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Diamanti E, López-Gallego F. Single-Particle and Single-Molecule Characterization of Immobilized Enzymes: A Multiscale Path toward Optimizing Heterogeneous Biocatalysts. Angew Chem Int Ed Engl 2024; 63:e202319248. [PMID: 38476019 DOI: 10.1002/anie.202319248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Heterogeneous biocatalysis is highly relevant in biotechnology as it offers several benefits and practical uses. To leverage the full potential of heterogeneous biocatalysts, the establishment of well-crafted protocols, and a deeper comprehension of enzyme immobilization on solid substrates are essential. These endeavors seek to optimize immobilized biocatalysts, ensuring maximal enzyme performance within confined spaces. For this aim, multidimensional characterization of heterogeneous biocatalysts is required. In this context, spectroscopic and microscopic methodologies conducted at different space and temporal scales can inform about the intraparticle enzyme kinetics, the enzyme spatial distribution, and the mass transport issues. In this Minireview, we identify enzyme immobilization, enzyme catalysis, and enzyme inactivation as the three main processes for which advanced characterization tools unveil fundamental information. Recent advances in operando characterization of immobilized enzymes at the single-particle (SP) and single-molecule (SM) levels inform about their functional properties, unlocking the full potential of heterogeneous biocatalysis toward biotechnological applications.
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Affiliation(s)
- Eleftheria Diamanti
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-, Basque Research and Technology Alliance (BRTA), Paseo Miramón, 194, 20014, Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-, Basque Research and Technology Alliance (BRTA), Paseo Miramón, 194, 20014, Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain
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2
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Ivanović M, Knez Ž, Leitgeb M. Influence of Supercritical Carbon Dioxide on the Activity and Conformational Changes of α-Amylase, Lipase, and Peroxidase in the Solid State Using White Wheat Flour as an Example. Foods 2023; 12:4499. [PMID: 38137304 PMCID: PMC10743174 DOI: 10.3390/foods12244499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Green technologies using renewable and alternative sources, including supercritical carbon dioxide (sc-CO2), are becoming a priority for researchers in a variety of fields, including the control of enzyme activity which, among other applications, is extremely important in the food industry. Namely, extending shelf life of e.g., flour could be reached by tuning the present enzymes activity. In this study, the effect of different sc-CO2 conditions such as temperature (35-50 °C), pressure (200 bar and 300 bar), and exposure time (1-6 h) on the inactivation and structural changes of α-amylase, lipase, and horseradish peroxidase (POD) from white wheat flour and native enzymes was investigated. The total protein (TPC) content and residual activities of the enzymes were determined by standard spectrophotometric methods, while the changes in the secondary structures of the enzymes were determined by circular dichroism spectrometry (CD). The present work is therefore concerned for the first time with the study of the stability and structural changes of the enzyme molecules dominant in white wheat flour under sc-CO2 conditions at different pressures and temperatures. In addition, the changes in aggregation or dissociation of the enzyme molecules were investigated based on the changes in particle size distribution and ζ-potential. The results of the activity assays showed a decrease in the activity of native POD and lipase under optimal exposure conditions (6 h and 50 °C; and 1 h and 50 °C) by 22% and 16%, respectively. In contrast, no significant changes were observed in α-amylase activity. Consequently, analysis of the CD spectra of POD and lipase confirmed a significant effect on secondary structure damage (changes in α-helix, β-sheet, and β-turn content), whereas the secondary structure of α-amylase retained its original configuration. Moreover, the changes in particle size distribution and ζ-potential showed a significant effect of sc-CO2 treatment on the aggregation and dissociation of the selected enzymes. The results of this study confirm that sc-CO2 technology can be effectively used as an environmentally friendly technology to control the activity of major flour enzymes by altering their structures.
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Affiliation(s)
- Milena Ivanović
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
| | - Željko Knez
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Maja Leitgeb
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
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3
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Khumsupan D, Lin SP, Hsieh CW, Santoso SP, Chou YJ, Hsieh KC, Lin HW, Ting Y, Cheng KC. Current and Potential Applications of Atmospheric Cold Plasma in the Food Industry. Molecules 2023; 28:4903. [PMID: 37446565 DOI: 10.3390/molecules28134903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
The cost-effectiveness and high efficiency of atmospheric cold plasma (ACP) incentivise researchers to explore its potentials within the food industry. Presently, the destructive nature of this nonthermal technology can be utilised to inactivate foodborne pathogens, enzymatic ripening, food allergens, and pesticides. However, by adjusting its parameters, ACP can also be employed in other novel applications including food modification, drying pre-treatment, nutrient extraction, active packaging, and food waste processing. Relevant studies were conducted to investigate the impacts of ACP and posit that reactive oxygen and nitrogen species (RONS) play the principal roles in achieving the set objectives. In this review article, operations of ACP to achieve desired results are discussed. Moreover, the recent progress of ACP in food processing and safety within the past decade is summarised while current challenges as well as its future outlook are proposed.
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Affiliation(s)
- Darin Khumsupan
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 106319, Taiwan
| | - Shin-Ping Lin
- School of Food Safety, Taipei Medical University, Taipei City 110, Taiwan
| | - Chang-Wei Hsieh
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung City 402, Taiwan
| | | | - Yu-Jou Chou
- Institute of Food Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 106319, Taiwan
| | - Kuan-Chen Hsieh
- Institute of Food Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 106319, Taiwan
| | - Hui-Wen Lin
- Department of Optometry, Asia University, Taichung City 41354, Taiwan
| | - Yuwen Ting
- Institute of Food Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 106319, Taiwan
| | - Kuan-Chen Cheng
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 106319, Taiwan
- Institute of Food Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 106319, Taiwan
- Department of Optometry, Asia University, Taichung City 41354, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung City 404327, Taiwan
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Seebach H, Radow G, Brunek M, Schulz F, Piotrowski M, Krämer U. Arabidopsis Nicotianamine Synthases (NAS) comprise a common core-NAS domain fused to a variable auto-inhibitory C-terminus. J Biol Chem 2023:104732. [PMID: 37086785 DOI: 10.1016/j.jbc.2023.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/07/2023] [Accepted: 04/12/2023] [Indexed: 04/24/2023] Open
Abstract
Nicotianamine Synthase (NAS) catalyzes the biosynthesis of the low-molecular-mass metal chelator nicotianamine (NA) from the 2-aminobutyrate moieties of three S-adenosylmethionine molecules. NA has central roles in metal nutrition and metal homeostasis of flowering plants. The enzymatic function of NAS remains poorly understood. Crystal structures are available of archaeal and bacterial NAS-like proteins that carry out simpler aminobutanoyl transferase reactions. Here we report amino acids essential for the activity of AtNAS1 based on structural modeling and site-directed mutagenesis. Using a newly developed enzyme-coupled continuous activity assay, we compare differing NAS proteins identified through multiple sequence alignments and phylogenetic analyses. In most NAS of dicotyledonous and monocotyledonous plants (class Ia and Ib), the core-NAS domain is fused to a variable C-terminal domain. Compared to fungal and moss NAS that comprise merely a core-NAS domain (class III), NA biosynthetic activities of the four paralogous Arabidopsis thaliana NAS proteins were far lower. C-terminally trimmed core-AtNAS variants exhibited strongly elevated activities. Of 320 amino acids of AtNAS1, twelve, 287-TRGCMFMPCNCS-298, accounted for the auto-inhibitory effect of the C-terminus, of which approximately one-third was attributed to N296 within a CNCS motif that is fully conserved in Arabidopsis. No detectable NA biosynthesis was mediated by two representative plant NAS proteins that naturally lack the C-terminal domain, class Ia Arabidopsis halleri NAS5, and Medicago truncatula NAS2 of class II which is found in dicots and diverged early during the evolution of flowering plants. Next we will address a possible post-translational release of auto-inhibition in class I NAS proteins.
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Affiliation(s)
- Hiroyuki Seebach
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Radow
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Brunek
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Frank Schulz
- Chemistry and Biochemistry of Natural Products, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Markus Piotrowski
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
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Okawa K, Tabata E, Kida Y, Uno K, Suzuki H, Kamaya M, Bauer PO, Oyama F. Irreversible evolutionary loss of chitin-degrading ability in the chitinase-like protein Ym1 under positive selection in rodents. Protein Sci 2023; 32:e4620. [PMID: 36883357 PMCID: PMC10031810 DOI: 10.1002/pro.4620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Ym1 (chitinase-like 3, Chil3) expressed in mice is a nonenzymatic chitinase-like protein, which shows 67% identity with mouse acidic chitinase (Chia). Similar to Chia, Ym1 is overexpressed in asthma and parasitic infections in mouse lungs. Due to the lack of chitin-degrading activity, the biomedical role of Ym1 under these pathophysiological conditions remains to be determined. In this study, we investigated what region and amino acid changes in Ym1 resulted in the loss of enzymatic activity. Replacing two amino acids at the catalytic motif to obtain a Chia-like sequence (N136D and Q140E; MT-Ym1) did not activate the protein. We conducted a comparative study of Ym1 and Chia. We found that three protein segments-(i) the catalytic motif residues, (ii) exons 6 and 7, and (iii) exon 10-are responsible for chitinase activity loss in Ym1. We show that replacing each of these three segments in Chia that are also involved in substrate recognition and binding by the Ym1 sequence can fully abolish the enzymatic activity. In addition, we show that there have been extensive gene duplication events at the Ym1 locus specific to the rodent lineages. Consistent with this result, Ym1 orthologs from the rodent genome were under positive selection when analyzed through the CODEML program. These data suggest that numerous amino acid substitutions in the regions involved in the chitin recognition, binding, and degradation ability of the ancestor Ym1 molecule lead to the irreversible inactivation of the protein.
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Affiliation(s)
- Kazuaki Okawa
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Eri Tabata
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
- Japan Society for the Promotion of Science (PD)TokyoJapan
| | - Yuta Kida
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Kyohei Uno
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Hidetoshi Suzuki
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Minori Kamaya
- Department of Applied ChemistryKogakuin UniversityTokyoJapan
| | | | - Fumitaka Oyama
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
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Leitgeb M, Knez Ž, Hojnik Podrepšek G. Effect of Green Food Processing Technology on the Enzyme Activity in Spelt Flour. Foods 2022; 11:foods11233832. [PMID: 36496639 PMCID: PMC9737601 DOI: 10.3390/foods11233832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
In this research, a new approach to enzyme inactivation in flour was presented by supercritical technology, considered a sustainable technology with lower energy consumption compared to other technologies that use ultra-high temperature processing. Total protein concentration and the activity of enzymes α-amylase, lipase, peroxidase, polyphenol oxidase, and protease were determined in flour pre-treated with scCO2. During the study, it was observed that the activity of enzymes such as lipase and polyphenol oxidase, was significantly reduced under certain conditions of scCO2 treatment, while the enzymes α-amylase and protease show better stability. In particular, polyphenol oxidase was effectively inactivated below the 60% of preserved activity at 200 bar and 3 h, whereas α-amylase under the same conditions retained its activity. Additionally, the moisture content of the scCO2-treated spelt flour was reduced by 5%, and the fat content was reduced by 58%, while the quality of scCO2-treated flour was maintained. In this regard, the sustainable scCO2 process could be a valuable tool for controlling the enzymatic activity of spelt flour since the use of scCO2 technology has a positive effect on the quality of flour, which was verified by the baking performance of spelt flour with the baked spelt bread as an indicator of quality.
