1
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Shen W, Hou Y, Yi Y, Li F, He C, Wang J. G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets. J Am Chem Soc 2024; 146:12778-12789. [PMID: 38679963 DOI: 10.1021/jacs.4c02901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
MicroRNAs (miRNAs) play indispensable roles in post-transcriptional gene regulation. The identification of target mRNAs is essential for dissecting the recognition basis, dynamics, and regulatory mechanism of miRNA-mRNA interactions. However, the lack of an unbiased method for detecting weak miRNA-mRNA interactions remains a long-standing obstacle for miRNA research. Here, we develop and provide proof-of-concept evidence demonstrating a chemical G-clamp-enhanced photo-cross-linking strategy for covalent capture of intracellular miRNA targets in different cell lines. This approach relies on an aryl-diazirine-G-clamp-modified-nucleoside (ARAGON) miRNA probe containing an alkynyl group that improves the thermal stability of miRNA-target mRNA duplex molecules and can rapidly cross-link with the complementary strand upon UV 365 nm activation, enhancing the transient capture of mRNA targets. After validating the accuracy and binding properties of ARAGON-based miRNA probes through the successful enrichment for the known targets of miR-106a, miR-21, and miR-101, we then extend ARAGON's application to screen for previously unknown targets of different miRNAs in various cell lines. Ultimately, results in this study uncover GAB1 as a target of miR-101 in H1299 lung cancer cells and show that miR-101 silencing of GAB1 can promote apoptosis in H1299 cells, suggesting an oncogenic mechanism of GAB1. This study thus provides a powerful and versatile tool for enhanced screening of global miRNA targets in cells to facilitate investigations of miRNA functions in fundamental cellular processes and disease pathogenesis.
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Affiliation(s)
- Weiguo Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yongkang Hou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yunpeng Yi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Fei Li
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Shields SWJ, Canez CR, Rosales CA, Roberts JA, Bourgaize H, Pallister PJ, Manthorpe JM, Smith JC. Optimized 13C-TrEnDi Enhances the Sensitivity of Plasmenyl Ether Glycerophospholipids and Demonstrates Compatibility with Other Derivatization Strategies. J Am Soc Mass Spectrom 2024; 35:972-981. [PMID: 38551491 DOI: 10.1021/jasms.4c00015] [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] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The identification and quantitation of plasmalogen glycerophospholipids is challenging due to their isobaric overlap with plasmanyl ether-linked glycerophospholipids, susceptibility to acid degradation, and their typically low abundance in biological samples. Trimethylation enhancement using diazomethane (TrEnDi) can be used to significantly enhance the signal of glycerophospholipids through the creation of quaternary ammonium groups producing fixed positive charges using 13C-diazomethane in complex lipid extracts. Although TrEnDi requires a strong acid for complete methylation, we report an optimized protocol using 10 mM HBF4 with the subsequent addition of a buffer solution that prevents acidic hydrolysis of plasmalogen species and enables the benefits of TrEnDi to be realized for this class of lipids. These optimized conditions were applied to aliquots of bovine liver extract (BLE) to achieve permethylation of plasmalogen lipids within a complex mixture. Treating aliquots of unmodified and TrEnDi-derivatized BLE samples with 80% formic acid and comparing their liquid chromatography mass spectrometry (LCMS) results to analogous samples not treated with formic acid, enabled the identification of 29 plasmalogen species. On average, methylated plasmalogen species from BLE demonstrated 2.81-fold and 28.1-fold sensitivity gains over unmodified counterparts for phosphatidylcholine and phosphatidylethanolamine plasmalogen species, respectively. Furthermore, the compatibility of employing 13C-TrEnDi and a previously reported iodoacetalization strategy was demonstrated to effectively identify plasmenyl-ether lipids in complex biological extracts at greater levels of sensitivity. Overall, we detail an optimized 13C-TrEnDi derivatization strategy that enables the analysis of plasmalogen glycerophospholipids with no undesired cleavage of radyl groups, boosting their sensitivity in LCMS and LCMS/MS analyses.
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Affiliation(s)
- Samuel W J Shields
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Carlos R Canez
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Christian A Rosales
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Joshua A Roberts
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Hillary Bourgaize
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Peter J Pallister
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Jeffrey M Manthorpe
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Jeffrey C Smith
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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Cabanero DC, Kariofillis SK, Johns AC, Kim J, Ni J, Park S, Parker DL, Ramil CP, Roy X, Shah NH, Rovis T. Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light. J Am Chem Soc 2024; 146:1337-1345. [PMID: 38165744 DOI: 10.1021/jacs.3c09545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
State-of-the-art methods in photoproximity labeling center on the targeted generation and capture of short-lived reactive intermediates to provide a snapshot of local protein environments. Diazirines are the current gold standard for high-resolution proximity labeling, generating short-lived aryl(trifluoromethyl) carbenes. Here, we present a method to access aryl(trifluoromethyl) carbenes from a stable diazo source via tissue-penetrable, deep red to near-infrared light (600-800 nm). The operative mechanism of this activation involves Dexter energy transfer from photoexcited osmium(II) photocatalysts to the diazo, thus revealing an aryl(trifluoromethyl) carbene. The labeling preferences of the diazo probe with amino acids are studied, showing high reactivity toward heteroatom-H bonds. Upon the synthesis of a biotinylated diazo probe, labeling studies are conducted on native proteins as well as proteins conjugated to the Os photocatalyst. Finally, we demonstrate that the conjugation of a protein inhibitor to the photocatalyst also enables selective protein labeling in the presence of spectator proteins and achieves specific labeling of a membrane protein on the surface of mammalian cells via a two-antibody photocatalytic system.
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Affiliation(s)
- David C Cabanero
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Stavros K Kariofillis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Andrew C Johns
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jinwoo Kim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jizhi Ni
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sangho Park
- Discovery Biology, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Dann L Parker
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carlo P Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Xavier Roy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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4
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Rosales CA, Sheedy KL, Wasslen KV, Manthorpe JM, Smith JC. Trimethylation Enhancement Using Diazomethane (TrEnDi) Enables Enhanced Detection of Glufosinate and 3-(Methylphosphinico)propionic Acid from Complex Canola Samples. J Am Soc Mass Spectrom 2024; 35:140-150. [PMID: 38127770 DOI: 10.1021/jasms.3c00376] [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] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Over the past century, agriculture practices have transitioned from manual cultivation to the use of an array of chemical herbicides for weed control including phosphinothricin, or glufosinate (GLUF). Consequently, the potential for long-term residual GLUF exposure in the food chain has increased, highlighting the need for improved analytical strategies for its detection, as well as the detection of its main breakdown product 3-(methylphosphinico)propionic acid (MPPA). Chemical derivatization strategies have been developed to improve the detection of GLUF and MPPA via liquid chromatography tandem mass spectrometry analyses. Herein, we employ trimethylation enhancement using diazomethane (TrEnDi) for the first time as a means to confer analytical advantages via quantitatively derivatizing these analytes into permethylated GLUF ([GLUFTr]+) and MPPA ([MPPATr+H]+). Comparing [GLUFTr]+ and [MPPATr+H]+ to underivatized counterparts, TrEnDi yields 2.8-fold and 1.7-fold improvements in reversed-phase chromatographic retention, respectively, while MS-based sensitivity is enhanced 4.1-fold and 11.0-fold, respectively. Successful analyte derivatization (with >99% yields) was further demonstrated on a commercial herbicide solution imparting consistent analytical enhancements. To investigate the benefits of TrEnDi in a bona fide agricultural scenario, simple aqueous extractions from distinct parts of field-grown canola plants were performed to quantify GLUF and MPPA before and after TrEnDi derivatization. In their underivatized forms, GLUF and MPPA were undetectable in all field samples, whereas [GLUFTr]+ and [MPPATr+H]+ were readily quantifiable using the same analysis conditions. Our results demonstrate that TrEnDi continues to be a useful tool to enhance the analytical characteristics of organic molecules that are traditionally difficult to detect.
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Affiliation(s)
- Christian A Rosales
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Krysten L Sheedy
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Karl V Wasslen
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Jeffrey M Manthorpe
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Jeffrey C Smith
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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5
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Roberts JA, Rosales CA, Wasslen KV, Radnoff AS, Godbout E, Diallo JS, Manthorpe JM, Smith JC. An In Silico Database for Automated Feature Identification of High-Resolution Tandem Mass Spectrometry 13C-Trimethylation Enhancement Using Diazomethane ( 13C-TrEnDi)-Modified Lipid Data. J Am Soc Mass Spectrom 2023; 34:2722-2730. [PMID: 37929927 DOI: 10.1021/jasms.3c00273] [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] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
13C-Trimethylation enhancement using diazomethane (13C-TrEnDi) is a chemical derivatization technique that uses 13C-labeled diazomethane to increase mass spectrometry (MS) signal intensities for phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid classes, both of which are of major interest in biochemistry. In silico mass spectrometry databases have become mainstays in lipidomics experiments; however, 13C-TrEnDi-modified PC and PE species have altered m/z and fragmentation patterns from their native counterparts. To build a database of 13C-TrEnDi-modified PC and PE species, a lipid extract from nutritional yeast was derivatized and fragmentation spectra of modified PC and PE species were mined using diagnostic fragmentation filtering by searching 13C-TrEnDi-modified headgroups with m/z 199 (PC) and 202 (PE). Identities of 25 PC and 10 PE species were assigned after comparing to predicted masses from the Lipid Maps Structure Database with no false positive identifications observed; neutral lipids could still be annotated after derivatization. Collision energies from 16 to 52 eV were examined, resulting in three additional class-specific fragment ions emerging, as well as a combined sn-1/sn-2 fragment ion, allowing sum-composition level annotations to be assigned. Using the Lipid Blast templates, a NIST-compatible 13C-TrEnDi database was produced based on fragmentation spectra observed at 36 eV and tested on HEK 293T cell lipid extracts, identifying 47 PC and 24 PE species, representing a 1.8-fold and 2.2-fold increase in annotations, respectively. The 13C-TrEnDi database is freely available, MS vendor-independent, and widely compatible with MS data processing pipelines, increasing the throughput and accessibility of TrEnDi for lipidomics applications.
