aminotriazole [Musah, R. A., and Goodin, D. B. (1997) Biochemistry 36, 11665-11674]. Accordingly, while Tyr71 acts as a true reactive intermediate for the oxidation of certain small substrates that bind at a site remote from the heme, the surface-exposed Tyr236 would be more likely related to oxidative stress signaling, as previously proposed. Our findings reinforce the view that CcP is the monofunctional peroxidase that most closely resembles its ancestor enzymes, the catalase-peroxidases, in terms of the higher complexity of the peroxidase reaction [Colin, J., et al. (2009) J. Am. Chem. Soc. 131, 8557-8563]. The strategy used to identify the elusive Tyr radical sites in CcP may be applied to other heme enzymes containing a large number of Tyr and Trp residues and for which Tyr (or Trp) radicals have been proposed to be involved in their peroxidase or peroxidase-like reaction.
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Affiliation(s)
- Kyle D Miner
- CNRS, Unité de Recherche Mixte CNRS/CEA/Université Paris-Sud (UMR 8221), Laboratoire de Bioénergétique, Métalloprotéines et Stress. Centre d'Etudes de Saclay, iBiTec-S, 91191 Gif-sur-Yvette, France
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18
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Ravikiran B, Mahalakshmi R. Unusual post-translational protein modifications: the benefits of sophistication. RSC Adv 2014. [DOI: 10.1039/c4ra04694c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review summarizes the “seemingly bizarre”, yet naturally occurring, covalent non-disulphide cross-links in enzymatic and scaffolding proteins and their functions.
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Affiliation(s)
- Boddepalli Ravikiran
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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19
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Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 2013; 339:1328-1331. [PMID: 23371551 DOI: 10.1126/science.1230593] [Citation(s) in RCA: 875] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microscopy and mass spectrometry (MS) are complementary techniques: The former provides spatiotemporal information in living cells, but only for a handful of recombinant proteins at a time, whereas the latter can detect thousands of endogenous proteins simultaneously, but only in lysed samples. Here, we introduce technology that combines these strengths by offering spatially and temporally resolved proteomic maps of endogenous proteins within living cells. Our method relies on a genetically targetable peroxidase enzyme that biotinylates nearby proteins, which are subsequently purified and identified by MS. We used this approach to identify 495 proteins within the human mitochondrial matrix, including 31 not previously linked to mitochondria. The labeling was exceptionally specific and distinguished between inner membrane proteins facing the matrix versus the intermembrane space (IMS). Several proteins previously thought to reside in the IMS or outer membrane, including protoporphyrinogen oxidase, were reassigned to the matrix by our proteomic data and confirmed by electron microscopy. The specificity of peroxidase-mediated proteomic mapping in live cells, combined with its ease of use, offers biologists a powerful tool for understanding the molecular composition of living cells.
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Affiliation(s)
- Hyun-Woo Rhee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peng Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Jeffrey D Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Molecular Biology, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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20
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Estey T, Chen Y, Carpenter JF, Vasiliou V. Structural and functional modifications of corneal crystallin ALDH3A1 by UVB light. PLoS One 2010; 5:e15218. [PMID: 21203538 PMCID: PMC3006428 DOI: 10.1371/journal.pone.0015218] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 10/29/2010] [Indexed: 11/18/2022] Open
Abstract
As one of the most abundantly expressed proteins in the mammalian corneal epithelium, aldehyde dehydrogenase 3A1 (ALDH3A1) plays critical and multifaceted roles in protecting the cornea from oxidative stress. Recent studies have demonstrated that one protective mechanism of ALDH3A1 is the direct absorption of UV-energy, which reduces damage to other corneal proteins such as glucose-6-phosphate dehydrogenase through a competition mechanism. UV-exposure, however, leads to the inactivation of ALDH3A1 in such cases. In the current study, we demonstrate that UV-light caused soluble, non-native aggregation of ALDH3A1 due to both covalent and non-covalent interactions, and that the formation of the aggregates was responsible for the loss of ALDH3A1 enzymatic activity. Spectroscopic studies revealed that as a result of aggregation, the secondary and tertiary structure of ALDH3A1 were perturbed. LysC peptide mapping using MALDI-TOF mass spectrometry shows that UV-induced damage to ALDH3A1 also includes chemical modifications to Trp, Met, and Cys residues. Surprisingly, the conserved active site Cys of ALDH3A1 does not appear to be affected by UV-exposure; this residue remained intact after exposure to UV-light that rendered the enzyme completely inactive. Collectively, our data suggest that the UV-induced inactivation of ALDH3A1 is a result of non-native aggregation and associated structural changes rather than specific damage to the active site Cys.
