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Moleri P, Wilkins BJ. Unnatural Amino Acid Crosslinking for Increased Spatiotemporal Resolution of Chromatin Dynamics. Int J Mol Sci 2023; 24:12879. [PMID: 37629060 PMCID: PMC10454095 DOI: 10.3390/ijms241612879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The utilization of an expanded genetic code and in vivo unnatural amino acid crosslinking has grown significantly in the past decade, proving to be a reliable system for the examination of protein-protein interactions. Perhaps the most utilized amino acid crosslinker, p-benzoyl-(l)-phenylalanine (pBPA), has delivered a vast compendium of structural and mechanistic data, placing it firmly in the upper echelons of protein analytical techniques. pBPA contains a benzophenone group that is activated with low energy radiation (~365 nm), initiating a diradical state that can lead to hydrogen abstraction and radical recombination in the form of a covalent bond to a neighboring protein. Importantly, the expanded genetic code system provides for site-specific encoding of the crosslinker, yielding spatial control for protein surface mapping capabilities. Paired with UV-activation, this process offers a practical means for spatiotemporal understanding of protein-protein dynamics in the living cell. The chromatin field has benefitted particularly well from this technique, providing detailed mapping and mechanistic insight for numerous chromatin-related pathways. We provide here a brief history of unnatural amino acid crosslinking in chromatin studies and outlooks into future applications of the system for increased spatiotemporal resolution in chromatin related research.
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Affiliation(s)
| | - Bryan J. Wilkins
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Riverdale, NY 10471, USA
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2
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Abstract
Multiple reports over the past 2 years have provided the first complete structural analyses for the essential yeast chromatin remodeler, RSC, providing elaborate molecular details for its engagement with the nucleosome. However, there still remain gaps in resolution, particularly within the many RSC subunits that harbor histone binding domains. Solving contacts at these interfaces is crucial because they are regulated by posttranslational modifications that control remodeler binding modes and function. Modifications are dynamic in nature often corresponding to transcriptional activation states and cell cycle stage, highlighting not only a need for enriched spatial resolution but also temporal understanding of remodeler engagement with the nucleosome. Our recent work sheds light on some of those gaps by exploring the binding interface between the RSC catalytic motor protein, Sth1, and the nucleosome, in the living nucleus. Using genetically encoded photo-activatable amino acids incorporated into histones of living yeast we are able to monitor the nucleosomal binding of RSC, emphasizing the regulatory roles of histone modifications in a spatiotemporal manner. We observe that RSC prefers to bind H2B SUMOylated nucleosomes in vivo and interacts with neighboring nucleosomes via H3K14ac. Additionally, we establish that RSC is constitutively bound to the nucleosome and is not ejected during mitotic chromatin compaction but alters its binding mode as it progresses through the cell cycle. Our data offer a renewed perspective on RSC mechanics under true physiological conditions.
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Affiliation(s)
- Heinz Neumann
- Department of Structural Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany.
| | - Bryan J Wilkins
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Bronx, NY, 10471, USA.
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Jain N, Tamborrini D, Evans B, Chaudhry S, Wilkins BJ, Neumann H. Interaction of RSC Chromatin Remodeling Complex with Nucleosomes Is Modulated by H3 K14 Acetylation and H2B SUMOylation In Vivo. iScience 2020; 23:101292. [PMID: 32623337 PMCID: PMC7334588 DOI: 10.1016/j.isci.2020.101292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 01/04/2023] Open
Abstract
Chromatin remodeling complexes are multi-subunit nucleosome translocases that reorganize chromatin in the context of DNA replication, repair, and transcription. To understand how these complexes find their target sites on chromatin, we use genetically encoded photo-cross-linker amino acids to map the footprint of Sth1, the catalytic subunit of the RSC complex, on nucleosomes in living yeast. We find that H3 K14 acetylation induces the interaction of the Sth1 bromodomain with the H3 tail and mediates the interaction of RSC with neighboring nucleosomes rather than recruiting it to chromatin. RSC preferentially resides on H2B SUMOylated nucleosomes in vivo and shows a moderately enhanced affinity due to this modification in vitro. Furthermore, RSC is not ejected from chromatin in mitosis, but changes its mode of nucleosome binding. Our in vivo analyses show that RSC recruitment to specific chromatin targets involves multiple histone modifications likely in combination with histone variants and transcription factors.
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Affiliation(s)
- Neha Jain
- Department of Structural Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Davide Tamborrini
- Department of Structural Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Brian Evans
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Bronx, NY 10471, USA
| | - Shereen Chaudhry
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Bronx, NY 10471, USA
| | - Bryan J Wilkins
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Bronx, NY 10471, USA.
| | - Heinz Neumann
- Department of Structural Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295 Darmstadt, Germany.