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Affiliation(s)
- Joshua A Roberts
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Christian A Rosales
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Karl V Wasslen
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Angela S Radnoff
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Elena Godbout
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6, Canada
| | - Jean-Simon Diallo
- Centre for Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6, Canada
| | - Jeffrey M Manthorpe
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Jeffrey C Smith
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
- Carleton Mass Spectrometry Centre, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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6
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Murai Y, Hashimoto M. Heteroaromatic Diazirines Are Essential Building Blocks for Material and Medicinal Chemistry. Molecules 2023; 28:molecules28031408. [PMID: 36771073 PMCID: PMC9921084 DOI: 10.3390/molecules28031408] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
In materials (polymer) science and medicinal chemistry, heteroaromatic derivatives play the role of the central skeleton in development of novel devices and discovery of new drugs. On the other hand, (3-trifluoromethyl)phenyldiazirine (TPD) is a crucial chemical method for understanding biological processes such as ligand-receptor, nucleic acid-protein, lipid-protein, and protein-protein interactions. In particular, use of TPD has increased in recent materials science to create novel electric and polymer devices with comparative ease and reduced costs. Therefore, a combination of heteroaromatics and (3-trifluoromethyl)diazirine is a promising option for creating better materials and elucidating the unknown mechanisms of action of bioactive heteroaromatic compounds. In this review, a comprehensive synthesis of (3-trifluoromethyl)diazirine-substituted heteroaromatics is described.
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Affiliation(s)
- Yuta Murai
- Graduate School of Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
- Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
- Correspondence: (Y.M.); (M.H.); Tel.: +81-11-706-9030 (Y.M.); +81-11-706-3849 (M.H.)
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Correspondence: (Y.M.); (M.H.); Tel.: +81-11-706-9030 (Y.M.); +81-11-706-3849 (M.H.)
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Korn P, Schwieger C, Gruhle K, Garamus VM, Meister A, Ihling C, Drescher S. Azide- and diazirine-modified membrane lipids: Physicochemistry and applicability to study peptide/lipid interactions via cross-linking/mass spectrometry. Biochim Biophys Acta Biomembr 2022; 1864:184004. [PMID: 35841926 DOI: 10.1016/j.bbamem.2022.184004] [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] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Although the incorporation of photo-activatable lipids into membranes potentially opens new avenues for studying interactions with peptides and proteins, the question of whether azide- or diazirine-modified lipids are suitable for such studies remains controversial. We have recently shown that diazirine-modified lipids can indeed form cross-links to membrane peptides after UV activation and that these cross-links can be precisely determined in their position by mass spectrometry (MS). However, we also observed an unexpected backfolding of the lipid's diazirine-containing stearoyl chain to the membrane interface challenging the potential application of this modified lipid for future cross-linking (XL)-MS studies of protein/lipid interactions. In this work, we compared an azide- (AzidoPC) and a diazirine-modified (DiazPC) membrane lipid regarding their self-assembly properties, their mixing behavior with saturated bilayer-forming phospholipids, and their reactivity upon UV activation using differential scanning calorimetry (DSC), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and MS. Mixtures of both modified lipids with DMPC were further used for photo-chemically induced XL experiments with a transmembrane model peptide (KLAW23) to elucidate similarities and differences between the azide and the diazirine moiety. We showed that both photo-reactive lipids can be used to study lipid/peptide and lipid/protein interactions. The AzidoPC proved easier to handle, whereas the DiazPC had fewer degradation products and a higher cross-linking yield. However, the problem of backfolding occurs in both lipids; thus, it seems to be a general phenomenon.
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Affiliation(s)
- Patricia Korn
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Schwieger
- Institute of Chemistry, MLU Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Vasil M Garamus
- Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Biochemistry and Biotechnology-Physical Biotechnology, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany; Phospholipid Research Center, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany.
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8
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Cheng YS, Zhang T, Ma X, Pratuangtham S, Zhang GC, Ondrus AA, Mafi A, Lomenick B, Jones JJ, Ondrus AE. A proteome-wide map of 20(S)-hydroxycholesterol interactors in cell membranes. Nat Chem Biol 2021; 17:1271-1280. [PMID: 34799735 PMCID: PMC8607797 DOI: 10.1038/s41589-021-00907-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/25/2021] [Indexed: 12/28/2022]
Abstract
Oxysterols (OHCs) are hydroxylated cholesterol metabolites that play ubiquitous roles in health and disease. Due to the non-covalent nature of their interactions and their unique partitioning in membranes, the analysis of live-cell, proteome-wide interactions of OHCs remains an unmet challenge. Here, we present a structurally precise chemoproteomics probe for the biologically active molecule 20(S)-hydroxycholesterol (20(S)-OHC) and provide a map of its proteome-wide targets in the membranes of living cells. Our target catalog consolidates diverse OHC ontologies and demonstrates that OHC-interacting proteins cluster with specific processes in immune response and cancer. Competition experiments reveal that 20(S)-OHC is a chemo-, regio- and stereoselective ligand for the protein transmembrane protein 97 (Tmem97/the σ2 receptor), enabling us to reconstruct the 20(S)-OHC-Tmem97 binding site. Our results demonstrate that multiplexed, quantitative analysis of cellular target engagement can expose new dimensions of metabolite activity and identify actionable targets for molecular therapy.
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Affiliation(s)
- Yu-Shiuan Cheng
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tianyi Zhang
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xiang Ma
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sarida Pratuangtham
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grace C Zhang
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexander A Ondrus
- Mathematics Department, Northern Alberta Institute of Technology, Edmonton, Alberta, Canada
| | - Amirhossein Mafi
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Jeffrey J Jones
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Alison E Ondrus
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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9
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Cuthbert TJ, Ennis S, Musolino SF, Buckley HL, Niikura M, Wulff JE, Menon C. Covalent functionalization of polypropylene filters with diazirine-photosensitizer conjugates producing visible light driven virus inactivating materials. Sci Rep 2021; 11:19029. [PMID: 34561486 PMCID: PMC8463589 DOI: 10.1038/s41598-021-98280-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/07/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
The SARS-CoV-2 pandemic has highlighted the weaknesses of relying on single-use mask and respirator personal protective equipment (PPE) and the global supply chain that supports this market. There have been no major innovations in filter technology for PPE in the past two decades. Non-woven textiles used for filtering PPE are single-use products in the healthcare environment; use and protection is focused on preventing infection from airborne or aerosolized pathogens such as Influenza A virus or SARS-CoV-2. Recently, C-H bond activation under mild and controllable conditions was reported for crosslinking commodity aliphatic polymers such as polyethylene and polypropylene. Significantly, these are the same types of polymers used in PPE filtration systems. In this report, we take advantage of this C-H insertion method to covalently attach a photosensitizing zinc-porphyrin to the surface of a melt-blow non-woven textile filter material. With the photosensitizer covalently attached to the surface of the textile, illumination with visible light was expected to produce oxidizing 1O2/ROS at the surface of the material that would result in pathogen inactivation. The filter was tested for its ability to inactivate Influenza A virus, an enveloped RNA virus similar to SARS-CoV-2, over a period of four hours with illumination of high intensity visible light. The photosensitizer-functionalized polypropylene filter inactivated our model virus by 99.99% in comparison to a control.
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Affiliation(s)
- T J Cuthbert
- Department of Health Sciences and Technology, ETH Zürich, 8008, Zürich, Switzerland.
- Schools of Mechatronic Systems Engineering and Engineering Science, Simon Fraser University, Metro Vancouver, BC, V5A 1S6, Canada.
| | - S Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - S F Musolino
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - H L Buckley
- Department of Civil Engineering, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - M Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - J E Wulff
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - C Menon
- Department of Health Sciences and Technology, ETH Zürich, 8008, Zürich, Switzerland
- Schools of Mechatronic Systems Engineering and Engineering Science, Simon Fraser University, Metro Vancouver, BC, V5A 1S6, Canada
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10
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Zhang X, Spiegel J, Martínez Cuesta S, Adhikari S, Balasubramanian S. Chemical profiling of DNA G-quadruplex-interacting proteins in live cells. Nat Chem 2021; 13:626-633. [PMID: 34183817 PMCID: PMC8245323 DOI: 10.1038/s41557-021-00736-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [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: 01/20/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022]
Abstract
DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential to understand the underlying regulatory mechanisms on a molecular level. Here we describe a co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in native chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We first showed the robustness of CMPP by proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we then identified hundreds of putative G4-interacting proteins from various functional classes. Next, we confirmed a high G4-binding affinity and selectivity for several newly discovered G4 interactors in vitro, and we validated direct G4 interactions for a functionally important candidate in cellular chromatin using an independent approach. Our studies provide a chemical strategy to map protein interactions of specific nucleic acid features in living cells.
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Affiliation(s)
- Xiaoyun Zhang
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Sergio Martínez Cuesta
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | | | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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11
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Pan M, Qin C, Han X. Quantitative Analysis of Polyphosphoinositide, Bis(monoacylglycero)phosphate, and Phosphatidylglycerol Species by Shotgun Lipidomics After Methylation. Methods Mol Biol 2021; 2306:77-91. [PMID: 33954941 PMCID: PMC8287892 DOI: 10.1007/978-1-0716-1410-5_6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phospholipids play important roles in biological process even at a very low level. For example, bis(monoacylglycerol)phosphate (BMP) is involved in the pathogenesis of lysosomal storage diseases, and polyphosphoinositides (PPI) play critical roles in cellular signaling and functions. Phosphatidylglycerol (PG), a structural isomer of BMP, mediates lipid-protein and lipid-lipid interactions, and inhibits platelet activating factor and phosphatidylcholine transferring. However, due to their low abundance, the analysis of these phospholipids from biological samples is technically challenging. Therefore, the cellular function and metabolism of these phospholipids are still elusive. This chapter overviews a novel method of shotgun lipidomics after methylation with trimethylsilyl-diazomethane (TMS-D) for accurate and comprehensive analysis of these phospholipid species in biological samples. Firstly, a modified Bligh and Dyer procedure is performed to extract tissue lipids for PPI analysis, whereas modified methyl-tert-butylether (MTBE) extraction and modified Folch extraction methods are described to extract tissue lipids for PPI analysis. Secondly, TMS-D methylation is performed to derivatize PG/BMP and PPI, respectively. Then, we described the shotgun lipidomics strategies that can be used as cost-effective and relatively high-throughput methods to determine BMP, PG, and PPI species and isomers with different phosphate position(s) and fatty acyl chains. The described method of shotgun lipidomics after methylation achieves feasible and reliable quantitative analysis of low-abundance lipid classes. The application of this novel method should enable us to reveal the metabolism and functions of these phospholipids in healthy and disease states.