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Affiliation(s)
- Tia Estey
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Ying Chen
- Molecular Toxicology & Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - John F. Carpenter
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Vasilis Vasiliou
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
- Molecular Toxicology & Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
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21
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Abu Tarboush N, Jensen LMR, Feng M, Tachikawa H, Wilmot CM, Davidson VL. Functional importance of tyrosine 294 and the catalytic selectivity for the bis-Fe(IV) state of MauG revealed by replacement of this axial heme ligand with histidine . Biochemistry 2010; 49:9783-91. [PMID: 20929212 DOI: 10.1021/bi101254p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diheme enzyme MauG catalyzes the posttranslational modification of a precursor protein of methylamine dehydrogenase (preMADH) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. It catalyzes three sequential two-electron oxidation reactions which proceed through a high-valent bis-Fe(IV) redox state. Tyr294, the unusual distal axial ligand of one c-type heme, was mutated to His, and the crystal structure of Y294H MauG in complex with preMADH reveals that this heme now has His-His axial ligation. Y294H MauG is able to interact with preMADH and participate in interprotein electron transfer, but it is unable to catalyze the TTQ biosynthesis reactions that require the bis-Fe(IV) state. This mutation affects not only the redox properties of the six-coordinate heme but also the redox and CO-binding properties of the five-coordinate heme, despite the 21 Å separation of the heme iron centers. This highlights the communication between the hemes which in wild-type MauG behave as a single diheme unit. Spectroscopic data suggest that Y294H MauG can stabilize a high-valent redox state equivalent to Fe(V), but it appears to be an Fe(IV)═O/π radical at the five-coordinate heme rather than the bis-Fe(IV) state. This compound I-like intermediate does not catalyze TTQ biosynthesis, demonstrating that the bis-Fe(IV) state, which is stabilized by Tyr294, is specifically required for this reaction. The TTQ biosynthetic reactions catalyzed by wild-type MauG do not occur via direct contact with the Fe(IV)═O heme but via long-range electron transfer through the six-coordinate heme. Thus, a critical feature of the bis-Fe(IV) species may be that it shortens the electron transfer distance from preMADH to a high-valent heme iron.
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Affiliation(s)
- Nafez Abu Tarboush
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
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22
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Pipirou Z, Guallar V, Basran J, Metcalfe CL, Murphy EJ, Bottrill AR, Mistry SC, Raven EL. Peroxide-Dependent Formation of a Covalent Link between Trp51 and the Heme in Cytochrome c Peroxidase. Biochemistry 2009; 48:3593-9. [DOI: 10.1021/bi802210g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zoi Pipirou
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Victor Guallar
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Jaswir Basran
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Clive L. Metcalfe
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Emma J. Murphy
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Andrew R. Bottrill
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Sharad C. Mistry
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Emma Lloyd Raven
- Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, England, ICREA, Life Science Department, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain, Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England, and Protein and Nucleic Acid Chemistry Laboratory, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
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Vidossich P, Alfonso-Prieto M, Carpena X, Loewen PC, Fita I, Rovira C. Versatility of the Electronic Structure of Compound I in Catalase-Peroxidases. J Am Chem Soc 2007; 129:13436-46. [DOI: 10.1021/ja072245i] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pietro Vidossich
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Xavi Carpena
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Peter C. Loewen
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Ignacio Fita
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Carme Rovira
- Contribution from the Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Institut de Biologia Molecular (IBMB-CSIC), Institut de Recerca Biomèdica (IRB), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain, Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada, Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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Pipirou Z, Bottrill AR, Metcalfe CM, Mistry SC, Badyal SK, Rawlings BJ, Raven EL. Autocatalytic formation of a covalent link between tryptophan 41 and the heme in ascorbate peroxidase. Biochemistry 2007; 46:2174-80. [PMID: 17263562 DOI: 10.1021/bi062274q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electronic spectroscopy, HPLC analyses, and mass spectrometry (MALDI-TOF and MS/MS) have been used to show that a covalent link from the heme to the distal Trp41 can occur on exposure of ascorbate peroxidase (APX) to H2O2 under noncatalytic conditions. Parallel analyses with the W41A variant and with APX reconstituted with deuteroheme clearly indicate that the covalent link does not form in the absence of either Trp41 or the heme vinyl groups. The presence of substrate also precludes formation of the link. Formation of a protein radical at Trp41 is implicated, in a reaction mechanism that is analogous to that proposed [Ghiladi, R. A., et al. (2005) Biochemistry 44, 15093-15105] for formation of a covalent Trp-Tyr-Met link in the closely related catalase peroxidase (KatG) enzymes. Collectively, the data suggest that radical formation at the distal tryptophan position is not an exclusive feature of the KatG enzymes and may be used more widely across other members of the class I heme peroxidase family.