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Affiliation(s)
- Maja Leitgeb
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia
- Correspondence: ; Tel.: +386-2-2294-462
| | - Željko Knez
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia
| | - Gordana Hojnik Podrepšek
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
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Souza PMP, Carballares D, Gonçalves LRB, Fernandez-Lafuente R, Rodrigues S. Immobilization of Lipase B from Candida antarctica in Octyl-Vinyl Sulfone Agarose: Effect of the Enzyme-Support Interactions on Enzyme Activity, Specificity, Structure and Inactivation Pathway. Int J Mol Sci 2022; 23:ijms232214268. [PMID: 36430745 PMCID: PMC9697615 DOI: 10.3390/ijms232214268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/21/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Lipase B from Candida antarctica was immobilized on heterofunctional support octyl agarose activated with vinyl sulfone to prevent enzyme release under drastic conditions. Covalent attachment was established, but the blocking step using hexylamine, ethylenediamine or the amino acids glycine (Gly) and aspartic acid (Asp) altered the results. The activities were lower than those observed using the octyl biocatalyst, except when using ethylenediamine as blocking reagent and p-nitrophenol butyrate (pNPB) as substrate. The enzyme stability increased using these new biocatalysts at pH 7 and 9 using all blocking agents (much more significantly at pH 9), while it decreased at pH 5 except when using Gly as blocking agent. The stress inactivation of the biocatalysts decreased the enzyme activity versus three different substrates (pNPB, S-methyl mandelate and triacetin) in a relatively similar fashion. The tryptophane (Trp) fluorescence spectra were different for the biocatalysts, suggesting different enzyme conformations. However, the fluorescence spectra changes during the inactivation were not too different except for the biocatalyst blocked with Asp, suggesting that, except for this biocatalyst, the inactivation pathways may not be so different.
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Affiliation(s)
- Priscila M. P. Souza
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Food Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 858, Fortaleza CEP 60440-900, CE, Brazil
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
| | - Luciana R. B. Gonçalves
- Chemical Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 709, Fortaleza CEP 60440-900, CE, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Center of Excellence in Bionanoscience Research, Member of the External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (R.F.-L.); (S.R.)
| | - Sueli Rodrigues
- Food Engineering Department, Federal University of Ceará, Campus do Pici, Bloco 858, Fortaleza CEP 60440-900, CE, Brazil
- Correspondence: (R.F.-L.); (S.R.)
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8
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Ko MS, Cohen SN, Polley S, Mahata SK, Biswas T, Huxford T, Ghosh G. Regulatory subunit NEMO promotes polyubiquitin-dependent induction of NF-κB through a targetable second interaction with upstream activator IKK2. J Biol Chem 2022; 298:101864. [PMID: 35339487 PMCID: PMC9035715 DOI: 10.1016/j.jbc.2022.101864] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/16/2023] Open
Abstract
Canonical NF-κB signaling through the inhibitor of κB kinase (IKK) complex requires induction of IKK2/IKKβ subunit catalytic activity via specific phosphorylation within its activation loop. This process is known to be dependent upon the accessory ubiquitin (Ub)-binding subunit NF-κB essential modulator (NEMO)/IKKγ as well as poly-Ub chains. However, the mechanism through which poly-Ub binding serves to promote IKK catalytic activity is unclear. Here, we show that binding of NEMO/IKKγ to linear poly-Ub promotes a second interaction between NEMO/IKKγ and IKK2/IKKβ, distinct from the well-characterized interaction of the NEMO/IKKγ N terminus to the "NEMO-binding domain" at the C terminus of IKK2/IKKβ. We mapped the location of this second interaction to a stretch of roughly six amino acids immediately N-terminal to the zinc finger domain in human NEMO/IKKγ. We also showed that amino acid residues within this region of NEMO/IKKγ are necessary for binding to IKK2/IKKβ through this secondary interaction in vitro and for full activation of IKK2/IKKβ in cultured cells. Furthermore, we identified a docking site for this segment of NEMO/IKKγ on IKK2/IKKβ within its scaffold-dimerization domain proximal to the kinase domain-Ub-like domain. Finally, we showed that a peptide derived from this region of NEMO/IKKγ is capable of interfering specifically with canonical NF-κB signaling in transfected cells. These in vitro biochemical and cell culture-based experiments suggest that, as a consequence of its association with linear poly-Ub, NEMO/IKKγ plays a direct role in priming IKK2/IKKβ for phosphorylation and that this process can be inhibited to specifically disrupt canonical NF-κB signaling.
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Affiliation(s)
- Myung Soo Ko
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA; Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Samantha N Cohen
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Smarajit Polley
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Sushil K Mahata
- Department of Medicine, University of California, San Diego, La Jolla, California, USA; Medicine, VA San Diego Health Care System, San Diego, California, USA
| | - Tapan Biswas
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA.
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9
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Mangiagalli M, Ami D, de Divitiis M, Brocca S, Catelani T, Natalello A, Lotti M. Short-chain alcohols inactivate an immobilized industrial lipase through two different mechanisms. Biotechnol J 2022; 17:e2100712. [PMID: 35188703 DOI: 10.1002/biot.202100712] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/26/2022] [Accepted: 02/18/2022] [Indexed: 11/07/2022]
Abstract
Broadly used in biocatalysis as acyl acceptors or (co)-solvents, short-chain alcohols often cause irreversible loss of enzyme activity. Understanding the mechanisms of inactivation is a necessary step toward the optimization of biocatalytic reactions and the design of enzyme-based sustainable processes. In this work, we explored the functional and structural response of an immobilized enzyme, Novozym 435, exposed to methanol, ethanol, and tert-butanol. N-435 consists of Candida antarctica lipase B (CALB) adsorbed on polymethacrylate beads and finds application in a variety of processes involving the presence of short-chain alcohols. The nature of the N-435 material required the development of an ad hoc method of structural analysis, based on Fourier transform infrared microspectroscopy, which was complemented by catalytic activity assays and by morphological observation by transmission electron microscopy. We found that the inactivation of N-435 is highly dependent on alcohol concentration and occurs through two different mechanisms. Short-chain alcohols induce conformational changes leading to CALB aggregation, which is only partially prevented by immobilization. Moreover, alcohol modifies the texture of the solid support promoting the enzyme release. Overall, knowledge of the molecular mechanisms underlying Novozym 435 inactivation induced by short-chain alcohols promises to overcome the limitations that usually occur during industrial processes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Tiziano Catelani
- Microscopy Facility, University of Milano-Bicocca, Milan, 20126, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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10
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Andorfer MC, Backman LRF, Li PL, Ulrich EC, Drennan CL. Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein. J Biol Chem 2021; 297:101423. [PMID: 34801558 DOI: 10.1016/j.jbc.2021.101423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.
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11
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Kuusk S, Väljamäe P. Kinetics of H 2O 2-driven catalysis by a lytic polysaccharide monooxygenase from the fungus Trichoderma reesei. J Biol Chem 2021; 297:101256. [PMID: 34597668 PMCID: PMC8528726 DOI: 10.1016/j.jbc.2021.101256] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 01/17/2023] Open
Abstract
Owing to their ability to break glycosidic bonds in recalcitrant crystalline polysaccharides such as cellulose, the catalysis effected by lytic polysaccharide monooxygenases (LPMOs) is of major interest. Kinetics of these reductant-dependent, monocopper enzymes is complicated by the insoluble nature of the cellulose substrate and parallel, enzyme-dependent, and enzyme-independent side reactions between the reductant and oxygen-containing cosubstrates. Here, we provide kinetic characterization of cellulose peroxygenase (oxidative cleavage of glycosidic bonds in cellulose) and reductant peroxidase (oxidation of the reductant) activities of the LPMO TrAA9A of the cellulose-degrading model fungus Trichoderma reesei. The catalytic efficiency (kcat/Km(H2O2)) of the cellulose peroxygenase reaction (kcat = 8.5 s−1, and Km(H2O2)=30μM) was an order of magnitude higher than that of the reductant (ascorbic acid) peroxidase reaction. The turnover of H2O2 in the ascorbic acid peroxidase reaction followed the ping-pong mechanism and led to irreversible inactivation of the enzyme with a probability of 0.0072. Using theoretical analysis, we suggest a relationship between the half-life of LPMO, the values of kinetic parameters, and the concentrations of the reactants.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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12
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Luan C, Zhang M, Fan K, Devahastin S. Effective pretreatment technologies for fresh foods aimed for use in central kitchen processing. J Sci Food Agric 2021; 101:347-363. [PMID: 32564354 DOI: 10.1002/jsfa.10602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 06/14/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
The central kitchen concept is a new trend in the food industry, where centralized preparation and processing of fresh foods and the distribution of finished or semi-finished products to catering chains or related units take place. Fresh foods processed by a central kitchen mainly include fruit and vegetables, meat, aquatic products, and edible fungi; these foods have high water activities and thermal sensitivities and must be processed with care. Appropriate pretreatments are generally required for these food materials; typical pretreatment processes include cleaning, enzyme inactivation, and disinfection, as well as packaging and coating. To improve the working efficiency of a central kitchen, novel efficient pretreatment technologies are needed. This article systematically reviews various high-efficiency pretreatment technologies for fresh foods. These include ultrasonic cleaning technologies, physical-field enzyme inactivation technologies, non-thermal disinfection technologies, and modified-atmosphere packagings and coatings. Mechanisms, applications, influencing factors, and advantages and disadvantages of these technologies, which can be used in a central kitchen, are outlined and discussed. Possible solutions to problems related to central-kitchen food processing are addressed, including low cleaning efficiency and automation feasibility, high nutrition loss, high energy consumption, and short shelf life of products. These should lead us to the next step of fresh food processing for a highly demanding modern society. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Chunning Luan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Min Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Jiangsu Province Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, Wuxi, China
| | - Kai Fan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Yechun Food Production and Distribution Co., Ltd, Yangzhou, China
| | - Sakamon Devahastin
- Advanced Food Processing Research Laboratory, Department of Food Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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13
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Latorre-Muro P, Baeza J, Hurtado-Guerrero R, Hicks T, Delso I, Hernández-Ruiz C, Velázquez-Campoy A, Lawton AJ, Angulo J, Denu JM, Carrodeguas JA. Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity. J Biol Chem 2021; 296:100205. [PMID: 33334880 PMCID: PMC7948413 DOI: 10.1074/jbc.ra120.015103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/12/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Acetylation is known to regulate the activity of cytosolic phosphoenolpyruvate carboxykinase (PCK1), a key enzyme in gluconeogenesis, by promoting the reverse reaction of the enzyme (converting phosphoenolpyruvate to oxaloacetate). It is also known that the histone acetyltransferase p300 can induce PCK1 acetylation in cells, but whether that is a direct or indirect function was not known. Here we initially set out to determine whether p300 can acetylate directly PCK1 in vitro. We report that p300 weakly acetylates PCK1, but surprisingly, using several techniques including protein crystallization, mass spectrometry, isothermal titration calorimetry, saturation-transfer difference nuclear magnetic resonance and molecular docking, we found that PCK1 is also able to acetylate itself using acetyl-CoA independently of p300. This reaction yielded an acetylated recombinant PCK1 with a 3-fold decrease in kcat without changes in Km for all substrates. Acetylation stoichiometry was determined for 14 residues, including residues lining the active site. Structural and kinetic analyses determined that site-directed acetylation of K244, located inside the active site, altered this site and rendered the enzyme inactive. In addition, we found that acetyl-CoA binding to the active site is specific and metal dependent. Our findings provide direct evidence for acetyl-CoA binding and chemical reaction with the active site of PCK1 and suggest a newly discovered regulatory mechanism of PCK1 during metabolic stress.
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Affiliation(s)
- Pedro Latorre-Muro
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.
| | - Josue Baeza
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Ignacio Delso
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, Zaragoza, Spain
| | - Cristina Hernández-Ruiz
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Adrian Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; Biomedical Research Network Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain; IIS Aragón, Zaragoza, Spain
| | - Alexis J Lawton
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich, UK; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-Universidad de Sevilla), Sevilla, Spain
| | - John M Denu
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, School of Medicine and Public Health-Madison, Madison, Wisconsin, USA
| | - José A Carrodeguas
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain; IIS Aragón, Zaragoza, Spain.