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Affiliation(s)
- Meixia Pan
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Chao Qin
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Department of Medicine-Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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12
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Curry AM, Barton E, Kang W, Mongeluzi DV, Cen Y. Development of Second Generation Activity-Based Chemical Probes for Sirtuins. Molecules 2020; 26:molecules26010011. [PMID: 33375102 PMCID: PMC7792806 DOI: 10.3390/molecules26010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
NAD+ (nicotinamide adenine dinucleotide)-dependent protein deacylases, namely, the sirtuins, are important cell adaptor proteins that alter cell physiology in response to low calorie conditions. They are thought to mediate the beneficial effects of calorie restriction to extend longevity and improve health profiles. Novel chemical probes are highly desired for a better understanding of sirtuin’s roles in various biological processes. We developed a group of remarkably simple activity-based chemical probes for the investigation of active sirtuin content in complex native proteomes. These probes harbor a thioacyllysine warhead, a diazirine photoaffinity tag, as well as a terminal alkyne bioorthogonal functional group. Compared to their benzophenone-containing counterparts, these new probes demonstrated improved labeling efficiency and sensitivity, shortened irradiation time, and reduced background signal. They were applied to the labeling of individual recombinant proteins, protein mixtures, and whole cell lysate. These cell permeable small molecule probes also enabled the cellular imaging of sirtuin activity change. Taken together, our study provides new chemical biology tools and future drug discovery strategies for perturbing the activity of different sirtuin isoforms.
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Affiliation(s)
- Alyson M. Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Elizabeth Barton
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Wenjia Kang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Daniel V. Mongeluzi
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
- Correspondence: ; Tel.: +1-804-828-7405
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13
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Salah M, Belghiti ME, Aitouna AO, Zeroual A, Jorio S, El Alaoui Abdellaoui H, El Hadki H, Marakchi K, Komiha N. MEDT study of the 1,3-DC reaction of diazomethane with Psilostachyin and investigation about the interactions of some pyrazoline derivatives with protease (M pro) of nCoV-2. J Mol Graph Model 2020; 102:107763. [PMID: 33069124 PMCID: PMC7515590 DOI: 10.1016/j.jmgm.2020.107763] [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: 07/08/2020] [Revised: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023]
Abstract
The molecular electronic density theory (MEDT) was invested to elucidate the chemo-, regio- and stereo-selectivity of the 1,3-dipolar cycloaddition between Diazomethane (DZM) and Psilostachyin (PSH). The DFT method at B3LYP/6-31 + G (d,p) level of theory was used. Reactivity indices, transition structures theory, IGM and ELF analysis were employed to reveal the mechanism of the reaction. The addition of DZM to PSH takes place through a one-step mechanism and an asynchronous transition states. Eight possible addition channels of reaction were investigated (addition of C (sp2) to Diazomethane at C4, C5, C6 or C7). The addition of C (sp2) at C5 leading to P1 product is the preferred channel. The addition of ether does not affect the chemo-, regio- and stereo-selectivity of the reaction. Analysis of transfer of charges along the IRC path associated with the P1 product shows a polar character for the studied reaction. We have also used the noncovalent interaction (NCI) which is very helpful to reveal the most favored addition channel of the reaction, by analyzing the weak interactions in different TSs. Finally, we investigate about the potential of inhibition of some pyrazoline compounds against COVID-19-Mpro by performing a molecular docking calculations. The 1,3-DC reaction between Diazomethane and Psilostachyin has been investigated by MEDT. The asynchronicity of TSs has been revealed by IGM and Wiberg indices. The electronic description of mechanism of reaction has been performed by ELF analysis. The NCI analysis allow a deep description of weak interactions. The pyrazolines products possess a potential effect against COVID-19.
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Affiliation(s)
- M Salah
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco; LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco.
| | - M E Belghiti
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - A O Aitouna
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - A Zeroual
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - S Jorio
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - H El Alaoui Abdellaoui
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - H El Hadki
- LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco
| | - K Marakchi
- LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco
| | - N Komiha
- LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco
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14
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Hu Z, Rolt A, Hu X, Ma CD, Le DJ, Park SB, Houghton M, Southall N, Anderson DE, Talley DC, Lloyd JR, Marugan JC, Liang TJ. Chlorcyclizine Inhibits Viral Fusion of Hepatitis C Virus Entry by Directly Targeting HCV Envelope Glycoprotein 1. Cell Chem Biol 2020; 27:780-792.e5. [PMID: 32386595 PMCID: PMC7368827 DOI: 10.1016/j.chembiol.2020.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 12/06/2019] [Revised: 03/04/2020] [Accepted: 04/13/2020] [Indexed: 12/22/2022]
Abstract
Chlorcyclizine (CCZ) is a potent hepatitis C virus (HCV) entry inhibitor, but its molecular mechanism is unknown. Here, we show that CCZ directly targets the fusion peptide of HCV E1 and interferes with the fusion process. Generation of CCZ resistance-associated substitutions of HCV in vitro revealed six missense mutations in the HCV E1 protein, five being in the putative fusion peptide. A viral fusion assay demonstrated that CCZ blocked HCV entry at the membrane fusion step and that the mutant viruses acquired resistance to CCZ's action in blocking membrane fusion. UV cross-linking of photoactivatable CCZ-diazirine-biotin in both HCV-infected cells and recombinant HCV E1/E2 protein demonstrated direct binding to HCV E1 glycoprotein. Mass spectrometry analysis revealed that CCZ cross-linked to an E1 sequence adjacent to the putative fusion peptide. Docking simulations demonstrate a putative binding model, wherein CCZ binds to a hydrophobic pocket of HCV E1 and forms extensive interactions with the fusion peptide.
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Affiliation(s)
- Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Adam Rolt
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Xin Hu
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Christopher D Ma
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Derek J Le
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Michael Houghton
- Li Ka Shing Virology Institute, University of Alberta, Edmonton, Canada
| | - Noel Southall
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - D Eric Anderson
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Daniel C Talley
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - John R Lloyd
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Juan C Marugan
- Division of Pre-Clinical Innovations, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
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15
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Hassan MM, Olaoye OO. Recent Advances in Chemical Biology Using Benzophenones and Diazirines as Radical Precursors. Molecules 2020; 25:E2285. [PMID: 32414020 PMCID: PMC7288102 DOI: 10.3390/molecules25102285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022] Open
Abstract
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein-protein, protein-nucleic acid, protein-ligand (drug, probe), and protein-co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Olasunkanmi O. Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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16
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Ziemianowicz DS, MacCallum JL, Schriemer DC. Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:207-216. [PMID: 32031402 DOI: 10.1021/jasms.9b00083] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The functional properties of a protein are strongly influenced by its topography, or the solvent-facing contour map of its surface. Together with crosslinking, covalent labeling mass spectrometry (CL-MS) has the potential to contribute topographical data through the measurement of surface accessibility. However, recent efforts to correlate measures of surface accessibility with labeling yield have been met with mixed success. Most applications of CL-MS involve differential analysis of protein interactions (i.e., footprinting experiments) where such inconsistencies have limited effect. Extending CL-MS into structural analysis requires an improved evaluation of the relationship between labeling and surface exposure. In this study, we applied recently developed diazirine reagents to obtain deep coverage of the large motor domain of Eg5 (a mitotic kinesin), and together with computational methods we correlated labeling yields with accessibility data in a number of ways. We observe that correlations can indeed be seen at a local structural level, but these correlations do not extend across the structure. The lack of correlation arises from the influence of protein dynamics and chemical composition on reagent partitioning and, thus, also on labeling yield. We conclude that our use of CL-MS data should be considered in light of "chemical accessibility" rather than "solvent accessibility" and suggest that CL-MS data would be a useful tool in the fundamental study of protein-solute interactions.
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Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - Justin L MacCallum
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
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17
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Abstract
Ultraviolent crosslinking is a key experimental step in the numerous protocols that have been developed for capturing and dissecting RNA-protein interactions in living cells. UV crosslinking covalently stalls dynamic interactions between RNAs and the directly contacting RNA-binding proteins and enables stringent denaturing downstream purification conditions needed for the enrichment and biochemical analysis of RNA-protein complexes. Despite its popularity, conventional 254 nm UV crosslinking possesses a set of intrinsic drawbacks, with the low photochemical efficiency being the central caveat. Here we show that genetically encoded photoreactive unnatural amino acids bearing a dialkyl diazirine photoreactive group can address this problem. Using the human iron regulatory protein 1 (IRP1) as a model RNA-binding protein, we show that the photoreactive amino acids can be introduced into the protein without diminishing its RNA-binding properties. A sevenfold increase in the crosslinking efficiency compared to conventional 254 nm UV crosslinking was achieved using the diazirine-based unnatural amino acid DiAzKs. This finding opens an avenue for new applications of the unnatural amino acids in studying RNA-protein interactions.