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Affiliation(s)
- Zoi Pipirou
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, England
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25
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Ouellet H, Ranguelova K, Labarre M, Wittenberg JB, Wittenberg BA, Magliozzo RS, Guertin M. Reaction of Mycobacterium tuberculosis truncated hemoglobin O with hydrogen peroxide: evidence for peroxidatic activity and formation of protein-based radicals. J Biol Chem 2007; 282:7491-503. [PMID: 17218317 DOI: 10.1074/jbc.m609155200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, we investigated the reaction of ferric Mycobacterium tuberculosis truncated hemoglobin O (trHbO) with hydrogen peroxide. Stopped-flow spectrophotometric experiments under single turnover conditions showed that trHbO reacts with H(2)O(2) to give transient intermediate(s), among which is an oxyferryl heme, different from a typical peroxidase Compound I (oxyferryl heme pi-cation radical). EPR spectroscopy indicated evidence for both tryptophanyl and tyrosyl radicals, whereas redox titrations demonstrated that the peroxide-treated protein product retains 2 oxidizing eq. We propose that Compound I formed transiently is reduced with concomitant oxidation of Trp(G8) to give the detected oxoferryl heme and a radical on Trp(G8) (detected by EPR of the trHbO Tyr(CD1)Phe mutant). In the wild-type protein, the Trp(G8) radical is in turn reduced rapidly by Tyr(CD1). In a second cycle, Trp(G8) may be reoxidized by the ferryl heme to yield ferric heme and two protein radicals. In turn, these migrate to form tyrosyl radicals on Tyr(55) and Tyr(115), which lead, in the absence of a reducing substrate, to oligomerization of the protein. Steady-state kinetics in the presence of H(2)O(2) and the one-electron donor 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) indicated that trHbO has peroxidase activity, in accord with the presence of typical peroxidase intermediates. These findings suggest an oxidation/reduction function for trHbO and, by analogy, for other Group II trHbs.