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14
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Zhang L, Liu W, Ji J, Deng L, Feng Q, Shi W, Gao J. Inactivation of Inulinase and Marination of High-Quality Jerusalem Artichoke ( Helianthus tuberosus L.) Pickles With Screened Dominant Strains. Front Bioeng Biotechnol 2021; 8:626861. [PMID: 33553130 PMCID: PMC7855583 DOI: 10.3389/fbioe.2020.626861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/18/2020] [Indexed: 11/13/2022] Open
Abstract
Freshly harvested Jerusalem artichoke tubers contain inulinase, an enzyme that requires inactivation, because of its ability to hydrolysis inulin into fructose, which can be consumed by microorganism during marination. As the traditional pickling process takes 6 months, and involves the addition of a large amount of salt (18-20%), this production strategy is uneconomical and increases the nitrite intake. Additionally, miscellaneous bacteria produced during pickling affect the product taste. In this study, the enzyme inactivation effects of NaCl, NaHCO3, and ultrasound were evaluated. NaHCO3 treatment results in the highest degree of enzyme inactivation; however, the quality and flavor of the obtained Jerusalem artichoke pickles were not ideal. The Jerusalem artichoke pickles in which the enzymes were inactivated using a combination of NaCl and ultrasound exhibited better flavor than those exposed to NaHCO3; further, this combination reduced the inulinase activity of the Jerusalem artichokes to 2.50 U/mL, and maintained the inulin content at 61.22%. The strains LS3 and YS2, identified as Enterococcus faecalis and the salt-tolerant yeast Meyerozyma guilliermondii, respectively, were the dominant microorganisms isolated from the pickle juice. Jerusalem artichokes with inactivated inulinase were pickled with microbial powder, separated, purified, and dried to remove the natural Jerusalem artichoke sauce. This process shortened the fermentation cycle and improved product quality.
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Affiliation(s)
| | | | | | | | | | | | - Jian Gao
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
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15
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Hojnik Podrepšek G, Knez Ž, Leitgeb M. The Influence of Supercritical Carbon Dioxide on Graham Flour Enzyme Polyphenol Oxidase Activity. Molecules 2020; 25:molecules25245981. [PMID: 33348622 PMCID: PMC7767152 DOI: 10.3390/molecules25245981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
Graham flour is a form of whole wheat flour made by grinding the endosperm and is thus also the most nutritious. Generally, the enzyme polyphenol oxidase (PPO) catalyzes two different reactions in the presence of molecular oxygen: the hydroxylation of monophenols to ortho-diphenol and the oxidation of o-diphenol to o-quinone. The purpose of the work was to inactivate PPO activity to extend the shelf life of graham flour and at the same time preserve all the of its high-quality properties. The influence of supercritical CO2 (scCO2) treatment on PPO activity in graham flour was investigated. First, graham flour was exposed to scCO2 conditions, then the proteins were extracted, and in the last step the concentration of total proteins and the specific activity of the PPO enzyme were determined by spectrophotometric assay. PPO activity decreased with an increase in treatment pressure. Furthermore, the flour quality characteristics that meet all needs for wheat end-use products after scCO2 treatment have been preserved. No major changes in the structure of the granulate or shape of the flour particles were observed. A slightly reduced value of the moisture content in scCO2-treated graham flour also implies an extension of the shelf life.
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Affiliation(s)
- Gordana Hojnik Podrepšek
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (G.H.P.); (Ž.K.)
| | - Željko Knez
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (G.H.P.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Maja Leitgeb
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (G.H.P.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
- Correspondence: ; Tel.: +386-22294462
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16
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Ferreira JC, Khrbtli AR, Shetler CL, Mansoor S, Ali L, Sensoy O, Rabeh WM. Linker residues regulate the activity and stability of hexokinase 2, a promising anticancer target. J Biol Chem 2020; 296:100071. [PMID: 33187984 PMCID: PMC7949118 DOI: 10.1074/jbc.ra120.015293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Hexokinase (HK) catalyzes the first step in glucose metabolism, making it an exciting target for the inhibition of tumor initiation and progression due to their elevated glucose metabolism. The upregulation of hexokinase-2 (HK2) in many cancers and its limited expression in normal tissues make it a particularly attractive target for the selective inhibition of cancer growth and the eradication of tumors with limited side effects. The design of such safe and effective anticancer therapeutics requires the development of HK2-specific inhibitors that will not interfere with other HK isozymes. As HK2 is unique among HKs in having a catalytically active N-terminal domain (NTD), we have focused our attention on this region. We previously found that NTD activity is affected by the size of the linker helix-α13 that connects the N- and C-terminal domains of HK2. Three nonactive site residues (D447, S449, and K451) at the beginning of the linker helix-α13 have been found to regulate the NTD activity of HK2. Mutation of these residues led to increased dynamics, as shown via hydrogen deuterium exchange analysis and molecular dynamic simulations. D447A contributed the most to the enhanced dynamics of the NTD, with reduced calorimetric enthalpy of HK2. Similar residues exist in the C-terminal domain (CTD) but are unnecessary for HK1 and HK2 activity. Thus, we postulate these residues serve as a regulatory site for HK2 and may provide new directions for the design of anticancer therapeutics that reduce the rate of glycolysis in cancer through specific inhibition of HK2.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Abdul-Rahman Khrbtli
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Cameron L Shetler
- Department of Chemistry, New York University Shanghai, Shanghai, China
| | - Samman Mansoor
- The School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Liaqat Ali
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Campus, Abu Dhabi, United Arab Emirates
| | - Ozge Sensoy
- The School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey; Regenerative and Restorative Medicine Research Center (REMER), Istanbul Medipol University, Istanbul, Turkey; Research Institute for Health Sciences and Technologies (SABITA), İstanbul Medipol University, Istanbul, Turkey
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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17
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Marcinkowska M, Jeleń HH. Inactivation of Thioglucosidase from Sinapis alba (White Mustard) Seed by Metal Salts. Molecules 2020; 25:molecules25194363. [PMID: 32977439 PMCID: PMC7582697 DOI: 10.3390/molecules25194363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 11/27/2022] Open
Abstract
The glucosinolates which are specialized plant metabolites of Brassica vegetables are prone to hydrolysis catalyzed by an endogenous enzyme myrosinase (thioglycoside hydrolase, thioglucosidase) that exists in Brassica plant tissue causing volatile isothiocyanates release. Currently existing literature data on the inactivation of myrosinase is insufficient in particular for use in the analysis of volatile and odor compounds in vegetables rich in glucosinolates. In this study, the impact of different metal salts in effective inactivation of enzyme activity was investigated by solid-phase microextraction (SPME) and GC/MS system in aqueous samples and kohlrabi matrix. A saturated solution of calcium chloride which is commonly used to stop enzyme activity in plant tissue inactivates the myrosinase–glucosinolate system. However, even without the participation of myrosinase, it changes the reaction pathway towards nitrile formation. The model experiment shows that optimum efficiency in inhibition of the enzyme system shows iron(III) ions, silver ions, and anhydride sodium sulfate resulting in no volatile products derived from glucosinolates. However, in the kohlrabi matrix, the strongest enzyme inhibition effect was observed for silver salt resulting in no volatile products, also both anhydrous Na2SO4 and saturated CaCl2 solution seem to be useful inhibitors in flavor studies.
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18
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Ravala SK, Hopkins JB, Plescia CB, Allgood SR, Kane MA, Cash JN, Stahelin RV, Tesmer JJG. The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding. J Biol Chem 2020; 295:12635-12647. [PMID: 32661198 DOI: 10.1074/jbc.ra120.014534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/08/2020] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylinositol (3,4,5)-trisphosphate (PIP3)-dependent Rac exchanger 1 (P-Rex1) catalyzes the exchange of GDP for GTP on Rac GTPases, thereby triggering changes in the actin cytoskeleton and in transcription. Its overexpression is highly correlated with the metastasis of certain cancers. P-Rex1 recruitment to the plasma membrane and its activity are regulated via interactions with heterotrimeric Gβγ subunits, PIP3, and protein kinase A (PKA). Deletion analysis has further shown that domains C-terminal to its catalytic Dbl homology (DH) domain confer autoinhibition. Among these, the first dishevelled, Egl-10, and pleckstrin domain (DEP1) remains to be structurally characterized. DEP1 also harbors the primary PKA phosphorylation site, suggesting that an improved understanding of this region could substantially increase our knowledge of P-Rex1 signaling and open the door to new selective chemotherapeutics. Here we show that the DEP1 domain alone can autoinhibit activity in context of the DH/PH-DEP1 fragment of P-Rex1 and interacts with the DH/PH domains in solution. The 3.1 Å crystal structure of DEP1 features a domain swap, similar to that observed previously in the Dvl2 DEP domain, involving an exposed basic loop that contains the PKA site. Using purified proteins, we show that although DEP1 phosphorylation has no effect on the activity or solution conformation of the DH/PH-DEP1 fragment, it inhibits binding of the DEP1 domain to liposomes containing phosphatidic acid. Thus, we propose that PKA phosphorylation of the DEP1 domain hampers P-Rex1 binding to negatively charged membranes in cells, freeing the DEP1 domain to associate with and inhibit the DH/PH module.
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Affiliation(s)
- Sandeep K Ravala
- Departments of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,The Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Jesse B Hopkins
- Biophysics Collaborative Access Team, Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA
| | - Caroline B Plescia
- The Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Samantha R Allgood
- Departments of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Madison A Kane
- College of Engineering, California State University, Long Beach, California, USA
| | - Jennifer N Cash
- Department of Biological Chemistry & Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert V Stahelin
- The Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - John J G Tesmer
- Departments of Biological Sciences, Purdue University, West Lafayette, Indiana, USA .,The Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
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19
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Toro-Uribe S, Godoy-Chivatá J, Villamizar-Jaimes AR, Perea-Flores MDJ, López-Giraldo LJ. Insight of Polyphenol Oxidase Enzyme Inhibition and Total Polyphenol Recovery from Cocoa Beans. Antioxidants (Basel) 2020; 9:antiox9060458. [PMID: 32471228 PMCID: PMC7346217 DOI: 10.3390/antiox9060458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
A full factorial design (ascorbic acid/l-cysteine inhibitors, temperature, and time as factors) study was conducted to enhance inhibition of polyphenol oxidase (PPO) activity without decreasing cocoa polyphenol concentrations. The data obtained were modelled through a new equation, represented by Γ, which correlates both high polyphenol content with reduced specific PPO activity. At optimized values (70 mM inhibitory solution at 96 °C for 6.4 min, Γ = 11.6), 93.3% PPO inhibition and total polyphenol of 94.9 mg GAE/g were obtained. In addition, microscopy images confirmed the cell morphological changes measured as the fractal dimension and explained the possible cell lysis and denaturation as a result of heat treatment and chemical inhibitors. Results also showed that PPO enzyme was most suitable (higher vmax/Km ratio) for catechol, with a reduction in its affinity of 13.7-fold after the inhibition heat treatment. Overall, this work proposed a suitable and food-safe procedure for obtaining enriched polyphenol extract with low enzyme activity.
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Affiliation(s)
- Said Toro-Uribe
- School of Chemical Engineering, Food Science & Technology Research Center (CICTA), Universidad Industrial de Santander, Carrera 27, Calle 9, 68002 Bucaramanga, Colombia; (S.T.-U.); (J.G.-C.)
| | - Jhair Godoy-Chivatá
- School of Chemical Engineering, Food Science & Technology Research Center (CICTA), Universidad Industrial de Santander, Carrera 27, Calle 9, 68002 Bucaramanga, Colombia; (S.T.-U.); (J.G.-C.)
| | - Arley René Villamizar-Jaimes
- Food Science & Technology Research Center (CICTA), Universidad Industrial de Santander, Carrera 27, Calle 9, 68002 Bucaramanga, Colombia;
| | - María de Jesús Perea-Flores
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Luis Enrique Erro s/n, Unidad, Profesional Adolfo López Mateos, Col. Zacatenco, C.P. 07738 Ciudad de México, Mexico;
| | - Luis J. López-Giraldo
- School of Chemical Engineering, Food Science & Technology Research Center (CICTA), Universidad Industrial de Santander, Carrera 27, Calle 9, 68002 Bucaramanga, Colombia; (S.T.-U.); (J.G.-C.)