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Wilkins BJ, Jain N, Evans B, Chaudhry S, Neumann H. Histone H3 K14 acetylation and H2B SUMOylation help regulate binding of the RSC remodeler complex to the nucleosome. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Neha Jain
- MPI for Molecular Physiology Dortmund
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Kruitwagen T, Denoth-Lippuner A, Wilkins BJ, Neumann H, Barral Y. Axial contraction and short-range compaction of chromatin synergistically promote mitotic chromosome condensation. eLife 2015; 4:e1039. [PMID: 26615018 PMCID: PMC4755758 DOI: 10.7554/elife.10396] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/27/2015] [Indexed: 11/16/2022] Open
Abstract
The segregation of eukaryotic chromosomes during mitosis requires their extensive folding into units of manageable size for the mitotic spindle. Here, we report on how phosphorylation at serine 10 of histone H3 (H3 S10) contributes to this process. Using a fluorescence-based assay to study local compaction of the chromatin fiber in living yeast cells, we show that chromosome condensation entails two temporally and mechanistically distinct processes. Initially, nucleosome-nucleosome interaction triggered by H3 S10 phosphorylation and deacetylation of histone H4 promote short-range compaction of chromatin during early anaphase. Independently, condensin mediates the axial contraction of chromosome arms, a process peaking later in anaphase. Whereas defects in chromatin compaction have no observable effect on axial contraction and condensin inactivation does not affect short-range chromatin compaction, inactivation of both pathways causes synergistic defects in chromosome segregation and cell viability. Furthermore, both pathways rely at least partially on the deacetylase Hst2, suggesting that this protein helps coordinating chromatin compaction and axial contraction to properly shape mitotic chromosomes. DOI:http://dx.doi.org/10.7554/eLife.10396.001 DNA in humans, yeast and other eukaryotic organisms is packaged in structures called chromosomes. When a cell divides these chromosomes are copied and then the matching pairs are separated so that each daughter cell has a full set of its genome. To enable these events to take place, the DNA must become more tightly packed so that the chromosomes become rigid units with projections called arms. Any failure in this chromosome “condensation” leads to the loss of chromosomes during cell division. Within a chromosome, sections of DNA are wrapped around groups of proteins to make a series of linked units called nucleosomes, which resemble beads on a string. These units and other scaffold proteins together make a structure called chromatin and establish the overall shape of the chromosome. However, it is not exactly clear how the nucleosomes and scaffold proteins are rearranged during condensation. Kruitwagen et al. used microscopy to study chromosome condensation in budding yeast. The experiments reveal that condensation involves two separate processes. First, modifications to the nucleosomes result in these units becoming more tightly packed in a process called short-range compaction. Second, a group of proteins called condensin is responsible for rearranging the compacted chromatin to enforce higher-order structure on the arms of the condensed chromosome (long-range contraction). Further experiments suggest that an enzyme called Hst2 may help to co-ordinate these processes to ensure that chromosomes adopt the right shape before the cell divides. For example, Hst2 ensures that longer chromosomes condense more than shorter ones. A future challenge will be to find out whether chromosome condensation works in a similar way in humans and other large eukaryotes, which form much larger chromosomes with more complicated structures than yeast. DOI:http://dx.doi.org/10.7554/eLife.10396.002
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Affiliation(s)
- Tom Kruitwagen
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Annina Denoth-Lippuner
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Bryan J Wilkins
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg- August University Göttingen, Göttingen, Germany
| | - Heinz Neumann
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg- August University Göttingen, Göttingen, Germany
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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Wilkins BJ, Hahn LE, Heitmüller S, Frauendorf H, Valerius O, Braus GH, Neumann H. Genetically encoding lysine modifications on histone H4. ACS Chem Biol 2015; 10:939-44. [PMID: 25590375 DOI: 10.1021/cb501011v] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Post-translational modifications of proteins are important modulators of protein function. In order to identify the specific consequences of individual modifications, general methods are required for homogeneous production of modified proteins. The direct installation of modified amino acids by genetic code expansion facilitates the production of such proteins independent of the knowledge and availability of the enzymes naturally responsible for the modification. The production of recombinant histone H4 with genetically encoded modifications has proven notoriously difficult in the past. Here, we present a general strategy to produce histone H4 with acetylation, propionylation, butyrylation, and crotonylation on lysine residues. We produce homogeneous histone H4 containing up to four simultaneous acetylations to analyze the impact of the modifications on chromatin array compaction. Furthermore, we explore the ability of antibodies to discriminate between alternative lysine acylations by incorporating these modifications in recombinant histone H4.