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Affiliation(s)
- Hugues Ouellet
- Department of Biochemistry and Microbiology, Laval University, Quebec G1K 7P4, Canada
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26
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Ranguelova K, Girotto S, Gerfen GJ, Yu S, Suarez J, Metlitsky L, Magliozzo RS. Radical sites in Mycobacterium tuberculosis KatG identified using electron paramagnetic resonance spectroscopy, the three-dimensional crystal structure, and electron transfer couplings. J Biol Chem 2007; 282:6255-64. [PMID: 17204474 PMCID: PMC1885898 DOI: 10.1074/jbc.m607309200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidase (KatG) from Mycobacterium tuberculosis, a Class I peroxidase, exhibits high catalase activity and peroxidase activity with various substrates and is responsible for activation of the commonly used antitubercular drug, isoniazid (INH). KatG readily forms amino acid-based radicals during turnover with alkyl peroxides, and this work focuses on extending the identification and characterization of radicals forming on the millisecond to second time scale. Rapid freeze-quench electron paramagnetic resonance spectroscopy (RFQ-EPR) reveals a change in the structure of the initially formed radical in the presence of INH. Heme pocket binding of the drug and knowledge that KatG[Y229F] lacks this signal provides evidence for radical formation on residue Tyr(229). High field RFQ-EPR spectroscopy confirmed a tryptophanyl radical signal, and new analyses of X-band RFQ-EPR spectra also established its presence. High field EPR spectroscopy also confirmed that the majority radical species is a tyrosyl radical. Site-directed mutagenesis, along with simulations of EPR spectra based on x-ray structural data for particular tyrosine and tryptophan residues, enabled assignments based on predicted hyperfine coupling parameters. KatG mutants W107F, Y229F, and the double mutant W107F/Y229F showed alteration in type and yield of radical species. Results are consistent with formation of a tyrosyl radical reasonably assigned to residue Tyr(229) within the first few milliseconds of turnover. This is followed by a mixture of tyrosyl and tryptophanyl radical species and finally to only a tyrosyl radical on residue Tyr(353), which lies more distant from the heme. The radical processing of enzyme lacking the Trp(107)-Tyr(229)-Met(255) adduct (found as a unique structural feature of catalase-peroxidases) is suggested to be a reasonable assignment of the phenomena.
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Affiliation(s)
- Kalina Ranguelova
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Stefania Girotto
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Gary J. Gerfen
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Shengwei Yu
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Javier Suarez
- Department of Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
| | - Leonid Metlitsky
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
- Department of Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
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27
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Kapetanaki SM, Zhao X, Yu S, Magliozzo RS, Schelvis JPM. Modification of the active site of Mycobacterium tuberculosis KatG after disruption of the Met-Tyr-Trp cross-linked adduct. J Inorg Biochem 2006; 101:422-33. [PMID: 17188362 PMCID: PMC1885897 DOI: 10.1016/j.jinorgbio.2006.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 11/01/2006] [Accepted: 11/02/2006] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis catalase-peroxidase (Mtb KatG) is a bifunctional enzyme that possesses both catalase and peroxidase activities and is responsible for the activation of the antituberculosis drug isoniazid. Mtb KatG contains an unusual adduct in its distal heme-pocket that consists of the covalently linked Trp107, Tyr229, and Met255. The KatG(Y229F) mutant lacks this adduct and has decreased steady-state catalase activity and enhanced peroxidase activity. In order to test a potential structural role of the adduct that supports catalase activity, we have used resonance Raman spectroscopy to probe the local heme environment of KatG(Y229F). In comparison to wild-type KatG, resting KatG(Y229F) contains a significant amount of 6-coordinate, low-spin heme and a more planar heme. Resonance Raman spectroscopy of the ferrous-CO complex of KatG(Y229F) suggest a non-linear Fe-CO binding geometry that is less tilted than in wild-type KatG. These data provide evidence that the Met-Tyr-Trp adduct imparts structural stability to the active site of KatG that seems to be important for sustaining catalase activity.
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Affiliation(s)
- Sofia M. Kapetanaki
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003
| | - Xiangbo Zhao
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210-2889
| | - Shengwei Yu
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210-2889
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210-2889
| | - Johannes P. M. Schelvis
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003
- *Corresponding author. Tel.: +1 212 998 3597; fax: +1 212 260 7905. E-mail address:
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28
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Carpena X, Wiseman B, Deemagarn T, Singh R, Switala J, Ivancich A, Fita I, Loewen PC. A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases. EMBO Rep 2006; 6:1156-62. [PMID: 16211084 PMCID: PMC1369206 DOI: 10.1038/sj.embor.7400550] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/29/2005] [Accepted: 09/09/2005] [Indexed: 11/08/2022] Open
Abstract
The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidation and one that activates oxoferryl heme reduction by H(2)O(2), facilitating the catalatic pathway in a peroxidase. The influence of the arginine is imparted to the heme through its association with or dissociation from a tyrosinate that modulates reactivity through a Met-Tyr-Trp crosslinked adduct and a pi electron interaction of the heme with the adduct Trp.