- Correspondence: ; Tel.: +57-300-377-8801
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20
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Kalous KS, Wynia-Smith SL, Summers SB, Smith BC. Human sirtuins are differentially sensitive to inhibition by nitrosating agents and other cysteine oxidants. J Biol Chem 2020; 295:8524-8536. [PMID: 32371394 DOI: 10.1074/jbc.ra119.011988] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/29/2020] [Indexed: 01/25/2023] Open
Abstract
Sirtuins (e.g. human Sirt1-7) catalyze the removal of acyl groups from lysine residues in proteins in an NAD+-dependent manner, and loss of sirtuin deacylase activity correlates with the development of aging-related diseases. Although multiple reports suggest that sirtuin activity is regulated by oxidative post-translational modifications of cysteines during inflammation and aging, no systematic comparative study of potential direct sirtuin cysteine oxidative modifications has been performed. Here, using IC50 and k inact/KI analyses, we quantified the ability of nitrosothiols (S-nitrosoglutathione and S-nitroso-N-acetyl-d,l-penicillamine), nitric oxide, oxidized GSH, and hydrogen peroxide to post-translationally modify and inhibit the deacylase activity of Sirt1, Sirt2, Sirt3, Sirt5, and Sirt6. The inhibition was correlated with cysteine modification and assessed with chemical-probe and blot-based assays for cysteine S-nitrosation, sulfenylation, and glutathionylation. We show that the primarily nuclear sirtuins Sirt1 and Sirt6, as well as the primarily cytosolic sirtuin Sirt2, are modified and inhibited by cysteine S-nitrosation in response to exposure to both free nitric oxide and nitrosothiols (k inact/KI ≥ 5 m-1 s-1), which is the first report of Sirt2 and Sirt6 inhibition by S-nitrosation. Surprisingly, the mitochondrial sirtuins Sirt3 and Sirt5 were resistant to inhibition by cysteine oxidants. Collectively, these results suggest that nitric oxide-derived oxidants may causatively link nuclear and cytosolic sirtuin inhibition to aging-related inflammatory disease development.
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Affiliation(s)
- Kelsey S Kalous
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sarah L Wynia-Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Steven B Summers
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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21
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Umair M, Jabbar S, Nasiru MM, Sultana T, Senan AM, Awad FN, Hong Z, Zhang J. Exploring the Potential of High-Voltage Electric Field Cold Plasma (HVCP) Using a Dielectric Barrier Discharge (DBD) as a Plasma Source on the Quality Parameters of Carrot Juice. Antibiotics (Basel) 2019; 8:E235. [PMID: 31775237 PMCID: PMC6963332 DOI: 10.3390/antibiotics8040235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/20/2019] [Accepted: 10/21/2019] [Indexed: 12/03/2022] Open
Abstract
The main aim of the current investigation was to contemplate the impact of high-voltage electric field cold plasma (HVCP) on different quality characteristics (enzymes, microbial activities, coloring pigments, ascorbic acid, polyphenolic compounds, °Brix, acidity, and color index) of carrot juice in correlation with thermal processing. A carrot juice (250 mL) sample sealed in pre-sterilized food-grade bottles, which placed between two dielectric quartz plates for HVCP treatment. The gap between the plates was 30 mm, and a stable and uniform plasma dielectric barrier discharge (DBD) generated for 3 and 4 min at 60, 70, and 80 kV. Air was used as a working gas during the DBD-based plasma treatment. The observed rise in temperature was 2-5 °C during the HVCP treatment. A water bath was used to carry out thermal treatment (100 °C for 5 min). The maximum inactivation of enzymes and microorganisms was achieved with thermal treatment and then with HVCP treatment at 70 kV for 4 min. However, maximum retention of coloring compounds, ascorbic acid, total phenols, flavonoids, and tannins was found following HVCP (70 kV for 4 min) treatment compared to thermal treatment. The °Brix, pH, and acidity remained unchanged irrespective of treatments. These findings suggest that HVCP treatment at 70 kV for 4 min may be a good alternative to thermal treatment, and it may successfully be applied in carrot juice production, resulting in reduced enzymes, lower microbial activity, and improved bioactive compounds. The prospects of overcoming the existing conventional physical and chemical methods for sterilization make it a novel and more economical technique to maintain food's natural nourishment, composition, appearance, structure, and freshness.
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Affiliation(s)
- Muhammad Umair
- National Center of Meat Quality and Safety Control, Synergetic Innovation Center of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.U.); (M.M.N.); (A.M.S.); (F.N.A.)
| | - Saqib Jabbar
- Food Science Research Institute (FSRI), National Agricultural Research Centre (NARC), Islamabad 44000, Pakistan;
| | - Mustapha Muhammad Nasiru
- National Center of Meat Quality and Safety Control, Synergetic Innovation Center of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.U.); (M.M.N.); (A.M.S.); (F.N.A.)
| | - Tayyaba Sultana
- College of Public Administration, Nanjing Agriculture University Nanjing, Nanjing 210095, China;
| | - Ahmed M. Senan
- National Center of Meat Quality and Safety Control, Synergetic Innovation Center of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.U.); (M.M.N.); (A.M.S.); (F.N.A.)
| | - Faisal Nureldin Awad
- National Center of Meat Quality and Safety Control, Synergetic Innovation Center of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.U.); (M.M.N.); (A.M.S.); (F.N.A.)
| | - Zhuang Hong
- Quality & Safety Assessment Research Unit, USDA-ARS, Athens, GA 30605, USA;
| | - Jianhao Zhang
- National Center of Meat Quality and Safety Control, Synergetic Innovation Center of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.U.); (M.M.N.); (A.M.S.); (F.N.A.)
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22
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Roche-Hakansson H, Vansarla G, Marks LR, Hakansson AP. The human milk protein-lipid complex HAMLET disrupts glycolysis and induces death in Streptococcus pneumoniae. J Biol Chem 2019; 294:19511-19522. [PMID: 31694917 DOI: 10.1074/jbc.ra119.009930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/29/2019] [Indexed: 12/25/2022] Open
Abstract
HAMLET is a complex of human α-lactalbumin (ALA) and oleic acid and kills several Gram-positive bacteria by a mechanism that bears resemblance to apoptosis in eukaryotic cells. To identify HAMLET's bacterial targets, here we used Streptococcus pneumoniae as a model organism and employed a proteomic approach that identified several potential candidates. Two of these targets were the glycolytic enzymes fructose bisphosphate aldolase (FBPA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Treatment of pneumococci with HAMLET immediately inhibited their ATP and lactate production, suggesting that HAMLET inhibits glycolysis. This observation was supported by experiments with recombinant bacterial enzymes, along with biochemical and bacterial viability assays, indicating that HAMLET's activity is partially inhibited by high glucose-mediated stimulation of glycolysis but enhanced in the presence of the glycolysis inhibitor 2-deoxyglucose. Both HAMLET and ALA bound directly to each glycolytic enzyme in solution and solid-phase assays and effectively inhibited their enzymatic activities. In contrast, oleic acid alone had little to no inhibitory activity. However, ALA alone also exhibited no bactericidal activity and did not block glycolysis in whole cells, suggesting a role for the lipid moiety in the internalization of HAMLET into the bacterial cells to reach its target(s). This was verified by inhibition of enzyme activity in whole cells after HAMLET but not ALA exposure. The results of this study suggest that part of HAMLET's antibacterial activity relates to its ability to target and inhibit glycolytic enzymes, providing an example of a natural antimicrobial agent that specifically targets glycolysis.
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Affiliation(s)
- Hazeline Roche-Hakansson
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14203
| | - Goutham Vansarla
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University, SE-21428 Malmö, Sweden
| | - Laura R Marks
- Department of Medicine, Barnes-Jewish Hospital, Washington University, St. Louis, Missouri 63110
| | - Anders P Hakansson
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University, SE-21428 Malmö, Sweden
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23
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Hemmerlin A, Huchelmann A, Tritsch D, Schaller H, Bach TJ. The specific molecular architecture of plant 3-hydroxy-3-methylglutaryl-CoA lyase. J Biol Chem 2019; 294:16186-16197. [PMID: 31515272 DOI: 10.1074/jbc.ra119.008839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/20/2019] [Indexed: 11/06/2022] Open
Abstract
3-Hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase (HMGL) is involved in branched-chain amino acid catabolism leading to acetyl-CoA production. Here, using bioinformatics analyses and protein sequence alignments, we found that in Arabidopsis thaliana a single gene encodes two HMGL isoforms differing in size (51 kDa, HMGL51 and 46 kDa, HMGL46). Similar to animal HMGLs, both isoforms comprised a C-terminal type 1 peroxisomal retention motif, and HMGL51 contained a mitochondrial leader peptide. We observed that only a shortened HMGL (35 kDa, HMGL35) is conserved across all kingdoms of life. Most notably, all plant HMGLs also contained a specific N-terminal extension (P100) that is located between the N-terminal mitochondrial targeting sequence TP35 and HMGL35 and is absent in bacteria and other eukaryotes. Interestingly, using HMGL enzyme assays, we found that rather than HMGL46, homodimeric recombinant HMGL35 is the active enzyme catalyzing acetyl-CoA and acetoacetate synthesis when incubated with (S)-HMG-CoA. This suggested that the plant-specific P100 peptide may inactivate HMGL according to specific physiological requirements. Therefore, we investigated whether the P100 peptide in HMGL46 alters its activity, possibly by modifying the HMGL46 structure. We found that induced expression of a cytosolic HMGL35 version in A. thaliana delays germination and leads to rapid wilting and chlorosis in mature plants. Our results suggest that in plants, P100-mediated HMGL inactivation outside of peroxisomes or mitochondria is crucial, protecting against potentially cytotoxic effects of HMGL activity while it transits to these organelles.
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Affiliation(s)
- Andréa Hemmerlin
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Alexandre Huchelmann
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Denis Tritsch
- Institut de Chimie de Strasbourg, 4 rue Blaise Pascal, F-67081 Strasbourg, France
| | - Hubert Schaller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Thomas J Bach
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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24
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Thaz CJ, Jayaraman G. Calcium ion induced thermodynamic stability, bisubstrate specificity, and differential organic solvent tolerance of a predominantly β-sheet serine protease from Bacillus aquimaris VITP4. Biotechnol Appl Biochem 2019; 66:955-961. [PMID: 31486109 DOI: 10.1002/bab.1811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/01/2019] [Indexed: 01/22/2023]
Abstract
The present study was aimed to get insights on the role of calcium ions on the thermodynamic stability, substrate specificity, and organic solvent compatibility of the extracellular protease produced by Bacillus aquimaris VITP4. Presence of Ca2+ enhanced the activity of the enzyme in the temperature range of 30-60 °C and increased the half-life from 164 to 234 Min. Circular dichroism experiments indicated that the temperature of half-denaturation (Tm ) of the protease increased from 76 to 86 °C. As judged by fluorescence emission profiles, the overall fold of the enzyme around the tryptophan residues could be similar. Further, thermal inactivation experiments revealed that the enzyme followed first order kinetics, with increase in energy for inactivation (Eai ) by 24.2 ± 1.2 kJ mol -1 in the presence of Ca2+ . Studies with synthetic peptides as well as with bovine serum albumin signified preferential hydrolysis of the peptide bonds at the C-terminus of alanine residues (with a kcat /KM of 141,400 M-1 Sec-1 ) and at the C-terminus of arginine residues with a lower specificity (72,400 M-1 Sec-1 ), indicating bisubstrate specificity of the enzyme. The enzyme was found to be compatible with organic solvents (50%, v/v) such as acetonitrile and butanol, indicating possible application under demanding nonaqueous conditions.