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Affiliation(s)
- Dmytro Dziuba
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Jan‐Erik Hoffmann
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityL334, 3181 SW Sam Jackson Park RoadPortlandOR97239-3098USA
| | - Matthias W. Hentze
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityL334, 3181 SW Sam Jackson Park RoadPortlandOR97239-3098USA
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18
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Liu Y, Tureček F. Photodissociative Cross-Linking of Diazirine-Tagged Peptides with DNA Dinucleotides in the Gas Phase. J Am Soc Mass Spectrom 2019; 30:1992-2006. [PMID: 30945107 DOI: 10.1007/s13361-019-02189-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/15/2019] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Non-covalent complexes of DNA dinucleotides dAA, dAT, dGG, dGC, and dCG with diazirine-tagged Cys-Ala-Gln-Lys peptides were generated as singly charged ions in the gas phase. Laser photodissociation at 355 nm of the diazirine ring in the gas-phase complexes created carbene intermediates that underwent covalent cross-linking to the dinucleotides. The dinucleotides differed in the cross-linking yields, ranging from 27 to 36% for dAA and dAT up to 90-98% for dGG, dGC, and dCG. Collision-induced dissociation tandem mass spectrometry (CID-MS3) of the cross-linked conjugates revealed that fragmentation occurred chiefly in the dinucleotide moieties, resulting in a loss of a nucleobase and backbone cleavages. The CID-MS3 spectra further revealed that cross-links were primarily formed in the 3'-nucleotides for the dAT, dGC, and dCG combinations. Gas-phase and solution structures of dGG complexes with S-tagged CAQK were investigated by Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations. The low free-energy complexes had zwitterionic structures in which the peptide was protonated at the N-terminus and in the Lys residue whereas the carboxyl or dGG phosphate were deprotonated, corresponding to the respective (Cys+, Lys+, COO-)+ and (Cys+, Lys+, phosphate-)+ protomeric types. Both types preferred structures in which the peptide N-terminal cysteine carrying the S-photo-tag was aligned with the 3'-guanine moiety. BOMD trajectories at 310 K were analyzed for close contacts of the incipient peptide carbene with the positions in dGG that pointed to frequent contacts with the N-1, NH2, and N-7 atoms of 3'-guanine, in agreement with the cross-linking results. Carbene insertion to the guanine N-1-H and NH2 bonds was calculated by density functional and Møller-Plesset perturbational theory to be 350-380 kJ mol-1 exothermic. Based on calculations, we proposed a mechanism for the carbene reaction with guanine starting with an exothermic attack at N-7 to form a dipolar intermediate that can close an aziridine ring in another exothermic reaction, forming a stable covalent cross link. Graphical Abstract.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA.
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19
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Feltes M, Moores S, Gale SE, Krishnan K, Mydock-McGrane L, Covey DF, Ory DS, Schaffer JE. Synthesis and characterization of diazirine alkyne probes for the study of intracellular cholesterol trafficking. J Lipid Res 2019; 60:707-716. [PMID: 30617147 PMCID: PMC6399506 DOI: 10.1194/jlr.d091470] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 12/03/2018] [Revised: 12/28/2018] [Indexed: 02/05/2023] Open
Abstract
Cholesterol is an essential structural component of cellular membranes and precursor molecule for oxysterol, bile acid, and hormone synthesis. The study of intracellular cholesterol trafficking pathways has been limited in part due to a lack of suitable cholesterol analogues. Herein, we developed three novel diazirine alkyne cholesterol probes: LKM38, KK174, and KK175. We evaluated these probes as well as a previously described diazirine alkyne cholesterol analogue, trans-sterol, for their fidelity as cholesterol mimics and for study of cholesterol trafficking. LKM38 emerged as a promising cholesterol mimic because it both sustained the growth of cholesterol-auxotrophic cells and appropriately regulated key cholesterol homeostatic pathways. When presented as an ester in lipoprotein particles, LKM38 initially localized to the lysosome and subsequently trafficked to the plasma membrane and endoplasmic reticulum. LKM38 bound to diverse, established cholesterol binding proteins. Through a detailed characterization of the cellular behavior of a panel of diazirine alkyne probes using cell biological, biochemical trafficking assays and immunofluorescence approaches, we conclude that LKM38 can serve as a powerful tool for the study of cholesterol protein interactions and trafficking.
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Affiliation(s)
- McKenna Feltes
- Departments of Medicine Washington University School of Medicine, St. Louis, MO 63110
| | - Samantha Moores
- Departments of Medicine Washington University School of Medicine, St. Louis, MO 63110
| | - Sarah E Gale
- Departments of Medicine Washington University School of Medicine, St. Louis, MO 63110
| | - Kathiresan Krishnan
- Developmental Biology Washington University School of Medicine, St. Louis, MO 63110
| | | | - Douglas F Covey
- Developmental Biology Washington University School of Medicine, St. Louis, MO 63110
| | - Daniel S Ory
- Departments of Medicine Washington University School of Medicine, St. Louis, MO 63110
| | - Jean E Schaffer
- Departments of Medicine Washington University School of Medicine, St. Louis, MO 63110
- Developmental Biology Washington University School of Medicine, St. Louis, MO 63110
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20
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Nakamoto K, Akao Y, Ueno Y. Diazirine-containing tag-free RNA probes for efficient RISC-loading and photoaffinity labeling of microRNA targets. Bioorg Med Chem Lett 2018; 28:2906-2909. [PMID: 30021704 DOI: 10.1016/j.bmcl.2018.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 04/02/2018] [Revised: 05/17/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022]
Abstract
We designed and synthesized a photo-reactive and tag-free RNA probe for the identification of microRNA (miRNA) targets. To synthesize the RNA probe, we designed a novel nucleoside analog 1-O-[3-ethynyl-5-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-β-d-ribofuranose containing aryl trifluoromethyl diazirine and ethynyl moieties. The RNA probe containing this analog was observed to form crosslinks with complementary RNA by UV irradiation and was rapidly tagged by Cu-catalyzed azide alkyne cycloaddition (CuAAC). In addition, the tag-free and photo-reactive miRNA-145 probe showed comparable gene silencing activity to that of unmodified miRNA-145. Therefore, miRNA probes containing the nucleoside analog are promising candidates for the identification of target mRNAs of miRNAs.
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Affiliation(s)
- Kosuke Nakamoto
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukihiro Akao
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Faculty of Applied Biological Sciences, 1-1 Yanagido, Gifu 501-1193, Japan; Center of Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan.
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21
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Gao F, Djordjevic I, Pokholenko O, Zhang H, Zhang J, Steele TWJ. On-Demand Bioadhesive Dendrimers with Reduced Cytotoxicity. Molecules 2018; 23:E796. [PMID: 29601480 PMCID: PMC6017702 DOI: 10.3390/molecules23040796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 03/22/2018] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 01/11/2023] Open
Abstract
Tissue adhesives based on polyamidoamine (PAMAM) dendrimer, grafted with UV-sensitive aryldiazirine (PAMAM-g-diazirine) are promising new candidates for light active adhesion on soft tissues. Diazirine carbene precursors form interfacial and intermolecular covalent crosslinks with tissues after UV light activation that requires no premixing or inclusion of free radical initiators. However, primary amines on the PAMAM dendrimer surface present a potential risk due to their cytotoxic and immunological effects. PAMAM-g-diazirine formulations with cationic pendant amines converted into neutral amide groups were evaluated. In vitro toxicity is reduced by an order of magnitude upon amine capping while retaining bioadhesive properties. The in vivo immunological response to PAMAM-g-diazirine formulations was found to be optimal in comparison to standard poly(lactic-co-glycolic acid) (PLGA) thin films.
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Affiliation(s)
- Feng Gao
- School of Material Science and Engineering, Beijing University of Chemistry Technology, North Third Ring Road 15, Chaoyang District, Beijing 100029, China.
| | - Ivan Djordjevic
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, NL, Mexico.
| | - Oleksandr Pokholenko
- School of Materials Science and Engineering, Division of Materials Technology, Nanyang Technological University, Singapore 639798, Singapore.
| | - Haobo Zhang
- School of Material Science and Engineering, Beijing University of Chemistry Technology, North Third Ring Road 15, Chaoyang District, Beijing 100029, China.
| | - Junying Zhang
- School of Material Science and Engineering, Beijing University of Chemistry Technology, North Third Ring Road 15, Chaoyang District, Beijing 100029, China.
| | - Terry W J Steele
- School of Materials Science and Engineering, Division of Materials Technology, Nanyang Technological University, Singapore 639798, Singapore.
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22
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Ziemianowicz DS, Bomgarden R, Etienne C, Schriemer DC. Amino Acid Insertion Frequencies Arising from Photoproducts Generated Using Aliphatic Diazirines. J Am Soc Mass Spectrom 2017; 28:2011-2021. [PMID: 28799075 DOI: 10.1007/s13361-017-1730-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Mapping proteins with chemical reagents and mass spectrometry can generate a measure of accessible surface area, which in turn can be used to support the modeling and refinement of protein structures. Photolytically generated carbenes are a promising class of reagent for this purpose. Substituent effects appear to influence surface mapping properties, allowing for a useful measure of design control. However, to use carbene labeling data in a quantitative manner for modeling activities, we require a better understanding of their inherent amino acid reactivity, so that incorporation data can be normalized. The current study presents an analysis of the amino acid insertion frequency of aliphatic carbenes generated by the photolysis of three different diazirines: 3,3'-azibutyl-1-ammonium, 3,3'-azibutan-1-ol, and 4,4'-azipentan-1-oate. Leveraging an improved photolysis system for single-shot labeling of sub-microliter frozen samples, we used EThCD to localize insertion products in a large population of labeled peptides. Counting statistics were drawn from data-dependent LC-MS2 experiments and used to estimate the frequencies of insertion as a function of amino acid. We observed labeling of all 20 amino acids over a remarkably narrow range of insertion frequencies. However, the nature of the substituent could influence relative insertion frequencies, within a general preference for larger polar amino acids. We confirm a large (6-fold) increase in labeling yield when carbenes were photogenerated in the solid phase (77 K) relative to the liquid phase (293 K), and we suggest that carbene labeling should always be conducted in the frozen state to avoid information loss in surface mapping experiments. Graphical Abstract ᅟ.
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Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Ryan Bomgarden
- Thermo Fisher Scientific, 3747 N. Meridian Rd., Rockford, IL, 61101, USA
| | - Chris Etienne
- Thermo Fisher Scientific, 3747 N. Meridian Rd., Rockford, IL, 61101, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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23
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Shaffer CJ, Andrikopoulos PC, Řezáč J, Rulíšek L, Tureček F. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler. J Am Soc Mass Spectrom 2016; 27:633-645. [PMID: 26817657 DOI: 10.1007/s13361-016-1338-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 12/27/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific (13)C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)(+) ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H](+) ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase. Graphical Abstract ᅟ.
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Affiliation(s)
- Christopher J Shaffer
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA
| | - Prokopis C Andrikopoulos
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 16610, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 16610, Prague, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, 16610, Prague, Czech Republic.
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA.