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Affiliation(s)
- Xavier Carpena
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Ben Wiseman
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Rahul Singh
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Anabella Ivancich
- Service de Bioénergétique, URA 2096 CNRS, Département de Biologie Joliot-Curie, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Ignacio Fita
- Departament de Biologia Estructural (IBMB-CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Peter C Loewen
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
- Tel: +1 204 474 8334; Fax: +1 204 474 7603; E-mail:
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29
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Pettigrew GW, Echalier A, Pauleta SR. Structure and mechanism in the bacterial dihaem cytochrome c peroxidases. J Inorg Biochem 2006; 100:551-67. [PMID: 16434100 DOI: 10.1016/j.jinorgbio.2005.12.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 12/13/2005] [Indexed: 11/21/2022]
Abstract
The bacterial cytochrome c peroxidases contain an electron-transferring haem c (E) and a peroxidatic haem c (P). Many are isolated in an inactive oxidised state. Reduction of the E haem promotes Ca(2+)-dependent spin state and coordination changes at the P haem rendering it accessible to ligand. Recent crystallographic work on the oxidised and mixed valence enzymes has suggested a mechanism by which an electron entering the E haem remotely triggers this activation of the P haem. Binding of hydrogen peroxide at the activated P haem leads to an intermediate catalytic form containing two oxidising equivalents, one of which is a ferryl oxene. This form of the enzyme is then reduced by two single electron transfers to the E haem delivered by small redox proteins such as cytochromes or cupredoxins. The binding of these small redox proteins is dominated by global electrostatic forces but the interfaces of the electron transfer complexes that are formed are largely hydrophobic and relatively non-specific. These features allow very high electron transfer rates in the steady state.
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Affiliation(s)
- Graham W Pettigrew
- Division of Veterinary Biomedical Sciences, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.
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30
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Ghiladi RA, Medzihradszky KF, Ortiz de Montellano PR. Role of the Met−Tyr−Trp Cross-Link in Mycobacterium tuberculosis Catalase-Peroxidase (KatG) As Revealed by KatG(M255I). Biochemistry 2005; 44:15093-105. [PMID: 16285713 DOI: 10.1021/bi051463q] [Citation(s) in RCA: 35] [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
Catalase-peroxidases (KatGs) are bifunctional enzymes possessing both catalase and peroxidase activities. Four crystal structures of different KatGs revealed the presence of a novel Met-Tyr-Trp cross-link which has been suggested to impart catalatic activity to the KatGs. To decipher the individual roles of the two cross-links in the Met-Tyr-Trp adduct, we have focused on recombinant Mycobacterium tuberculosis KatG(M255I). UV-visible spectroscopic and mass spectrometric studies of the peptide fragments resulting from tryptic digestion of KatG(M255I) confirmed the presence of the single Tyr-Trp cross-link, as well as a 2e- oxidized form which is postulated to be an intermediate generated during Met-Tyr-Trp cross-link formation. KatG(M255I) lacking the Tyr-Trp cross-link was also prepared, and incubation with peroxyacetic acid, but not 2-methyl-1-phenyl-2-propyl hydroperoxide, resulted in complete formation of the Tyr-Trp cross-link. A mechanism for Tyr-Trp autocatalytic formation by KatG compound I is proposed from these studies. Optical stopped-flow studies with KatG(M255I) were performed, allowing characterization of compounds I, II, and III. Interestingly, two compound II intermediates were identified: (KatG*)(Por)Fe(III)-OH, where KatG* represents a protein-based radical, and oxoferryl (KatG)(Por)Fe(IV)=O. Insight into the contributions of the individual Tyr-Trp and Met-Tyr cross-links to catalase activity is presented, as is the overall contribution of the Met-Tyr-Trp cross-link to the structure-function-spectroscopy relationship and catalase-peroxidase mechanism in KatG.