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Affiliation(s)
- Chittoor Jabeena Thaz
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Gurunathan Jayaraman
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
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25
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Duval R, Bui LC, Mathieu C, Nian Q, Berthelet J, Xu X, Haddad I, Vinh J, Dupret JM, Busi F, Guidez F, Chomienne C, Rodrigues-Lima F. Benzoquinone, a leukemogenic metabolite of benzene, catalytically inhibits the protein tyrosine phosphatase PTPN2 and alters STAT1 signaling. J Biol Chem 2019; 294:12483-12494. [PMID: 31248982 DOI: 10.1074/jbc.ra119.008666] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Protein tyrosine phosphatase, nonreceptor type 2 (PTPN2) is mainly expressed in hematopoietic cells, where it negatively regulates growth factor and cytokine signaling. PTPN2 is an important regulator of hematopoiesis and immune/inflammatory responses, as evidenced by loss-of-function mutations of PTPN2 in leukemia and lymphoma and knockout mice studies. Benzene is an environmental chemical that causes hematological malignancies, and its hematotoxicity arises from its bioactivation in the bone marrow to electrophilic metabolites, notably 1,4-benzoquinone, a major hematotoxic benzene metabolite. Although the molecular bases for benzene-induced leukemia are not well-understood, it has been suggested that benzene metabolites alter topoisomerases II function and thereby significantly contribute to leukemogenesis. However, several studies indicate that benzene and its hematotoxic metabolites may also promote the leukemogenic process by reacting with other targets and pathways. Interestingly, alterations of cell-signaling pathways, such as Janus kinase (JAK)/signal transducer and activator of transcription (STAT), have been proposed to contribute to benzene-induced malignant blood diseases. We show here that 1,4-benzoquinone directly impairs PTPN2 activity. Mechanistic and kinetic experiments with purified human PTPN2 indicated that this impairment results from the irreversible formation (k inact = 645 m-1·s-1) of a covalent 1,4-benzoquinone adduct at the catalytic cysteine residue of the enzyme. Accordingly, cell experiments revealed that 1,4-benzoquinone exposure irreversibly inhibits cellular PTPN2 and concomitantly increases tyrosine phosphorylation of STAT1 and expression of STAT1-regulated genes. Our results provide molecular and cellular evidence that 1,4-benzoquinone covalently modifies key signaling enzymes, implicating it in benzene-induced malignant blood diseases.
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Affiliation(s)
- Romain Duval
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Linh-Chi Bui
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Cécile Mathieu
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Qing Nian
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | | | - Ximing Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Iman Haddad
- ESPCI Paris, PSL Université, USR 3149, CNRS, F-75005 Paris, France
| | - Joelle Vinh
- ESPCI Paris, PSL Université, USR 3149, CNRS, F-75005 Paris, France
| | | | - Florent Busi
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Fabien Guidez
- Université de Paris, Institut de Recherche Saint-Louis, UMRS 1131, INSERM, F-75010 Paris, France
| | - Christine Chomienne
- Université de Paris, Institut de Recherche Saint-Louis, UMRS 1131, INSERM, F-75010 Paris, France; Service de Biologie Cellulaire, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint Louis, F-75010 Paris, France
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26
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Kang JH, Roh SH, Min SC. Inactivation of Potato Polyphenol Oxidase Using Microwave Cold Plasma Treatment. J Food Sci 2019; 84:1122-1128. [PMID: 30997932 DOI: 10.1111/1750-3841.14601] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/16/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
This study was conducted to examine the effects of microwave cold plasma (CP) treatment on inactivation of polyphenol oxidase (PPO) of potato. The PPO activity and treatment variables were fit to first-order kinetics, the Weibull model, and the second-order model. The optimum CP-generation power and treatment time for inactivating PPO in the PPO extract were found to be 900 W and 40 min, respectively, which resulted in the highest inactivation of PPO (49.5%). PPO activity after CP treatment of potato slices decreased from 72.4% to 59.0% as the sample surface-to-volume ratio increased from 7.1 to 9.0. CP treatment delayed the browning of potato slices. Microwave CP treatment effectively inactivated PPO in potatoes, demonstrating the potential of CP treatment for controlling PPO activity in foods. PRACTICAL APPLICATION: This study demonstrated that microwave CP treatment, a nonthermal food processing technology, inactivates PPO activity in potatoes. The results showed that the inactivation effect of CP treatment on PPO corresponded to the surface-to-volume ratio of potato slices. Furthermore, this study proposed an enzyme inactivation model that is suitable for predicting the inactivation of PPO activity and confirmed that CP treatment delayed browning in potatoes.
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Affiliation(s)
- Joo Hyun Kang
- Dept. of Food Science and Technology, Seoul Women's Univ., Seoul, 01797, Republic of Korea
| | - Si Hyeon Roh
- Dept. of Food Science and Technology, Seoul Women's Univ., Seoul, 01797, Republic of Korea
| | - Sea Cheol Min
- Dept. of Food Science and Technology, Seoul Women's Univ., Seoul, 01797, Republic of Korea
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27
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d'Andrea FB, Townsend CA. Late-Stage Conversion of Diphenylphosphonate to Fluorophosphonate Probes for the Investigation of Serine Hydrolases. Cell Chem Biol 2019; 26:878-884.e8. [PMID: 30982751 DOI: 10.1016/j.chembiol.2019.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/04/2019] [Accepted: 02/27/2019] [Indexed: 01/13/2023]
Abstract
Diphenylphosphonates (DPPs) have been used for 50 years to inactivate serine hydrolases, creating adducts representative of tetrahedral intermediates of this important class of enzymes. Failure to react at active site serine residues, however, can thwart their usefulness. Here, we describe a facile route and allied mechanistic studies to highly reactive, structurally complex organofluorophosphonates (FPs) by direct fluorinative hydrolysis of DPPs. Advantages over current preparations of FPs are exemplified by the synthesis of a β-lactam-containing peptide substrate analog capable of modifying the C-terminal, dual-function thioesterase involved in nocardicin A biosynthesis. Although this serine hydrolase was found to resist modification by classic DPP inhibitors, active site selective phosphonylation by the corresponding FP occurs rapidly to form a stable adduct. This simple, late-stage method enables the ready preparation of FP probes that retain important structural motifs of native substrates, thus promoting efforts in mechanistic enzymology by accessing biologically relevant enzyme-inhibitor co-structures.
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28
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Mascaró C, Ortega A, Carceller E, Ruiz Rodriguez R, Ciceri F, Lunardi S, Yu L, Hilbert M, Maes T. Chemoprobe-based assays of histone lysine demethylase 1A target occupation enable in vivo pharmacokinetics and pharmacodynamics studies of KDM1A inhibitors. J Biol Chem 2019; 294:8311-8322. [PMID: 30804215 DOI: 10.1074/jbc.ra118.006980] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Screening of cellular activity for inhibitors of histone lysine modifiers is most frequently performed indirectly by analyzing changes in the total levels of histone marks targeted by lysine methylases/demethylases. However, inhibition of histone lysine modifiers often leads to local rather than total changes in histone marks. Also, because histone modifications can be modulated by more than one cellular enzyme, it is not always clear whether changes in histone marks are a direct or indirect consequence of the inhibitor treatment applied. Direct assessment of target occupation can provide a useful tool to quantify the fraction of an epigenetic modifier that is bound to a pharmacological inhibitor (target engagement). Here, we developed and used a novel chemoprobe-based immunoassay to quantify target engagement in cells. Quantification of the fraction of free KDM1A was made possible, in an immune-based assay, by coupling a biotinylated chemoprobe to a warhead capable of selectively and irreversibly binding to the free active form of KDM1A. The results obtained confirmed that this approach is able to determine the degree of target engagement in a dose-dependent manner. Furthermore, the assay can be also used on tissue extracts to analyze the in vivo pharmacokinetics and pharmacodynamics relationship of KDM1A inhibitors, as has been exemplified with ORY-1001 (iadademstat), a potent and irreversible inhibitor of KDM1A. The principle of this assay may be applied to other targets, and the KDM1A probe may be employed in chemoproteomic analyses.
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Affiliation(s)
- Cristina Mascaró
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Alberto Ortega
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Elena Carceller
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Raquel Ruiz Rodriguez
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Filippo Ciceri
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Serena Lunardi
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain
| | - Li Yu
- Roche Innovation Center New York, New York, New York 10016
| | - Manuel Hilbert
- Roche Innovation Center Basel, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Tamara Maes
- From Oryzon Genomics S.A., Carrer Sant Ferran 74, Cornellà de Llobregat, Barcelona 08940, Spain.
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29
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Kuusk S, Kont R, Kuusk P, Heering A, Sørlie M, Bissaro B, Eijsink VGH, Väljamäe P. Kinetic insights into the role of the reductant in H 2O 2-driven degradation of chitin by a bacterial lytic polysaccharide monooxygenase. J Biol Chem 2018; 294:1516-1528. [PMID: 30514757 DOI: 10.1074/jbc.ra118.006196] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/23/2018] [Indexed: 12/13/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes that catalyze oxidative cleavage of glycosidic bonds in polysaccharides in the presence of an external electron donor (reductant). In the classical O2-driven monooxygenase reaction, the reductant is needed in stoichiometric amounts. In a recently discovered, more efficient H2O2-driven reaction, the reductant would be needed only for the initial reduction (priming) of the LPMO to its catalytically active Cu(I) form. However, the influence of the reductant on reducing the LPMO or on H2O2 production in the reaction remains undefined. Here, we conducted a detailed kinetic characterization to investigate how the reductant affects H2O2-driven degradation of 14C-labeled chitin by a bacterial LPMO, SmLPMO10A (formerly CBP21). Sensitive detection of 14C-labeled products and careful experimental set-ups enabled discrimination between the effects of the reductant on LPMO priming and other effects, in particular enzyme-independent production of H2O2 through reactions with O2 When supplied with H2O2, SmLPMO10A catalyzed 18 oxidative cleavages per molecule of ascorbic acid, suggesting a "priming reduction" reaction. The dependence of initial rates of chitin degradation on reductant concentration followed hyperbolic saturation kinetics, and differences between the reductants were manifested in large variations in their half-saturating concentrations (K mR app). Theoretical analyses revealed that K mR app decreases with a decreasing rate of polysaccharide-independent LPMO reoxidation (by either O2 or H2O2). We conclude that the efficiency of LPMO priming depends on the relative contributions of reductant reactivity, on the LPMO's polysaccharide monooxygenase/peroxygenase and reductant oxidase/peroxidase activities, and on reaction conditions, such as O2, H2O2, and polysaccharide concentrations.
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Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Piret Kuusk
- Institute of Molecular and Physics, University of Tartu, 51010 Tartu, Estonia
| | - Agnes Heering
- Institute of Molecular and Chemistry, University of Tartu, 51010 Tartu, Estonia
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia.
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30
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Abstract
The polyamines spermidine, spermine, and their precursor putrescine are organic polycations involved in various cellular processes and are absolutely essential for cellular proliferation. Because of their crucial function in the cell, their intracellular concentration must be maintained at optimal levels. To a large extent, this regulation is achieved through the activity of an autoregulatory loop that involves two proteins, antizyme (Az) and antizyme inhibitor (AzI), that regulate the first enzyme in polyamine biosynthesis, ornithine decarboxylase (ODC), and polyamine uptake activity in response to intracellular polyamine levels. In this Minireview, I will discuss what has been learned about the mechanism of Az expression and its physical interaction with both ODC and AzI in the regulation of polyamines.