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24
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Theis T, Ortiz GX, Logan AWJ, Claytor KE, Feng Y, Huhn WP, Blum V, Malcolmson SJ, Chekmenev EY, Wang Q, Warren WS. Direct and cost-efficient hyperpolarization of long-lived nuclear spin states on universal (15)N2-diazirine molecular tags. Sci Adv 2016; 2:e1501438. [PMID: 27051867 PMCID: PMC4820385 DOI: 10.1126/sciadv.1501438] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/05/2016] [Indexed: 05/17/2023]
Abstract
Conventional magnetic resonance (MR) faces serious sensitivity limitations which can be overcome by hyperpolarization methods, but the most common method (dynamic nuclear polarization) is complex and expensive, and applications are limited by short spin lifetimes (typically seconds) of biologically relevant molecules. We use a recently developed method, SABRE-SHEATH, to directly hyperpolarize (15)N2 magnetization and long-lived (15)N2 singlet spin order, with signal decay time constants of 5.8 and 23 minutes, respectively. We find >10,000-fold enhancements generating detectable nuclear MR signals that last for over an hour. (15)N2-diazirines represent a class of particularly promising and versatile molecular tags, and can be incorporated into a wide range of biomolecules without significantly altering molecular function.
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Affiliation(s)
- Thomas Theis
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
| | | | | | | | - Yesu Feng
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - William P. Huhn
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | | | - Eduard Y. Chekmenev
- Departments of Radiology and Biomedical Engineering, Vanderbilt University, Institute of Imaging Science, Nashville, TN 37232, USA
| | - Qiu Wang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
| | - Warren S. Warren
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Physics, Duke University, Durham, NC 27708, USA
- Departments of Radiology and Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Corresponding author. E-mail: (W.S.W.); (Q.W.); (T.T.)
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25
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Shaffer CJ, Marek A, Nguyen HTH, Tureček F. Combining Near-UV Photodissociation with Electron Transfer. Reduction of the Diazirine Ring in a Photomethionine-Labeled Peptide Ion. J Am Soc Mass Spectrom 2015; 26:1367-1381. [PMID: 25904063 DOI: 10.1007/s13361-015-1139-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/26/2015] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
Electron transfer dissociation of peptide ions with the diazirine-containing residue photomethionine (M*) results in side-chain dissociations by loss of C3H7N2 radicals in addition to standard backbone cleavages. The side-chain dissociations are particularly prominent upon activation of long-lived, charge-reduced, cation radicals (GM*GGR + 2H)(+•). Investigation of these cation radicals by near-UV photodissociation and collisional activation revealed different fragmentation products and mechanisms resulting from these ion activation modes. The dissociations observed for photomethionine were dramatically different from those previously reported for the lower homologue photoleucine; here, a difference by a single methylene group in the side chain had a large effect on the chemistries of the cation radicals upon ETD and further activation. ETD intermediates and products were probed by tandem 355-nm UV photodissociation-collision induced dissociation and found to contain chromophores that resulted from electron attachment to the diazirine ring. The nature of the newly formed chromophores and ion energetics and kinetics were investigated by electron structure calculations combining ab initio and density functional theory methods and Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The dramatic difference between the dissociations of L* and M* containing peptide cation radicals is explained by electronic effects that play a role in stabilizing critical reaction intermediates and steer the dissociations into kinetically favored reaction channels. In addition, a new alternating UVPD-ETD-UVPD MS(4) experiment is introduced and utilized for ion structure elucidation.
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Affiliation(s)
- Christopher J Shaffer
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA
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26
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Kino R, Araya T, Arai T, Sohma Y, Kanai M. Covalent modifier-type aggregation inhibitor of amyloid-β based on a cyclo-KLVFF motif. Bioorg Med Chem Lett 2015; 25:2972-5. [PMID: 26045033 DOI: 10.1016/j.bmcl.2015.05.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 04/20/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022]
Abstract
Inhibition of amyloid-β (Aβ) aggregation could be a drug development target for treating Alzheimer disease. Insufficient activity to inhibit aggregation, however, remains a key issue. Here, we report a covalent modifier-type aggregation inhibitor of Aβ, diazirine-equipped cyclo-KLVF(β-Ph)F (2). Due to the affinity of the cyclo-KLVFF motif for Aβ, 2 selectively reacted with Aβ1-42 under UV-light irradiation to form an irreversible covalent bond. The Tyr-10 residue of Aβ1-42 was identified as the covalent modification site with 2. The extent of cross-β-sheet structure, characteristics of amyloid aggregation, and toxicity of Aβ1-42 were strongly attenuated by this chemical modification.
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Affiliation(s)
- Ryuto Kino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takushi Araya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tadamasa Arai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ERATO (Japan) Science and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ERATO (Japan) Science and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ERATO (Japan) Science and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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27
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Pham ND, Fermaintt CS, Rodriguez AC, McCombs JE, Nischan N, Kohler JJ. Cellular metabolism of unnatural sialic acid precursors. Glycoconj J 2015; 32:515-29. [PMID: 25957566 DOI: 10.1007/s10719-015-9593-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 01/08/2015] [Revised: 04/10/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
Abstract
Carbohydrates, in addition to their metabolic functions, serve important roles as receptors, ligands, and structural molecules for diverse biological processes. Insight into carbohydrate biology and mechanisms has been aided by metabolic oligosaccharide engineering (MOE). In MOE, unnatural carbohydrate analogs with novel functional groups are incorporated into cellular glycoconjugates and used to probe biological systems. While MOE has expanded knowledge of carbohydrate biology, limited metabolism of unnatural carbohydrate analogs restricts its use. Here we assess metabolism of SiaDAz, a diazirine-modified analog of sialic acid, and its cell-permeable precursor, Ac4ManNDAz. We show that the efficiency of Ac4ManNDAz and SiaDAz metabolism depends on cell type. Our results indicate that different cell lines can have different metabolic roadblocks in the synthesis of cell surface SiaDAz. These findings point to roles for promiscuous intracellular esterases, kinases, and phosphatases during unnatural sugar metabolism and provide guidance for ways to improve MOE.
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Affiliation(s)
- Nam D Pham
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Charles S Fermaintt
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Andrea C Rodriguez
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Janet E McCombs
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jennifer J Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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28
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Peng T, Hang HC. Bifunctional fatty acid chemical reporter for analyzing S-palmitoylated membrane protein-protein interactions in mammalian cells. J Am Chem Soc 2015; 137:556-9. [PMID: 25575299 PMCID: PMC4303541 DOI: 10.1021/ja502109n] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Studying the functions of S-palmitoylated proteins in cells can be challenging due to the membrane targeting property and dynamic nature of protein S-palmitoylation. New strategies are therefore needed to specifically capture S-palmitoylated protein complexes in cellular membranes for dissecting their functions in vivo. Here we present a bifunctional fatty acid chemical reporter, x-alk-16, which contains an alkyne and a diazirine, for metabolic labeling of S-palmitoylated proteins and photo-cross-linking of their involved protein complexes in mammalian cells. We demonstrate that x-alk-16 can be metabolically incorporated into known S-palmitoylated proteins such as H-Ras and IFITM3, a potent antiviral protein, and induce covalent cross-linking of IFITM3 oligomerization as well as its specific interactions with other membrane proteins upon in-cell photoactivation. Moreover, integration of x-alk-16-induced photo-cross-linking with label-free quantitative proteomics allows identification of new IFITM3 interacting proteins.
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Affiliation(s)
- Tao Peng
- Laboratory of Chemical Biology and Bacterial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Howard C. Hang
- Laboratory of Chemical Biology and Bacterial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
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29
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Abstract
Diazo compounds are very versatile reagents in organic chemistry and meet the challenge of selective assembly of structurally complex molecules. Their leaving group is dinitrogen; therefore, they are very clean and atom-efficient reagents. However, diazo compounds are potentially explosive and extremely difficult to handle on an industrial scale. In this review, it is discussed how continuous flow technology can help to make these powerful reagents accessible on large scale. Microstructured devices can improve heat transfer greatly and help with the handling of dangerous reagents safely. The in situ formation and subsequent consumption of diazo compounds are discussed along with advances in handling diazomethane and ethyl diazoacetate. The potential large-scale applications of a given methodology is emphasized.
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Affiliation(s)
- Simon T R Müller
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT (UK)
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30
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Ortiz-León A, Torres-Valencia JM, Manríquez-Torres JJ, Alvarado-Rodríguez JG, Hernández-Balderas U, Cerda-García-Rojas CM, Joseph-Nathan P. Diastereoselective addition of diazomethane to zaluzanin A. Nat Prod Commun 2014; 9:753-756. [PMID: 25115070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
The diastereoselectivity of diazomethane addition to the conjugated double bond of alpha,beta-unsaturated sesquiterpene lactones was explored using zaluzanin A (1) as a model. Thus, the absolute configuration of 1 was assured by X-ray diffraction analysis including evaluation of Flack and Hooft parameters, and by vibrational circular dichroism spectroscopy of its diacetyl derivative 2, while the absolute configuration of the diazomethane addition product, zaluzanin A pyrazoline (3), was determined by evaluation of the 1H NMR chemical shift changes with respect to 1, and confirmed by X-ray diffraction analysis, again including evaluation of Flack and Hooft parameters.
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31
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Marek A, Tureček F. Collision-induced dissociation of diazirine-labeled peptide ions. Evidence for Brønsted-acid assisted elimination of nitrogen. J Am Soc Mass Spectrom 2014; 25:778-789. [PMID: 24549894 DOI: 10.1007/s13361-014-0832-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 12/26/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Gas-phase dissociations were investigated for several peptide ions containing the Gly-Leu* N-terminal motif where Leu* was a modified norleucine residue containing the photolabile diazirine ring. Collisional activation of gas-phase peptide cations resulted in facile N₂ elimination that competed with backbone dissociations. A free lysine ammonium group can act as a Brønsted acid to facilitate N₂ elimination. This dissociation was accompanied by insertion of a lysine proton in the side chain of the photoleucine residue, as established by deuterium labeling and gas-phase sequencing of the products. Electron structure calculations were used to provide structures and energies of reactants, intermediates, and transition states for Gly-Leu*-Gly-Gly-Lys amide ions that were combined with RRKM calculations of unimolecular rate constants. The calculations indicated that Brønsted acid-catalyzed eliminations were kinetically preferred over direct loss of N₂ from the diazirine ring. Mechanisms are proposed to explain the proton-initiated reactions and discuss the reaction products. The non-catalyzed diazirine ring cleavage and N₂ loss is proposed as a thermometer dissociation for peptide ion dissociations.