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Affiliation(s)
- Reza A Ghiladi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2280, USA
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31
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Ghiladi RA, Knudsen GM, Medzihradszky KF, Ortiz de Montellano PR. The Met-Tyr-Trp Cross-link in Mycobacterium tuberculosis Catalase-peroxidase (KatG). J Biol Chem 2005; 280:22651-63. [PMID: 15840564 DOI: 10.1074/jbc.m502486200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidases (KatG) are bifunctional enzymes possessing both catalase and peroxidase activities. Three crystal structures of different KatGs revealed the presence of a novel Met-Tyr-Trp cross-link that has been suggested to impart catalatic activity to the KatGs. High-performance liquid chromatographic separation of the peptide fragments resulting from tryptic digestion of recombinant Mycobacterium tuberculosis WT KatG identified a peptide with unusual UV-visible spectroscopic features attributable to the Met(255)-Tyr(229)-Trp(107) cross-link, whose structure was confirmed by mass spectrometry. WT KatG lacking the Met-Tyr-Trp cross-link was prepared, making possible studies of its formation under oxidizing conditions that generate either compound I (peroxyacetic acid, PAA) or compound II (2-methyl-1-phenyl-2-propyl hydroperoxide, MPPH). Incubation of this "cross-link-free" WT KatG with PAA revealed complete formation of the Met-Tyr-Trp structure after six equivalents of peracid were added, whereas MPPH was unable to promote cross-link formation. A mechanism for Met-Tyr-Trp autocatalytic formation by KatG compound I is proposed from these studies. Optical stopped-flow studies of WT KatG and KatG(Y229F), a mutant in which the cross-link cannot be formed, were performed with MPPH and revealed an unusual compound II spectrum for WT KatG, best described as (P.)Fe(III), where P. represents a protein-based radical. This contrasts with the oxoferryl compound II spectrum observed for KatG(Y229F) under identical conditions. The structure-function-spectroscopy relationship in KatG is discussed with relevance to the role that the Met-Tyr-Trp cross-link plays in the catalase-peroxidase mechanism.
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Affiliation(s)
- Reza A Ghiladi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA
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32
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Swain MD, Benson DE. Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs. Proteins 2005; 59:64-71. [PMID: 15696544 DOI: 10.1002/prot.20403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-derived cofactors that are composed of covalently crosslinked amino acid side chains are of increasing importance in protein science. These crosslinked protein-derived cofactors (CPDC) are formed either through direct oxidation by metal/O(2)-derived intermediates or through outer sphere oxidation by highly oxidizing cofactors. CPDCs that are formed by outer sphere oxidation do not require side-chain precursors to be coordinated by a metal center, and therefore are more difficult to identify than those formed by direct oxidation. To better understand the propensity for CPDC formation by outer sphere oxidation, the geometrical preferences of CPDCs were examined. The Dezymer algorithm has been used to identify all putative CPDC-forming mutations in 500 proteins. Geometrically, although chemically unrelated, these CPDCs were found to be similar to disulfide-bonded cysteine pairs. Additionally, the percentage of near-sequence pairs (i and i +1 to i and i + 5) increased as the average C(alpha)-C(alpha) distance between the amino acid pairs increased. This survey also examined the protein databank for proteins with pre-attack conformations for CPDCs, using non-bonded contacts reported by Procheck. A total of 323 unique proteins was identified, with 55 being near-sequence amino acid pairs. The high geometric propensity of near-sequence amino acid pairs for forming CPDCs is significant due to difficulties associated with detection by structural or mass spectrometric methods.
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Affiliation(s)
- Marla D Swain
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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33
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Pfister TD, Ohki T, Ueno T, Hara I, Adachi S, Makino Y, Ueyama N, Lu Y, Watanabe Y. Monooxygenation of an aromatic ring by F43W/H64D/V68I myoglobin mutant and hydrogen peroxide. Myoglobin mutants as a model for P450 hydroxylation chemistry. J Biol Chem 2005; 280:12858-66. [PMID: 15664991 DOI: 10.1074/jbc.m410853200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myoglobin (Mb) is used as a model system for other heme proteins and the reactions they catalyze. The latest novel function to be proposed for myoglobin is a P450 type hydroxylation activity of aromatic carbons (Watanabe, Y., and Ueno, T. (2003) Bull. Chem. Soc. Jpn. 76, 1309-1322). Because Mb does not contain a specific substrate binding site for aromatic compounds near the heme, an engineered tryptophan in the heme pocket was used to model P450 hydroxylation of aromatic compounds. The monooxygenation product was not previously isolated because of rapid subsequent oxidation steps (Hara, I., Ueno, T., Ozaki, S., Itoh, S., Lee, K., Ueyama, N., and Watanabe, Y. (2001) J. Biol. Chem. 276, 36067-36070). In this work, a Mb variant (F43W/H64D/V68I) is used to characterize the monooxygenated intermediate. A modified (+16 Da) species forms upon the addition of 1 eq of H2O2. This product was digested with chymotrypsin, and the modified peptide fragments were isolated and characterized as 6-hydroxytryptophan using matrix-assisted laser desorption ionization time-of-flight tandem mass spectroscopy and 1H NMR. This engineered Mb variant represents the first enzyme to preferentially hydroxylate the indole side chain of Trp at the C6 position. Finally, heme extraction was used to demonstrate that both the formation of the 6-hydroxytryptophan intermediate (+16 Da) and subsequent oxidation to form the +30 Da final product are catalyzed by the heme cofactor, most probably via the compound I intermediate. These results provide insight into the mechanism of hydroxylation of aromatic carbons by heme proteins, demonstrating that non-thiolate-ligated heme enzymes can perform this function. This establishes Mb compound I as a model for P450 type aromatic hydroxylation chemistry.