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Affiliation(s)
- Chaim Kahana
- From the Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Westh P, Borch K, Sørensen T, Tokin R, Kari J, Badino S, Cavaleiro MA, Røjel N, Christensen S, Vesterager CS, Schiano-di-Cola C. Thermoactivation of a cellobiohydrolase. Biotechnol Bioeng 2018; 115:831-838. [PMID: 29240229 DOI: 10.1002/bit.26513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/21/2017] [Accepted: 12/04/2017] [Indexed: 01/11/2023]
Abstract
We have measured activity and substrate affinity of the thermostable cellobiohydrolase, Cel7A, from Rasamsonia emersonii over a broad range of temperatures. For the wild type enzyme, which does not have a Carbohydrate Binding Module (CBM), higher temperature only led to moderately increased activity against cellulose, and we ascribed this to a pronounced, temperature induced desorption of enzyme from the substrate surface. We also tested a "high affinity" variant of R. emersonii Cel7A with a linker and CBM from a related enzyme. At room temperature, the activity of the variant was similar to the wild type, but the variant was more accelerated by temperature and about two-fold faster around 70 °C. This better thermoactivation of the high-affinity variant could not be linked to differences in stability or the catalytic process, but coincided with less desorption as temperature increased. Based on these observations and earlier reports on moderate thermoactivation of cellulases, we suggest that better cellulolytic activity at industrially relevant temperatures may be attained by engineering improved substrate affinity into enzymes that already possess good thermostability.
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Affiliation(s)
- Peter Westh
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | | | - Trine Sørensen
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Radina Tokin
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Jeppe Kari
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Silke Badino
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | | | - Nanna Røjel
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Stefan Christensen
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
| | - Cynthia S Vesterager
- Department of Science and Environment, INM, Universitetsvej 1, Roskilde, Denmark
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Peixoto ÁS, Geyer RR, Iqbal A, Truzzi DR, Soares Moretti AI, Laurindo FRM, Augusto O. Peroxynitrite preferentially oxidizes the dithiol redox motifs of protein-disulfide isomerase. J Biol Chem 2017; 293:1450-1465. [PMID: 29191937 DOI: 10.1074/jbc.m117.807016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/29/2017] [Indexed: 12/22/2022] Open
Abstract
Protein-disulfide isomerase (PDI) is a ubiquitous dithiol-disulfide oxidoreductase that performs an array of cellular functions, such as cellular signaling and responses to cell-damaging events. PDI can become dysfunctional by post-translational modifications, including those promoted by biological oxidants, and its dysfunction has been associated with several diseases in which oxidative stress plays a role. Because the kinetics and products of the reaction of these oxidants with PDI remain incompletely characterized, we investigated the reaction of PDI with the biological oxidant peroxynitrite. First, by determining the rate constant of the oxidation of PDI's redox-active Cys residues (Cys53 and Cys397) by hydrogen peroxide (k = 17.3 ± 1.3 m-1 s-1 at pH 7.4 and 25 °C), we established that the measured decay of the intrinsic PDI fluorescence is appropriate for kinetic studies. The reaction of these PDI residues with peroxynitrite was considerably faster (k = (6.9 ± 0.2) × 104 m-1 s-1), and both Cys residues were kinetically indistinguishable. Limited proteolysis, kinetic simulations, and MS analyses confirmed that peroxynitrite preferentially oxidizes the redox-active Cys residues of PDI to the corresponding sulfenic acids, which reacted with the resolving thiols at the active sites to produce disulfides (i.e. Cys53-Cys56 and Cys397-Cys400). A fraction of peroxynitrite, however, decayed to radicals that hydroxylated and nitrated other active-site residues (Trp52, Trp396, and Tyr393). Excess peroxynitrite promoted further PDI oxidation, nitration, inactivation, and covalent oligomerization. We conclude that these PDI modifications may contribute to the pathogenic mechanism of several diseases associated with dysfunctional PDI.
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Affiliation(s)
- Álbert Souza Peixoto
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - R Ryan Geyer
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - Asif Iqbal
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - Daniela R Truzzi
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
| | - Ana I Soares Moretti
- Vascular Biology Laboratory, Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, CEP 05403-000, Brazil
| | - Francisco R M Laurindo
- Vascular Biology Laboratory, Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, CEP 05403-000, Brazil
| | - Ohara Augusto
- From the Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, CEP 05508-000, Brazil and
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33
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Kuusk S, Bissaro B, Kuusk P, Forsberg Z, Eijsink VGH, Sørlie M, Väljamäe P. Kinetics of H 2O 2-driven degradation of chitin by a bacterial lytic polysaccharide monooxygenase. J Biol Chem 2017; 293:523-531. [PMID: 29138240 DOI: 10.1074/jbc.m117.817593] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/31/2017] [Indexed: 11/06/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides, such as cellulose and chitin, and are of interest in biotechnological utilization of these abundant biomaterials. It has recently been shown that LPMOs can use H2O2, instead of O2, as a cosubstrate. This peroxygenase-like reaction by a monocopper enzyme is unprecedented in nature and opens new avenues in chemistry and enzymology. Here, we provide the first detailed kinetic characterization of chitin degradation by the bacterial LPMO chitin-binding protein CBP21 using H2O2 as cosubstrate. The use of 14C-labeled chitin provided convenient and sensitive detection of the released soluble products, which enabled detailed kinetic measurements. The kcat for chitin oxidation found here (5.6 s-1) is more than an order of magnitude higher than previously reported (apparent) rate constants for reactions containing O2 but no added H2O2 The kcat/Km for H2O2-driven degradation of chitin was on the order of 106 m-1 s-1, indicating that LPMOs have catalytic efficiencies similar to those of peroxygenases. Of note, H2O2 also inactivated CBP21, but the second-order rate constant for inactivation was about 3 orders of magnitude lower than that for catalysis. In light of the observed CBP21 inactivation at higher H2O2 levels, we conclude that controlled generation of H2O2in situ seems most optimal for fueling LPMO-catalyzed oxidation of polysaccharides.
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Affiliation(s)
- Silja Kuusk
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Piret Kuusk
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway, and
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia,
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34
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Njuma OJ, Davis I, Ndontsa EN, Krewall JR, Liu A, Goodwin DC. Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron hole-hopping within the enzyme. J Biol Chem 2017; 292:18408-18421. [PMID: 28972181 DOI: 10.1074/jbc.m117.791202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/22/2017] [Indexed: 11/06/2022] Open
Abstract
KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H2O2-induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H2O2 to O2 and H2O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H2O2 disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting (i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H2O2 Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates.
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Affiliation(s)
- Olive J Njuma
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Ian Davis
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Elizabeth N Ndontsa
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Jessica R Krewall
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Aimin Liu
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and
| | - Douglas C Goodwin
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312,
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35
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Emptage RP, Schoenberger MJ, Ferguson KM, Marmorstein R. Intramolecular autoinhibition of checkpoint kinase 1 is mediated by conserved basic motifs of the C-terminal kinase-associated 1 domain. J Biol Chem 2017; 292:19024-19033. [PMID: 28972186 DOI: 10.1074/jbc.m117.811265] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/21/2017] [Indexed: 11/06/2022] Open
Abstract
Precise control of the cell cycle allows for timely repair of genetic material prior to replication. One factor intimately involved in this process is checkpoint kinase 1 (Chk1), a DNA damage repair inducing Ser/Thr protein kinase that contains an N-terminal kinase domain and a C-terminal regulatory region consisting of a ∼100-residue linker followed by a putative kinase-associated 1 (KA1) domain. We report the crystal structure of the human Chk1 KA1 domain, demonstrating striking structural homology with other sequentially diverse KA1 domains. Separately purified Chk1 kinase and KA1 domains are intimately associated in solution, which results in inhibition of Chk1 kinase activity. Using truncation mutants and site-directed mutagenesis, we define the inhibitory face of the KA1 domain as a series of basic residues residing on two conserved regions of the primary structure. These findings point to KA1-mediated intramolecular autoinhibition as a key regulatory mechanism of human Chk1, and provide new therapeutic possibilities with which to attack this validated oncology target with small molecules.
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Affiliation(s)
- Ryan P Emptage
- From the Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104,
| | - Megan J Schoenberger
- the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
| | - Kathryn M Ferguson
- the Department of Pharmacology and Cancer Biology Institute, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Ronen Marmorstein
- From the Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, .,the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and
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36
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Schardon CL, Tuley A, Er JAV, Swartzel JC, Fast W. Selective Covalent Protein Modification by 4-Halopyridines through Catalysis. Chembiochem 2017; 18:1551-1556. [PMID: 28470883 DOI: 10.1002/cbic.201700104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Indexed: 12/12/2022]
Abstract
We have investigated 4-halopyridines as selective, tunable, and switchable covalent protein modifiers for use in the development of chemical probes. Nonenzymatic reactivity of 4-chloropyridine with amino acids and thiols was ranked with respect to common covalent protein-modifying reagents and found to have reactivity similar to that of acrylamide, but could be switched to a reactivity similar to that of iodoacetamide upon stabilization of the positively charged pyridinium. Diverse, fragment-sized 4-halopyridines inactivated human dimethylarginine dimethylaminohydrolase-1 (DDAH1) through covalent modification of the active site cysteine, acting as quiescent affinity labels that required off-pathway catalysis through stabilization of the protonated pyridinium by a neighboring aspartate residue. A series of 2-fluoromethyl-substituted 4-chloropyridines demonstrated that the pKa and kinact /KI values could be predictably varied over several orders of magnitude. Covalent labeling of proteins in an Escherichia coli lysate was shown to require folded proteins, indicating that alternative proteins can be targeted, and modification is likely to be catalysisdependent. 4-Halopyridines, and quiescent affinity labels in general, represent an attractive strategy to develop reagents with switchable electrophilicity as selective covalent protein modifiers.
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Affiliation(s)
| | - Alfred Tuley
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA
| | - Joyce A V Er
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA
| | - Jake C Swartzel
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA.,LaMontagne Center for Infectious Disease, The University of Texas, Austin, TX, 78712, USA
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37
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Terzyan SS, Cook PF, Heroux A, Hanigan MH. Structure of 6-diazo-5-oxo-norleucine-bound human gamma-glutamyl transpeptidase 1, a novel mechanism of inactivation. Protein Sci 2017; 26:1196-1205. [PMID: 28378915 DOI: 10.1002/pro.3172] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 01/26/2023]
Abstract
Intense efforts are underway to identify inhibitors of the enzyme gamma-glutamyl transpeptidase 1 (GGT1) which cleaves extracellular gamma-glutamyl compounds and contributes to the pathology of asthma, reperfusion injury and cancer. The glutamate analog, 6-diazo-5-oxo-norleucine (DON), inhibits GGT1. DON also inhibits many essential glutamine metabolizing enzymes rendering it too toxic for use in the clinic as a GGT1 inhibitor. We investigated the molecular mechanism of human GGT1 (hGGT1) inhibition by DON to determine possible strategies for increasing its specificity for hGGT1. DON is an irreversible inhibitor of hGGT1. The second order rate constant of inactivation was 0.052 mM-1 min-1 and the Ki was 2.7 ± 0.7 mM. The crystal structure of DON-inactivated hGGT1 contained a molecule of DON without the diazo-nitrogen atoms in the active site. The overall structure of the hGGT1-DON complex resembled the structure of the apo-enzyme; however, shifts were detected in the loop forming the oxyanion hole and elements of the main chain that form the entrance to the active site. The structure of hGGT1-DON complex revealed two covalent bonds between the enzyme and inhibitor which were part of a six membered ring. The ring included the OG atom of Thr381, the reactive nucleophile of hGGT1 and the α-amine of Thr381. The structure of DON-bound hGGT1 has led to the discovery of a new mechanism of inactivation by DON that differs from its inactivation of other glutamine metabolizing enzymes, and insight into the activation of the catalytic nucleophile that initiates the hGGT1 reaction.