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Affiliation(s)
- Aleš Marek
- Department of Chemistry, University of Washington, Bagley Hall, Seattle, WA, 98195-1700, USA
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32
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Vervacke J, Funk AL, Wang YC, Strom M, Hrycyna CA, Distefano MD. Diazirine-containing photoactivatable isoprenoid: synthesis and application in studies with isoprenylcysteine carboxyl methyltransferase. J Org Chem 2014; 79:1971-8. [PMID: 24502619 PMCID: PMC3985442 DOI: 10.1021/jo402600b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 12/19/2022]
Abstract
Photoaffinity labeling is a useful technique employed to identify protein-ligand and protein-protein noncovalent interactions. Photolabeling experiments have been particularly informative for probing membrane-bound proteins where structural information is difficult to obtain. The most widely used classes of photoactive functionalities include aryl azides, diazocarbonyls, diazirines, and benzophenones. Diazirines are intrinsically smaller than benzophenones and generate carbenes upon photolysis that react with a broader range of amino acid side chains compared with the benzophenone-derived diradical; this makes diazirines potentially more general photoaffinity-labeling agents. In this article, we describe the development and application of a new isoprenoid analogue containing a diazirine moiety that was prepared in six steps and incorporated into an a-factor-derived peptide produced via solid-phase synthesis. In addition to the diazirine moiety, fluorescein and biotin groups were also incorporated into the peptide to aid in the detection and enrichment of photo-cross-linked products. This multifuctional diazirine-containing peptide was a substrate for Ste14p, the yeast homologue of the potential anticancer target Icmt, with K(m) (6.6 μM) and V(max) (947 pmol min(-1) mg(-1)) values comparable or better than a-factor peptides functionalized with benzophenone-based isoprenoids. Photo-cross-linking experiments demonstrated that the diazirine probe photo-cross-linked to Ste14p with observably higher efficiency than benzophenone-containing a-factor peptides.
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Affiliation(s)
- Jeffrey
S. Vervacke
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Amy L. Funk
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907−2084, United States
| | - Yen-Chih Wang
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark Strom
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christine A. Hrycyna
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907−2084, United States
| | - Mark D. Distefano
- Departments
of Chemistry and Medicinal Chemistry, University
of Minnesota, Minneapolis, Minnesota 55455, United States
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33
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Marek A, Pepin R, Peng B, Laszlo KJ, Bush MF, Tureček F. Electron transfer dissociation of photolabeled peptides. Backbone cleavages compete with diazirine ring rearrangements. J Am Soc Mass Spectrom 2013; 24:1641-1653. [PMID: 23633016 DOI: 10.1007/s13361-013-0630-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Gas-phase conformations and electron transfer dissociations of pentapeptide ions containing the photo-Leu residue (L*) were studied. Exhaustive conformational search including molecular dynamics force-field, semi-empirical, ab initio, and density functional theory calculations established that the photo-Leu residue did not alter the gas-phase conformations of (GL*GGK + 2H)(2+) and (GL*GGK-NH2 + H)(+) ions, which showed the same conformer energy ranking as the unmodified Leu-containing ions. This finding is significant in that it simplifies conformational analysis of photo-labeled peptide ions. Electron transfer dissociation mass spectra of (GL*GGK + 2H)(2+), (GL*GGK-NH2 + 2H)(2+),(GL*GGKK + 2H)(2+), (GL*GLK + 2H)(2+), and (GL*LGK + 2H)(2+) showed 16 %-21 % fragment ions originating by radical rearrangements and cleavages in the diazirine ring. These side-chain dissociations resulted in eliminations of N2H3, N2H4, [N2H5], and [NH4O] neutral fragments and were particularly abundant in long-lived charge-reduced cation-radicals. Deuterium labeling established that the neutral hydrazine molecules mainly contained two exchangeable and two nonexchangeable hydrogen atoms from the peptide and underwent further H/D exchange in an ion-molecule complex. Electron structure calculations on the charge-reduced ions indicated that the unpaired electron was delocalized between the diazirine and amide π* electronic systems in the low electronic states of the cation-radicals. The diazirine moiety in GL*GGK-NH2was calculated to have an intrinsic electron affinity of 1.5 eV, which was further increased by the Coulomb effect of the peptide positive charge. Mechanisms are proposed for the unusual elimination of hydrazine from the photo-labeled peptide ions.
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Affiliation(s)
- Aleš Marek
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
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Dubinsky L, Delago A, Amara N, Krief P, Rayo J, Zor T, Kravchenko VV, Meijler MM. Species selective diazirine positioning in tag-free photoactive quorum sensing probes. Chem Commun (Camb) 2013; 49:5826-8. [PMID: 23702727 PMCID: PMC3723129 DOI: 10.1039/c3cc43092h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The synthesis and comparison of activities of 'tag-free' probes with diazirines at various positions are described. Remarkable differences in their effects on P. aeruginosa and on human bronchial epithelial cells were observed, supporting the efforts to isolate and identify receptors for N-acyl homoserine lactones.
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Affiliation(s)
- Luba Dubinsky
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
| | - Antonia Delago
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
| | - Neri Amara
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
| | - Pnina Krief
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
| | - Josep Rayo
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
| | - Tsaffrir Zor
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Vladimir V. Kravchenko
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael M. Meijler
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er-Sheva 84105, Israel
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Nyholm JR, Gustafsson T, Östin A. Structural determination of nerve agent markers using gas chromatography mass spectrometry after derivatization with 3-pyridyldiazomethane. J Mass Spectrom 2013; 48:813-822. [PMID: 23832937 DOI: 10.1002/jms.3225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 02/05/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 06/02/2023]
Abstract
Nerve agents are a class of organophosphorous chemicals that are prohibited under the Chemical Weapons Convention. Their degradation products, phosphonic acids, are analyzed as markers of nerve agent contamination and use. Because the phosphonic acids are non-volatile and very polar, their identification by GC-MS requires a derivatization step prior to analysis. Standard derivatization methods for gas-chromatography electron-impact mass-spectrometry analysis give very similar spectra for many alkyl phosphonic acid isomers, which complicates the identification process. We present a new reagent, 3-pyridyldiazomethane, for preparing picolinyl ester derivatives of alkyl methylphosphonic acids facilitating the determination of their structure by enhancing predictable fragmentation of the O-alkyl chain. This fragmentation is directed by the nitrogen nucleus of the pyridyl moiety that abstracts hydrogen from the O-alkyl chain, inducing radical cleavage of the carbon-carbon bonds and thereby causing extensive fragmentation that can be used for detailed structure elucidation of the O-alkyl moiety. The separability of related isomers was tested by comparing the spectra of the picolinyl esters formed from twelve hexyl methylphosphonic acid isomers. Spectral library matches and principal component analysis showed that the picolinyl esters were more effectively separated than the corresponding trimethylsilyl derivatives used in the standard operating procedures. The suggested method will improve the unambiguous structural determination process for phosphonic acids.
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Affiliation(s)
- Jenny Rattfelt Nyholm
- Swedish Defence Research Agency, FOI CBRN Defence and Security, SE-907 82, Umeå, Sweden
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Kleigrewe K, Niehaus EM, Wiemann P, Tudzynski B, Humpf HU. New approach via gene knockout and single-step chemical reaction for the synthesis of isotopically labeled fusarin c as an internal standard for the analysis of this fusarium mycotoxin in food and feed samples. J Agric Food Chem 2012; 60:8350-8355. [PMID: 22877497 DOI: 10.1021/jf302534x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The gold standard for quantitation of contaminants with high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) is the use of isotopically labeled standards. Herein, we report a new strategy for the synthesis of isotopically labeled 21-d3-fusarin C via a genetically modified Fusarium strain, followed by a one-step derivatization reaction. Fusarin C is a Fusarium mycotoxin, which is mutagenic after metabolic activation. Its occurrence has been demonstrated recently in corn-based samples, but up to now, little is known about the contamination of other grain samples. To collect further data, the quantitation method was enhanced by application of the 21-d3-fusarin C and the use of a QTRAP 5500 mass spectrometer. This new method has a limit of detection (LOD) of 1 μg/kg, a limit of quantitation (LOQ) of 4 μg/kg, and a recovery rate of 99%. A total of 21 corn samples and 13 grain samples were analyzed, with resulting fusarin C levels varying from not detectable to 24.7 μg/kg.
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Affiliation(s)
- Karin Kleigrewe
- Institute of Food Chemistry, and ‡Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster , 48149 Münster, Germany
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Ghiassian S, Ismaili H, Lubbock BDW, Dube JW, Ragogna PJ, Workentin MS. Photoinduced carbene generation from diazirine modified task specific phosphonium salts to prepare robust hydrophobic coatings. Langmuir 2012; 28:12326-12333. [PMID: 22839497 DOI: 10.1021/la301975u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
3-Aryl-3-(trifluormethyl)diazirine functionalized highly fluorinated phosphonium salts (HFPS) were synthesized, characterized, and utilized as photoinduced carbene precursors for covalent attachment of the HFPS onto cotton/paper to impart hydrophobicity to these surfaces. Irradiation of cotton and paper, as proof of concept substrates, treated with the diazirine-HFPS leads to robust hydrophobic cotton and paper surfaces with antiwetting properties, whereas the corresponding control samples absorb water readily. The contact angles of water were determined to be 139° and 137° for cotton and paper, respectively. In contrast, water placed on the untreated or the control samples (those treated with the diazirine-HFPS but not irradiated) is simply absorbed into the surface. Additionaly, the chemically grafted hydrophobic coating showed high durability toward wash cycles and sonication in organic solvents. Because of the mode of activation to covalently tether the hydrophobic coating, it is amenable to photopatterning, which was demonstrated macroscopically.
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Affiliation(s)
- Sara Ghiassian
- Department of Chemistry and the Centre of Materials and Biomaterials Research (CAMBR), Western University, London, Ontario, Canada
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38
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Gómez GE, Mundo MR, Craig PO, Delfino JM. Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry. J Am Soc Mass Spectrom 2012; 23:30-42. [PMID: 22006407 DOI: 10.1007/s13361-011-0266-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/26/2011] [Accepted: 09/26/2011] [Indexed: 05/31/2023]
Abstract
Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites.