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Affiliation(s)
- Thomas D Pfister
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61820, USA
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34
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Duroux-Richard I, Vassault P, Subra G, Guichou JF, Richard E, Mouillac B, Barberis C, Marie J, Bonnafous JC. Crosslinking Photosensitized by a Ruthenium Chelate as a Tool for Labeling and Topographical Studies of G-Protein-Coupled Receptors. ACTA ACUST UNITED AC 2005; 12:15-24. [PMID: 15664511 DOI: 10.1016/j.chembiol.2004.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 09/24/2004] [Accepted: 10/07/2004] [Indexed: 11/30/2022]
Abstract
The purpose was to apply oxidative crosslinking reactions to the study of recognition and signaling mechanisms associated to G-protein-coupled receptors. Using a ruthenium chelate, Ru(bipy)(3)(2+), as photosensitizer and visible light irradiation, in the presence of ammonium persulfate, we performed fast and efficient covalent labeling of the B(2) bradykinin receptor by agonist or antagonist ligands possessing a radio-iodinated phenol moiety. The chemical and topographical specificities of these crosslinking experiments were investigated. The strategy could also be applied to the covalent labeling of the B(1) bradykinin receptor, the AT(1) angiotensin II receptor, the V(1a) vasopressin receptor and the oxytocin receptor. Interestingly, we demonstrated the possibility to covalently label the AT(1) and B(2) receptors with functionalized ligands. The potential applications of metal-chelate chemistry to receptor structural and signaling studies through intramolecular or intermolecular crosslinking are presented.
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Affiliation(s)
- Isabelle Duroux-Richard
- Centre de Biochimie Stucturale, Centre National de la Recherche Scientifique, UMR 5048, Université Montpellier 1, Institut National de la Santé et de la Recherche Médicale, U 554, 29 rue de Navacelles, 34090 Montpellier Cedex, France
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35
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Jakopitsch C, Kolarich D, Petutschnig G, Furtmüller PG, Obinger C. Distal side tryptophan, tyrosine and methionine in catalase-peroxidases are covalently linked in solution. FEBS Lett 2003; 552:135-40. [PMID: 14527675 DOI: 10.1016/s0014-5793(03)00901-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Distal side tryptophan and tyrosine have been shown to be essential in the catalase but not the peroxidase activity of bifunctional catalase-peroxidases (KatGs). Recently published crystal structures suggest that both residues could be part of a novel adduct including in addition a conserved methionine. A mass spectrometric analysis of the tryptic peptides from recombinant wild-type Synechocystis KatG and the variants Trp122Phe, Tyr249Phe and Met275Ile confirms that this novel adduct really exists in solution and thus may be common to all KatGs. Exchange of either Trp122 or Tyr249 prevents cross-linking, whereas exchange of Met275 still allowed bond formation between Trp122 and Tyr249. It is proposed that the covalent bond between Trp and Tyr may form before that between Tyr and Met. The findings are discussed with respect to the mechanism of cross-linking and its role in KatG catalysis.
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Affiliation(s)
- Christa Jakopitsch
- Institute of Chemistry, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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