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Affiliation(s)
- Simon S Terzyan
- Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104
| | - Paul F Cook
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019
| | - Annie Heroux
- Energy Sciences Directorate/Photon Science Division, Brookhaven National Laboratory, Upton, New York, 11973
| | - Marie H Hanigan
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104
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38
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Garzan A, Willby MJ, Ngo HX, Gajadeera CS, Green KD, Holbrook SYL, Hou C, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Combating Enhanced Intracellular Survival (Eis)-Mediated Kanamycin Resistance of Mycobacterium tuberculosis by Novel Pyrrolo[1,5-a]pyrazine-Based Eis Inhibitors. ACS Infect Dis 2017; 3:302-309. [PMID: 28192916 DOI: 10.1021/acsinfecdis.6b00193] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tuberculosis (TB) remains one of the leading causes of mortality worldwide. Hence, the identification of highly effective antitubercular drugs with novel modes of action is crucial. In this paper, we report the discovery and development of pyrrolo[1,5-a]pyrazine-based analogues as highly potent inhibitors of the Mycobacterium tuberculosis (Mtb) acetyltransferase enhanced intracellular survival (Eis), whose up-regulation causes clinically observed resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN). We performed a structure-activity relationship (SAR) study to optimize these compounds as potent Eis inhibitors both against purified enzyme and in mycobacterial cells. A crystal structure of Eis in complex with one of the most potent inhibitors reveals that the compound is bound to Eis in the AG binding pocket, serving as the structural basis for the SAR. These Eis inhibitors have no observed cytotoxicity to mammalian cells and are promising leads for the development of innovative AG adjuvant therapies against drug-resistant TB.
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Affiliation(s)
- Atefeh Garzan
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Laboratory Branch, Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Huy X. Ngo
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S. Gajadeera
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Laboratory Branch, Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
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39
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Garzan A, Willby MJ, Ngo HX, Gajadeera CS, Green KD, Holbrook SYL, Hou C, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Combating Enhanced Intracellular Survival (Eis)-Mediated Kanamycin Resistance of Mycobacterium tuberculosis by Novel Pyrrolo[1,5-a]pyrazine-Based Eis Inhibitors. ACS Infect Dis 2017. [PMID: 28192916 DOI: 10.1021/acsinfecdis.6b00193.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains one of the leading causes of mortality worldwide. Hence, the identification of highly effective antitubercular drugs with novel modes of action is crucial. In this paper, we report the discovery and development of pyrrolo[1,5-a]pyrazine-based analogues as highly potent inhibitors of the Mycobacterium tuberculosis (Mtb) acetyltransferase enhanced intracellular survival (Eis), whose up-regulation causes clinically observed resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN). We performed a structure-activity relationship (SAR) study to optimize these compounds as potent Eis inhibitors both against purified enzyme and in mycobacterial cells. A crystal structure of Eis in complex with one of the most potent inhibitors reveals that the compound is bound to Eis in the AG binding pocket, serving as the structural basis for the SAR. These Eis inhibitors have no observed cytotoxicity to mammalian cells and are promising leads for the development of innovative AG adjuvant therapies against drug-resistant TB.
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Affiliation(s)
- Atefeh Garzan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Melisa J Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30329, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S Gajadeera
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - James E Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30329, United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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40
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Machado LESF, Shen TL, Page R, Peti W. The KIM-family protein-tyrosine phosphatases use distinct reversible oxidation intermediates: Intramolecular or intermolecular disulfide bond formation. J Biol Chem 2017; 292:8786-8796. [PMID: 28389559 DOI: 10.1074/jbc.m116.774174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 04/07/2017] [Indexed: 11/06/2022] Open
Abstract
The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes hematopoietic protein-tyrosine phosphatase (HePTP), striatal-enriched protein-tyrosine phosphatase (STEP), and protein-tyrosine phosphatase receptor type R (PTPRR). KIM-PTPs bind and dephosphorylate mitogen-activated protein kinases (MAPKs) and thereby critically modulate cell proliferation and differentiation. PTP activity can readily be diminished by reactive oxygen species (ROS), e.g. H2O2, which oxidize the catalytically indispensable active-site cysteine. This initial oxidation generates an unstable sulfenic acid intermediate that is quickly converted into either a sulfinic/sulfonic acid (catalytically dead and irreversible inactivation) or a stable sulfenamide or disulfide bond intermediate (reversible inactivation). Critically, our understanding of ROS-mediated PTP oxidation is not yet sufficient to predict the molecular responses of PTPs to oxidative stress. However, identifying distinct responses will enable novel routes for PTP-selective drug design, important for managing diseases such as cancer and Alzheimer's disease. Therefore, we performed a detailed biochemical and molecular study of all KIM-PTP family members to determine their H2O2 oxidation profiles and identify their reversible inactivation mechanism(s). We show that despite having nearly identical 3D structures and sequences, each KIM-PTP family member has a unique oxidation profile. Furthermore, we also show that whereas STEP and PTPRR stabilize their reversibly oxidized state by forming an intramolecular disulfide bond, HePTP uses an unexpected mechanism, namely, formation of a reversible intermolecular disulfide bond. In summary, despite being closely related, KIM-PTPs significantly differ in oxidation profiles. These findings highlight that oxidation protection is critical when analyzing PTPs, for example, in drug screening.
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Affiliation(s)
| | | | - Rebecca Page
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912
| | - Wolfgang Peti
- From the Departments of Molecular Pharmacology, Physiology and Biotechnology, .,Chemistry, and
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41
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Abstract
Although the use of superheated steam has been known for quite a long time, only in the recent past has it emerged as a viable technology for food processing. Superheated steam, having higher enthalpy, can quickly transfer heat to the material being processed, resulting in its rapid heating. The major advantages of using superheated steam for food processing are better product quality (color, shrinkage, and rehydration characteristics), reduced oxidation losses, and higher energy efficiency. This review provides a comprehensive overview of recent studies on the application of superheated steam for food-processing operations such as drying, decontamination and microbial load reduction, parboiling, and enzyme inactivation. The review encompasses aspects such as the effect of superheated steam processing on product quality, mathematical models reported for superheated steam drying, and the future scope of application in food processing. Recent studies on process improvisation, wherein superheated steam is used at low pressure, in fluidized bed mode, sequential processing with hot air/infrared, and in combination with micro droplets of water have also been discussed.
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Affiliation(s)
- Anto Alfy
- a Department of Food Engineering, Council of Scientific and Industrial Research , Central Food Technological Research Institute , Mysore , India
| | - B V Kiran
- a Department of Food Engineering, Council of Scientific and Industrial Research , Central Food Technological Research Institute , Mysore , India
| | - G C Jeevitha
- a Department of Food Engineering, Council of Scientific and Industrial Research , Central Food Technological Research Institute , Mysore , India
| | - H Umesh Hebbar
- a Department of Food Engineering, Council of Scientific and Industrial Research , Central Food Technological Research Institute , Mysore , India
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42
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Hervé G, Evans HG, Fernado R, Patel C, Hachem F, Evans DR. Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure. J Biol Chem 2017; 292:629-637. [PMID: 27746403 DOI: 10.1074/jbc.m116.739862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/14/2016] [Indexed: 01/12/2023] Open
Abstract
Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO), which catalyzes the third step in de novo pyrimidine biosynthesis. The isolated protein, a 45-kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates. The loop is mostly disordered but is tethered to the active site region by several electrostatic and hydrogen bonds. This loop becomes ordered and is displaced from the active site upon formation of DHO-ATC complex. The application of pressure to the complex causes its time-dependent dissociation and the loss of both DHO and ATC activities. Pressure induced irreversible dissociation of the obligate ATC trimer, and as a consequence the DHO is also inactivated. However, moderate hydrostatic pressure applied to the isolated DHO subunit mimics the complex formation and reversibly activates the isolated subunit in the absence of ATC, suggesting that the loop has been displaced from the active site. This effect of pressure is explained by the negative volume change associated with the disruption of ionic interactions and exposure of ionized amino acids to the solvent (electrostriction). The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues.
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Affiliation(s)
- Guy Hervé
- From the Laboratoire BIOSIPE, Sorbonne Universités, Institut de Biologie Paris Seine, CNRS, Université Pierre et Marie Curie, 75005 Paris, France,
| | - Hedeel Guy Evans
- the Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan 48197, and.,the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Roshini Fernado
- the Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan 48197, and
| | - Chandni Patel
- the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Fatme Hachem
- the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - David R Evans
- the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
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43
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Virgen-Ortíz JJ, Pedrero SG, Fernandez-Lopez L, Lopez-Carrobles N, Gorines BC, Otero C, Fernandez-Lafuente R. Desorption of Lipases Immobilized on Octyl-Agarose Beads and Coated with Ionic Polymers after Thermal Inactivation. Stronger Adsorption of Polymers/Unfolded Protein Composites. Molecules 2017; 22:molecules22010091. [PMID: 28067789 PMCID: PMC6155924 DOI: 10.3390/molecules22010091] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 12/17/2022] Open
Abstract
Lipases from Candida antarctica (isoform B) and Rhizomucor miehei (CALB and RML) have been immobilized on octyl-agarose (OC) and further coated with polyethylenimine (PEI) and dextran sulfate (DS). The enzymes just immobilized on OC supports could be easily released from the support using 2% SDS at pH 7, both intact or after thermal inactivation (in fact, after inactivation most enzyme molecules were already desorbed). The coating with PEI and DS greatly reduced the enzyme release during thermal inactivation and improved enzyme stability. However, using OC-CALB/RML-PEI-DS, the full release of the immobilized enzyme to reuse the support required more drastic conditions: a pH value of 3, a buffer concentration over 2 M, and temperatures above 45 °C. However, even these conditions were not able to fully release the thermally inactivated enzyme molecules from the support, being necessary to increase the buffer concentration to 4 M sodium phosphate and decrease the pH to 2.5. The formation of unfolded protein/polymers composites seems to be responsible for this strong interaction between the octyl and some anionic groups of OC supports. The support could be reused five cycles using these conditions with similar loading capacity of the support and stability of the immobilized enzyme.
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Affiliation(s)
- Jose J Virgen-Ortíz
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD)-Centro de Innovación y Desarrollo Agroalimentario de Michoacán, A.C. (CIDAM), Km. 8 Antigua Carretera a Pátzcuaro s/n, C.P. 58341 Morelia, Michoacán, Mexico.
| | - Sara G Pedrero
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, C/Marie Curie 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
| | - Laura Fernandez-Lopez
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, C/Marie Curie 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
| | - Nerea Lopez-Carrobles
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, C/Marie Curie 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
| | - Beatriz C Gorines
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, C/Marie Curie 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
| | - Cristina Otero
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, C/Marie Curie 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, Instituto de Catálisis-CSIC, C/Marie Curie 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
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44
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Garzan A, Willby MJ, Green KD, Tsodikov OV, Posey JE, Garneau-Tsodikova S. Discovery and Optimization of Two Eis Inhibitor Families as Kanamycin Adjuvants against Drug-Resistant M. tuberculosis. ACS Med Chem Lett 2016; 7:1219-1221. [PMID: 27994767 DOI: 10.1021/acsmedchemlett.6b00261] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/15/2016] [Indexed: 11/29/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a global threat and innovative approaches such as using adjuvants of anti-TB therapeutics are required to combat it. High-throughput screening yielded two lead scaffolds of inhibitors of Mycobacterium tuberculosis (Mtb) acetyltransferase Eis, whose upregulation causes resistance to the anti-TB drug kanamycin (KAN). Chemical optimization on these scaffolds resulted in potent Eis inhibitors. One compound restored the activity of KAN in a KAN-resistant Mtb strain. Model structures of Eis-inhibitor complexes explain the structure-activity relationship.