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Affiliation(s)
- Gabriela E Gómez
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires e Instituto de Química y Fisicoquímica Biológica (IQUIFIB-CONICET), Junín 956, C1113AAD, Buenos Aires, Argentina
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Stewart DS, Savechenkov PY, Dostalova Z, Chiara DC, Ge R, Raines DE, Cohne JB, Forman SA, Bruzik KS, Miller KW. p-(4-Azipentyl)propofol: a potent photoreactive general anesthetic derivative of propofol. J Med Chem 2011; 54:8124-35. [PMID: 22029276 PMCID: PMC3580944 DOI: 10.1021/jm200943f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We synthesized 2,6-diisopropyl-4-[3-(3-methyl-3H-diazirin-3-yl)propyl]phenol (p-(4-azipentyl)propofol), or p-4-AziC5-Pro, a novel photoactivable derivative of the general anesthetic propofol. p-4-AziC5-Pro has an anesthetic potency similar to that of propofol. Like propofol, the compound potentiates inhibitory GABA(A) receptor current responses and allosterically modulates binding to both agonist and benzodiazepine sites, assayed on heterologously expressed GABA(A) receptors. p-4-AziC5-Pro inhibits excitatory current responses of nACh receptors expressed in Xenopus oocytes and photoincorporates into native nACh receptor-enriched Torpedo membranes. Thus, p-4-AziC5-Pro is a functional general anesthetic that both modulates and photoincorporates into Cys-loop ligand-gated ion channels, making it an excellent candidate for use in identifying propofol binding sites.
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Affiliation(s)
- Deirdre S. Stewart
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 32 Fruit Street, Boston, Massachusetts 02114
| | - Pavel Y. Savechenkov
- University of Illinois at Chicago, College of Pharmacy, 833 S. Wood Street (M/C 781), Chicago, IL 60612-7231
| | - Zuzana Dostalova
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 32 Fruit Street, Boston, Massachusetts 02114
| | - David C. Chiara
- Department of Neurobiology, 220 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115
| | - Rile Ge
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 32 Fruit Street, Boston, Massachusetts 02114
| | - Douglas E. Raines
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 32 Fruit Street, Boston, Massachusetts 02114
| | - Jonathan B. Cohne
- Department of Neurobiology, 220 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115
| | - Stuart A. Forman
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 32 Fruit Street, Boston, Massachusetts 02114
| | - Karol S. Bruzik
- University of Illinois at Chicago, College of Pharmacy, 833 S. Wood Street (M/C 781), Chicago, IL 60612-7231
| | - Keith W. Miller
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, 32 Fruit Street, Boston, Massachusetts 02114
- Department of Biological Chemistry and Molecular Pharmacology, 220 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115
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40
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van 't Erve TJ, Rautiainen R, Robertson L, Luthe G. Trimethylsilyldiazomethane: a safe non-explosive, cost effective and less-toxic reagent for phenol derivatization in GC applications. Environ Int 2010; 36:835-842. [PMID: 20385409 PMCID: PMC4090112 DOI: 10.1016/j.envint.2010.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/27/2010] [Accepted: 02/25/2010] [Indexed: 05/29/2023]
Abstract
Diazomethane is a highly explosive and toxic gas routinely employed for the quantitative and clean derivatization of phenols. We investigated the commercially available trimethylsilyldiazomethane in the presence of diisopropylethylamine as a safe, non-explosive and less-toxic alternative using six phenolic polychlorinated biphenyls as model analytes and fluoro-tagged analogues as internal standards. We compared yields and derivatization times of each method employing a liver microsomal extract as a real matrix. Steric hindrance and electronic properties of the analytes were also investigated. The alternative method afforded equal to higher derivatization yields with increased reaction times, up to 100 min, while explosion and toxic exposure risks were minimized and cost efficiency was increased above 25%. These findings demonstrate that non-explosive trimethylsilyl diazomethane produces comparable derivatization results to the dangerous diazomethane under the conditions studied.
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Affiliation(s)
- T. J. van 't Erve
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA
- Institute of Life Sciences, Saxion University of Applied Sciences, Enschede, The Netherlands
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA
| | - R.H. Rautiainen
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA
| | - L.W. Robertson
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA
| | - G. Luthe
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA
- Institute of Life Sciences, Saxion University of Applied Sciences, Enschede, The Netherlands
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA
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41
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Ismaili H, Lee S, Workentin MS. Diazirine-modified gold nanoparticle: template for efficient photoinduced interfacial carbene insertion reactions. Langmuir 2010; 26:14958-14964. [PMID: 20735050 DOI: 10.1021/la102621h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Photolysis of a 3-aryl-3-(trifluoromethyl)diazirine-modified monolayer-protected gold nanoparticles (2-C(12)MPNs), with a core size of 1.8 ± 0.3 nm, in the presence of model carbene trapping reagents leads to efficient, essentially quantitative, modification of the interface via carbene insertion reactions. The utility of carbene insertion reactions as a general approach for the modification of Au-MPNs to provide a breadth of new structures available was demonstrated using acetic acid, methanol, benzyl alcohol, phenol, benzylamine, methyl acrylate, and styrene (10a-g, respectively) as electrophilic carbene trapping agents to form the corresponding modified 3a-g-C(12)MPNs. The 1.8 ± 0.3 nm gold nanoparticles bearing a diazirine group (2-C(12)MPNs) were synthesized using the ligand exchange reaction with the requisite 3-aryl-3-(trifluoromethyl)diazirinealkylthiol. The 2-C(12)MPNs and the resulting products of the reaction on the MPN (3a-g-C(12)MPN) were fully characterized by IR, (1)H NMR, and (19)F NMR spectroscopy and, when applicable, transmission electron microscopy (TEM). Verification for the 3a-g-C(12)MPNs was accomplished by comparison of the spectral data to those of obtained for the photoreactions of 3-(3-methoxyphenyl)-3-(trifluoromethyl)-3H-diazirine as a model with 10a-g.
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Affiliation(s)
- Hossein Ismaili
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7
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42
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Gomes AF, Gozzo FC. Chemical cross-linking with a diazirine photoactivatable cross-linker investigated by MALDI- and ESI-MS/MS. J Mass Spectrom 2010; 45:892-9. [PMID: 20635431 DOI: 10.1002/jms.1776] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Crystallography and nuclear magnetic resonance are well-established methods to study protein tertiary structure and interactions. Despite their usefulness, such methods are not applicable to many protein systems. Chemical cross-linking of proteins coupled with mass spectrometry allows low-resolution characterization of proteins and protein complexes based on measuring distance constraints from cross-links. In this work, we have investigated cross-linking by means of a heterobifunctional cross-linker containing a traditional N-hydroxysuccinimide (NHS) ester and a UV photoactivatable diazirine group. Activation of the diazirine group yields a highly reactive carbene species, with potential to increase the number of cross-links compared with homobifunctional, NHS-based cross-linkers. Cross-linking reactions were performed on model systems such as synthetic peptides and equine myoglobin. After reduction of the disulfide bond, the formation of intra- and intermolecular cross-links was identified and the peptides modified with both NHS and diazirine moieties characterized. Fragmentation of these modified peptides reveals the presence of a marker ion for intramolecular cross-links, which facilitates identification.
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Affiliation(s)
- Alexandre F Gomes
- Institute of Chemistry, University of Campinas-UNICAMP and Instituto Nacional de Ciencia e Tecnologia de Bioanalitica, CP 6154, 13083-970, Campinas, Sao Paulo, Brazil
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Nirthanan S, Garcia G, Chiara DC, Husain SS, Cohen JB. Identification of binding sites in the nicotinic acetylcholine receptor for TDBzl-etomidate, a photoreactive positive allosteric effector. J Biol Chem 2008; 283:22051-62. [PMID: 18524766 PMCID: PMC2494931 DOI: 10.1074/jbc.m801332200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 05/30/2008] [Indexed: 11/06/2022] Open
Abstract
Etomidate, one of the most potent general anesthetics used clinically, acts at micromolar concentrations as an anesthetic and positive allosteric modulator of gamma-aminobutyric acid responses, whereas it inhibits muscle-type nicotinic acetylcholine receptors (nAChRs) at concentrations above 10 microm. We report here that TDBzl-etomidate, a photoreactive etomidate analog, acts as a positive allosteric nAChR modulator rather than an inhibitor, and we identify its binding sites by photoaffinity labeling. TDBzl-etomidate (>10 microm) increased the submaximal response to acetylcholine (10 microm) with a 2.5-fold increase at 60 microm. At higher concentrations, it inhibited the binding of the noncompetitive antagonists [(3)H]tetracaine and [(3)H]phencyclidine to Torpedo nAChR-rich membranes (IC(50) values of 0. 8 mm). nAChR-rich membranes were photolabeled with [(3)H]TDBzl-etomidate, and labeled amino acids were identified by Edman degradation. For nAChRs photolabeled in the absence of agonist (resting state), there was tetracaine-inhibitable photolabeling of amino acids in the ion channel at positions M2-9 (deltaLeu-265) and M2-13 (alphaVal-255 and deltaVal-269), whereas labeling of alphaM2-10 (alphaSer-252) was not inhibited by tetracaine but was enhanced 10-fold by proadifen or phencyclidine. In addition, there was labeling in gammaM3 (gammaMet-299), a residue that contributes to the same pocket in the nAChR structure as alphaM2-10. The pharmacological specificity of labeling of residues, together with their locations in the nAChR structure, indicate that TDBzl-etomidate binds at two distinct sites: one within the lumen of the ion channel (labeling of M2-9 and -13), an inhibitory site, and another at the interface between the alpha and gamma subunits (labeling of alphaM2-10 and gammaMet-299) likely to be a site for positive allosteric modulation.
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Frank RA, Kavanagh R, Kent Burnison B, Arsenault G, Headley JV, Peru KM, Van Der Kraak G, Solomon KR. Toxicity assessment of collected fractions from an extracted naphthenic acid mixture. Chemosphere 2008; 72:1309-1314. [PMID: 18555508 DOI: 10.1016/j.chemosphere.2008.04.078] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 04/01/2008] [Accepted: 04/16/2008] [Indexed: 05/26/2023]
Abstract
Recent expansion within the oil sands industry of the Athabasca Basin of Alberta, Canada has led to increased concern regarding process-affected wastewaters produced during bitumen extraction. Naphthenic acids (NAs) have been identified as the primary toxic constituents of oil sands process-affected waters (OSPW) and studies have shown that with time, microbial degradation of lower molecular weight NAs has led to a decrease in observed toxicity. As earlier studies identified the need for an "unequivocal demonstration" of lower molecular weight NAs being the primary contributors to mixture toxicity, a study was initiated to fractionate an extracted NA mixture by molecular weight and to assess each fraction's toxicity. Successful molecular weight fractionation of a methylated NA mixture was achieved using a Kugelrohr distillation apparatus, in which fractions collected at higher boiling points contained NAs with greater total carbon content as well as greater degree of cyclicity. Assays with Vibrio fischeri bioluminescence (via Microtox assay) revealed that the lowest molecular weight NAs collected had higher potency (EC50: 41.9+/-2.8 mg l(-1)) than the highest molecular weight NAs collected (EC50: 64.9+/-7.4 mg l(-1)). Although these results support field observations of microbial degradation of low molecular weight NAs decreasing OSPW toxicity, it is not clear why larger NAs, given their greater hydrophobicity, would be less toxic.