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Affiliation(s)
- Atefeh Garzan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Melisa J. Willby
- Mycobacteriology
Laboratory Branch, Division of Tuberculosis Elimination, National
Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Keith D. Green
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Oleg V. Tsodikov
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - James E. Posey
- Mycobacteriology
Laboratory Branch, Division of Tuberculosis Elimination, National
Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Sylvie Garneau-Tsodikova
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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45
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Bocedi A, Fabrini R, Lo Bello M, Caccuri AM, Federici G, Mannervik B, Cornish-Bowden A, Ricci G. Evolution of Negative Cooperativity in Glutathione Transferase Enabled Preservation of Enzyme Function. J Biol Chem 2016; 291:26739-26749. [PMID: 27815499 DOI: 10.1074/jbc.m116.749507] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/03/2016] [Indexed: 11/06/2022] Open
Abstract
Negative cooperativity in enzyme reactions, in which the first event makes subsequent events less favorable, is sometimes well understood at the molecular level, but its physiological role has often been obscure. Negative cooperativity occurs in human glutathione transferase (GST) GSTP1-1 when it binds and neutralizes a toxic nitric oxide adduct, the dinitrosyl-diglutathionyl iron complex (DNDGIC). However, the generality of this behavior across the divergent GST family and its evolutionary significance were unclear. To investigate, we studied 16 different GSTs, revealing that negative cooperativity is present only in more recently evolved GSTs, indicating evolutionary drift in this direction. In some variants, Hill coefficients were close to 0.5, the highest degree of negative cooperativity commonly observed (although smaller values of nH are theoretically possible). As DNDGIC is also a strong inhibitor of GSTs, we suggest negative cooperativity might have evolved to maintain a residual conjugating activity of GST against toxins even in the presence of high DNDGIC concentrations. Interestingly, two human isoenzymes that play a special protective role, safeguarding DNA from DNDGIC, display a classical half-of-the-sites interaction. Analysis of GST structures identified elements that could play a role in negative cooperativity in GSTs. Beside the well known lock-and-key and clasp motifs, other alternative structural interactions between subunits may be proposed for a few GSTs. Taken together, our findings suggest the evolution of self-preservation of enzyme function as a novel facility emerging from negative cooperativity.
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Affiliation(s)
- Alessio Bocedi
- From the Department of Chemical Sciences and Technologies
| | | | | | - Anna Maria Caccuri
- Department of Experimental Medicine and Surgery, University of Rome, Tor Vergata, Rome 00133, Italy
| | | | - Bengt Mannervik
- Department of Neurochemistry, Stockholm University SE-10691 Stockholm, Sweden, and
| | - Athel Cornish-Bowden
- Aix Marseille Université, CNRS, Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Giorgio Ricci
- From the Department of Chemical Sciences and Technologies,
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46
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Kalous KS, Wynia-Smith SL, Olp MD, Smith BC. Mechanism of Sirt1 NAD+-dependent Protein Deacetylase Inhibition by Cysteine S-Nitrosation. J Biol Chem 2016; 291:25398-25410. [PMID: 27756843 PMCID: PMC5207242 DOI: 10.1074/jbc.m116.754655] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Indexed: 11/06/2022] Open
Abstract
The sirtuin family of proteins catalyze the NAD+-dependent deacylation of acyl-lysine residues. Humans encode seven sirtuins (Sirt1-7), and recent studies have suggested that post-translational modification of Sirt1 by cysteine S-nitrosation correlates with increased acetylation of Sirt1 deacetylase substrates. However, the mechanism of Sirt1 inhibition by S-nitrosation was unknown. Here, we show that Sirt1 is transnitrosated and inhibited by the physiologically relevant nitrosothiol S-nitrosoglutathione. Steady-state kinetic analyses and binding assays were consistent with Sirt1 S-nitrosation inhibiting binding of both the NAD+ and acetyl-lysine substrates. Sirt1 S-nitrosation correlated with Zn2+ release from the conserved sirtuin Zn2+-tetrathiolate and a loss of α-helical structure without overall thermal destabilization of the enzyme. Molecular dynamics simulations suggested that Zn2+ loss due to Sirt1 S-nitrosation results in repositioning of the tetrathiolate subdomain away from the rest of the catalytic domain, thereby disrupting the NAD+ and acetyl-lysine-binding sites. Sirt1 S-nitrosation was reversed upon exposure to the thiol-based reducing agents, including physiologically relevant concentrations of the cellular reducing agent glutathione. Reversal of S-nitrosation resulted in full restoration of Sirt1 activity only in the presence of Zn2+, consistent with S-nitrosation of the Zn2+-tetrathiolate as the primary source of Sirt1 inhibition upon S-nitrosoglutathione treatment.
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Affiliation(s)
- Kelsey S Kalous
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Sarah L Wynia-Smith
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Michael D Olp
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Brian C Smith
- From the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
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47
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Ricq EL, Hooker JM, Haggarty SJ. Activity-dependent Regulation of Histone Lysine Demethylase KDM1A by a Putative Thiol/Disulfide Switch. J Biol Chem 2016; 291:24756-24767. [PMID: 27634040 DOI: 10.1074/jbc.m116.734426] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
Lysine demethylation of proteins such as histones is catalyzed by several classes of enzymes, including the FAD-dependent amine oxidases KDM1A/B. The KDM1 family is homologous to the mitochondrial monoamine oxidases MAO-A/B and produces hydrogen peroxide in the nucleus as a byproduct of demethylation. Here, we show KDM1A is highly thiol-reactive in vitro and in cellular models. Enzyme activity is potently and reversibly inhibited by the drug disulfiram and by hydrogen peroxide. Hydrogen peroxide produced by KDM1A catalysis reduces thiol labeling and inactivates demethylase activity over time. MALDI-TOF mass spectrometry indicates that hydrogen peroxide blocks labeling of cysteine 600, which we propose forms an intramolecular disulfide with cysteine 618 to negatively regulate the catalytic activity of KDM1A. This activity-dependent regulation is unique among histone-modifying enzymes but consistent with redox sensitivity of epigenetic regulators.
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Affiliation(s)
- Emily L Ricq
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138,; the Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, and; the Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Jacob M Hooker
- the Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, and
| | - Stephen J Haggarty
- the Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114.
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48
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Koo J, Shiigi S, Rohovie M, Mehta K, Swartz JR. Characterization of [FeFe] Hydrogenase O2 Sensitivity Using a New, Physiological Approach. J Biol Chem 2016; 291:21563-21570. [PMID: 27435671 DOI: 10.1074/jbc.m116.737122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/15/2016] [Indexed: 11/06/2022] Open
Abstract
[FeFe] hydrogenases catalyze rapid H2 production but are highly O2-sensitive. Developing O2-tolerant enzymes is needed for sustainable H2 production technologies, but the lack of a quantitative and predictive assay for O2 tolerance has impeded progress. We describe a new approach to provide quantitative assessment of O2 sensitivity by using an assay employing ferredoxin NADP+ reductase (FNR) to transfer electrons from NADPH to hydrogenase via ferredoxins (Fd). Hydrogenase inactivation is measured during H2 production in an O2-containing environment. An alternative assay uses dithionite (DTH) to provide reduced Fd. This second assay measures the remaining hydrogenase activity in periodic samples taken from the NADPH-driven reaction solutions. The second assay validates the more convenient NADPH-driven assay, which better mimics physiological conditions. During development of the NADPH-driven assay and while characterizing the Clostridium pasteurianum (Cp) [FeFe] hydrogenase, CpI, we detected significant rates of direct electron loss from reduced Fd to O2 However, this loss does not interfere with measurement of first order hydrogenase inactivation, providing rate constants insensitive to initial hydrogenase concentration. We show increased activity and O2 tolerance for a protein fusion between Cp ferredoxin (CpFd) and CpI mediated by a 15-amino acid linker but not for a longer linker. We suggest that this precise, solution phase assay for [FeFe] hydrogenase O2 sensitivity and the insights we provide constitute an important advance toward the discovery of the O2-tolerant [FeFe] hydrogenases required for photosynthetic, biological H2 production.
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Affiliation(s)
- Jamin Koo
- From the Departments of Chemical Engineering and
| | - Stacey Shiigi
- Bioengineering, Stanford University, Stanford, California 94305
| | | | - Kunal Mehta
- Bioengineering, Stanford University, Stanford, California 94305
| | - James R Swartz
- From the Departments of Chemical Engineering and .,Bioengineering, Stanford University, Stanford, California 94305
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49
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Li Y, Guo Z, Jin L, Wang D, Gao Z, Su X, Hou H, Dong Y. Mechanism of the allosteric regulation of Streptococcus mutans 2'-deoxycytidylate deaminase. Acta Crystallogr D Struct Biol 2016; 72:883-91. [PMID: 27377385 DOI: 10.1107/s2059798316009153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 06/07/2016] [Indexed: 01/24/2023]
Abstract
In cells, dUMP is the intermediate precursor of dTTP in its synthesis during deoxynucleotide metabolism. In Gram-positive bacteria and eukaryotes, zinc-dependent deoxycytidylate deaminases (dCDs) catalyze the conversion of dCMP to dUMP. The activity of dCD is allosterically activated by dCTP and inhibited by dTTP. Here, the crystal structure of Streptococcus mutans dCD (SmdCD) complexed with dTTP is presented at 2.35 Å resolution, thereby solving the first pair of activator-bound and inhibitor-bound structures from the same species to provide a more definitive description of the allosteric mechanism. In contrast to the dTTP-bound dCD from the bacteriophage S-TIM5 (S-TIM5-dCD), dTTP-bound SmdCD adopts an inactive conformation similar to the apo form. A structural comparison suggests that the distinct orientations of the triphosphate group in S-TIM5-dCD and SmdCD are a result of the varying protein binding environment. In addition, calorimetric data establish that the modulators bound to dCD can be mutually competitively replaced. The results reveal the mechanism underlying its regulator-specific activity and might greatly enhance the understanding of the allosteric regulation of other dCDs.
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Affiliation(s)
- Yanhua Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhen Guo
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing, People's Republic of China
| | - Li Jin
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing, People's Republic of China
| | - Deqiang Wang
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing, People's Republic of China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaodong Su
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Science, Peking University, Beijing 100871, People's Republic of China
| | - Haifeng Hou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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50
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Terefe NS, Buckow R, Versteeg C. Quality-related enzymes in plant-based products: effects of novel food-processing technologies part 3: ultrasonic processing. Crit Rev Food Sci Nutr 2015; 55:147-58. [PMID: 24915308 DOI: 10.1080/10408398.2011.586134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
High-power ultrasound is a versatile technology which can potentially be used in many food processing applications including food preservation. This is part 2 of a series of review articles dealing with the effectiveness of nonthermal food processing technologies in food preservation focusing on their effect on enzymes. Typically, ultrasound treatment alone does not efficiently cause microbial or enzyme inactivation sufficient for food preservation. However, combined with mild heat with or without elevated pressure (P ≤ 500 kPa), ultrasound can effectively inactivate enzymes and microorganisms. Synergistic effects between ultrasound and mild heat have been reported for the inactivation of both enzymes and microorganisms. The application of ultrasound has been shown to enhance the rate of inactivation of quality degrading enzymes including pectin methylesterase (PME), polygalacturonase (PG), peroxidase (POD), polyphenol oxidase (PPO), and lipoxygenase (LOX) at mild temperature by up to 400 times. Moreover, ultrasound enables the inactivation of relatively heat-resistant enzymes such as tomato PG1 and thermostable orange PME at mild temperature conditions. The extent to which ultrasound enhances the inactivation rate depends on the type of enzyme, the medium in which the enzyme is suspended, and the processing condition including frequency, ultrasonic intensity, temperature, and pressure. The physical and chemical effects of cavitation are considered to be responsible for the ultrasound-induced inactivation of enzymes, although the dominant mechanism depends on the structure of the enzyme.
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