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Affiliation(s)
- Richard A Frank
- Centre for Toxicology, University of Guelph, Guelph, ON, Canada.
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Noya Y, Mikami Y, Taneda S, Mori Y, Suzuki AK, Ohkura K, Yamaki K, Yoshino S, Seki KI. Improvement of an efficient separation method for chemicals in diesel exhaust particles: analysis for nitrophenols. Environ Sci Pollut Res Int 2008; 15:318-21. [PMID: 18437438 DOI: 10.1007/s11356-008-0006-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 03/21/2008] [Indexed: 05/14/2023]
Abstract
GOAL, SCOPE, AND BACKGROUND Diesel exhaust is believed to consist of thousands of organic constituents and is a major cause of urban pollution. We recently reported that a systematic separation procedure involving successive solvent extractions, followed by repeated column chromatography, resulted in the isolation of vasodilatory active nitrophenols. These findings indicated that the estimation of the amount of nitrophenols in the environment is important to evaluate their effect on human health. The isolation procedure, however, involved successive solvent extractions followed by tedious, repeated chromatography, resulting in poor fractionation and in a significant loss of accuracy and reliability. Therefore, it was crucial to develop an alternative, efficient, and reliable analytical method. Here, we describe a facile and efficient acid-base extraction procedure for the analysis of nitrophenols. MATERIALS AND METHODS Diesel exhaust particles (DEP) were collected from the exhaust of a 4JB1-type engine (ISUZU Automobile Co., Tokyo, Japan). Gas chromatography-mass spectrometry (GC-MS) analysis was performed with a GCMS-QP2010 instrument (Shimadzu, Kyoto, Japan). RESULTS A solution of DEP in 1-butanol was extracted with aqueous NaOH to afford a nitrophenol-rich oily extract. The resulting oil was methylated with trimethylsilyldiazomethane and subsequently subjected to GC-MS analysis, revealing that 4-nitrophenol, 3-methyl-4-nitrophenol, 2-methyl-4-nitrophenol, and 4-nitro-3-phenylphenol were present in significantly higher concentrations than those reported previously. DISCUSSION Simple acid-base extraction followed by the direct analysis of the resulting extract by GC-MS gave only broad peaks of nitrophenols with a poor detection limit, while the GC-MS analysis of the sample pretreated with (trimethylsilyl)diazomethane gave satisfactorily clear chromatograms with sharp peaks and with a significantly lowered detection limit (0.5 ng/ml, approximately 100 times). CONCLUSION The present method involving an acid-base extraction, in situ derivatization, and GC-MS analysis has shown to be a simple, efficient, and reliable method for the isolation and identification of the chemical substances in DEP.
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Affiliation(s)
- Yoichi Noya
- Central Institute of Isotope Science, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
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Kühnel E, Laffan DDP, Lloyd-Jones GC, Martínez Del Campo T, Shepperson IR, Slaughter JL. Mechanism of methyl esterification of carboxylic acids by trimethylsilyldiazomethane. Angew Chem Int Ed Engl 2008; 46:7075-8. [PMID: 17691089 DOI: 10.1002/anie.200702131] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Erik Kühnel
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS81TS, UK
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Moraes MCB, Birkett MA, Gordon-Weeks R, Smart LE, Martin JL, Pye BJ, Bromilow R, Pickett JA. cis-Jasmone induces accumulation of defence compounds in wheat, Triticum aestivum. Phytochemistry 2008; 69:9-17. [PMID: 17681563 DOI: 10.1016/j.phytochem.2007.06.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 06/14/2007] [Accepted: 06/15/2007] [Indexed: 05/16/2023]
Abstract
Liquid phase extraction (LPE) and vapor phase extraction (VPE) methodologies were used to evaluate the impact of the plant activator, cis-jasmone, on the secondary metabolism of wheat, Triticum aestivum, var. Solstice. LPE allowed the measurement of benzoxazinoids, i.e. 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), 2-hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA) and 6-methoxy-benzoxazolin-2-one (MBOA), and phenolic acids such as trans-p-coumaric acid, syringic acid, p-hydroxybenzoic acid, vanillic acid and cis- and trans-ferulic acid. Using LPE, a significantly higher level of DIMBOA was found in aerial parts and roots of T. aestivum following treatment with cis-jasmone, when compared with untreated plants. Similar results were obtained for phenolic acids, such as trans-ferulic acid and vanillic acid in roots. Using VPE, it was possible to measure levels of 2-hydroxy-7-methoxy-(2H)-1,4-benzoxazin-3(4H)-one (HBOA), benzoxazolin-2(3H)-one (BOA), ferulic acid, syringic acid and coumaric acid. The levels of HBOA in aerial parts and roots were significantly greater in cis-jasmone treated plants compared to untreated plants. cis-Jasmone is known to be a plant activator in terms of production of defence-related volatile semiochemicals that repel aphids and increase the foraging activity of aphid parasitoids. These results show, for the first time, that cis-jasmone also induces selective production of secondary metabolites that are capable of directly reducing development of pests, diseases and weeds.
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Affiliation(s)
- Maria C Blassioli Moraes
- Embrapa Genetic Resources and Biotechnology, Cx. Postal: 02372, Cep. 70849-970 Brasília-DF, Brazil
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Solbach C, Machulla HJ. Production of [11C]chloroform by direct chlorination of [11C]methane without catalyst support for the synthesis of [11C]diazomethane. Appl Radiat Isot 2007; 65:1345-9. [PMID: 17467278 DOI: 10.1016/j.apradiso.2007.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 01/12/2007] [Accepted: 02/23/2007] [Indexed: 11/22/2022]
Abstract
The preparation of [11C]chloroform by direct chlorination of [11C]methane using gaseous chlorine by variation of temperature and reaction time (inert gas flow) without catalyst support for the online production of [11C]diazomethane in a flow-through synthesis apparatus is described in this work. At an oven temperature of 400 degrees C and a He flow of 50 mL/min, [11C]chloroform was synthesized inside a quartz glass column in a radiochemical yield of 31+/-2% with respect to [11C]methane. The online preparation of [11C]diazomethane by reaction of [11C]chloroform with hydrazine in an ethanolic KOH solution with small amounts of 18-crown-6-crownether succeeded with a radiochemical yield of 20+/-3% with respect to [11C]methane. The product [11C]diazomethane was measured indirectly in the form of 4-nitrobenzoic acid[11C]methylester using the esterification of 4-nitrobenzoic acid as a monitor reaction.
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Affiliation(s)
- C Solbach
- Radiopharmacy, PET-Center, University Hospital Tübingen, Röntgenweg 15, D-72076 Tübingen, Germany.
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Ryzhikov S, Bahr BA. Gephyrin alterations due to protein accumulation stress are reduced by the lysosomal modulator Z-Phe-Ala-diazomethylketone. J Mol Neurosci 2007; 34:131-9. [PMID: 18204977 DOI: 10.1007/s12031-007-9009-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Accepted: 08/22/2007] [Indexed: 11/25/2022]
Abstract
Inhibitory neurotransmission is important for brain function and requires specific transmitter receptors that are organized in synaptic domains. Gephyrin is a cytoskeletal organization protein that binds tubulin and plays an important role in clustering and organizing select inhibitory neurotransmitter receptors. Here, we tested if gephyrin is altered by protein accumulation stress that is common in age-related neurodegenerative disorders. For this, we used the hippocampal slice model that has been shown to exhibit chloroquine (CQN)-induced protein accumulation, microtubule destabilization, transport failure, and declines in excitatory neurotransmitter receptors and their responses. In addition to the decreases in excitatory receptor subunits and other glutamatergic markers, we found that gephyrin isoforms were reduced across the CQN treatment period. Associated with this decline in gephyrin levels was the production of three gephyrin breakdown products (GBDPs) of 30, 38, and 48 kDa. The induced effects on gephyrin were tested for evidence of recovery through enhancement of lysosomal function that is known to promote protein clearance and microtubule integrity. Using the lysosomal modulator Z-Phe-Ala-diazomethylketone (PADK), gephyrin levels were completely restored in correspondence with the recovery of excitatory glutamatergic components. In addition, GBDPs were significantly reduced after the 2-day PADK treatment, to levels that were at or below those measured in control cultures. These findings suggest that receptor-clustering mechanisms for inhibitory synapses are compromised during protein accumulation events. They also indicate that a lysosomal enhancement strategy can protect gephyrin integrity, which may be vital for the balance between inhibitory and excitatory signaling during age-related diseases.
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Affiliation(s)
- Sophia Ryzhikov
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
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Taguchi H, Ohkubo A, Seio K, Sekine M. Synthesis of deoxycytidine derivatives and their use for the selective photo crosslinking with 5-methylcytosine. ACTA ACUST UNITED AC 2007:57-8. [PMID: 17150815 DOI: 10.1093/nass/nrl028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
New photoactivatable nucleosides, 4-N-[3-(trifluoromethyl)diazirinyl]benzoyldeoxycytidine derivatives and these corresponding phosphoramidite derivatives were synthesized for the use as photo crosslinking probes. The carbene species was generated by UV irradiation so that it could react with the benzylic C-H of toluene to give a cross-linking product. The diazirine modified DNA 12mer was successfully synthesized by our N-unprotected phosphoramidite method. We studied its hybridization and photo crosslinking abilities. When a 5-methyl deoxycytidine containing complementary DNA oligomer was irradiated in the presence of the DNA 12 mer, crosslinking products were observed.
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Affiliation(s)
- Haruhiko Taguchi
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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