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Affiliation(s)
- Bryan J. Wilkins
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Liljan E. Hahn
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Svenja Heitmüller
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Holm Frauendorf
- Institute
for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Oliver Valerius
- Institute
for Microbiology and Genetics, Georg-August University Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Gerhard H. Braus
- Institute
for Microbiology and Genetics, Georg-August University Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Heinz Neumann
- Free
Floater (Junior) Research Group “Applied Synthetic Biology”,
Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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Wilkins BJ, Rall NA, Ostwal Y, Kruitwagen T, Hiragami-Hamada K, Winkler M, Barral Y, Fischle W, Neumann H. A cascade of histone modifications induces chromatin condensation in mitosis. Science 2014; 343:77-80. [PMID: 24385627 DOI: 10.1126/science.1244508] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metaphase chromosomes are visible hallmarks of mitosis, yet our understanding of their structure and of the forces shaping them is rudimentary. Phosphorylation of histone H3 serine 10 (H3 S10) by Aurora B kinase is a signature event of mitosis, but its function in chromatin condensation is unclear. Using genetically encoded ultraviolet light-inducible cross-linkers, we monitored protein-protein interactions with spatiotemporal resolution in living yeast to identify the molecular details of the pathway downstream of H3 S10 phosphorylation. This modification leads to the recruitment of the histone deacetylase Hst2p that subsequently removes an acetyl group from histone H4 lysine 16, freeing the H4 tail to interact with the surface of neighboring nucleosomes and promoting fiber condensation. This cascade of events provides a condensin-independent driving force of chromatin hypercondensation during mitosis.
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Affiliation(s)
- Bryan J Wilkins
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
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Liu J, Castañeda CA, Wilkins BJ, Fushman D, Cropp TA. Condensed E. coli cultures for highly efficient production of proteins containing unnatural amino acids. Bioorg Med Chem Lett 2010; 20:5613-6. [PMID: 20805030 DOI: 10.1016/j.bmcl.2010.08.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 08/07/2010] [Accepted: 08/10/2010] [Indexed: 11/29/2022]
Abstract
Current biosynthetic methods for producing proteins containing site-specifically incorporated unnatural amino acids are inefficient because the majority of the amino acid goes unused. Here we present a universal approach to improve the efficiency of such processes using condensed Escherichia coli cultures.
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Affiliation(s)
- Jia Liu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Wilkins BJ, Marionni S, Young DD, Liu J, Wang Y, Di Salvo ML, Deiters A, Cropp TA. Site-Specific Incorporation of Fluorotyrosines into Proteins in Escherichia coli by Photochemical Disguise. Biochemistry 2010; 49:1557-9. [DOI: 10.1021/bi100013s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bryan J. Wilkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Samuel Marionni
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Douglas D. Young
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Jia Liu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Yan Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Martino L. Di Salvo
- Dipartimento di Scienze Biochimiche and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro, 5-00185 Roma, Italy
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - T. Ashton Cropp
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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Wilkins BJ, Yang X, Cropp TA. Photochemical control of FlAsH labeling of proteins. Bioorg Med Chem Lett 2009; 19:4296-8. [DOI: 10.1016/j.bmcl.2009.05.072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 05/19/2009] [Accepted: 05/20/2009] [Indexed: 11/26/2022]
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Wilkins BJ, Daggett KA, Cropp TA. Peptide mass fingerprinting using isotopically encoded photo-crosslinking amino acids. Mol BioSyst 2008; 4:934-6. [DOI: 10.1039/b801512k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Daggett KA, Wilkins BJ, Cropp TA. A novel random mutagenesis method and the incorporation of an isotopic label into a protein. FASEB J 2007. [DOI: 10.1096/fasebj.21.6.lb17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kelly A Daggett
- Chemistry and BiochemistryUniversity of Maryland0107 Chemistry BuildingCollege ParkMD20742
| | - Bryan J. Wilkins
- Chemistry and BiochemistryUniversity of Maryland0107 Chemistry BuildingCollege ParkMD20742
| | - T. Ashton Cropp
- Chemistry and BiochemistryUniversity of Maryland0107 Chemistry BuildingCollege ParkMD20742
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Lee DW, Zhang K, Ning ZQ, Raabe EH, Tintner S, Wieland R, Wilkins BJ, Kim JM, Blough RI, Arceci RJ. Proliferation-associated SNF2-like gene (PASG): a SNF2 family member altered in leukemia. Cancer Res 2000; 60:3612-22. [PMID: 10910076] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
To identify genes involved in cell growth and/or apoptosis in leukemia, differential display was used to identify mRNAs that showed altered expression levels after cytokine withdrawal from the cytokine-dependent MO7e cell line. Sequence analysis of one transcript that showed a profound decrease in expression after cytokine withdrawal revealed it to be a member of the SNF2 family of chromatin remodeling ATPases. This cDNA had a 2514-nucleotide (838-amino acid) open reading frame and encoded an additional 230 amino acids at the NH2 terminus compared with the murine homologue, lsh, and the human counterpart, Hells. This gene locus has been designated SMARCA6 (SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6). The highest levels of mRNA expression in humans are observed in proliferative tissues such as the thymus, testis, and bone marrow. Whereas cytokine withdrawal in MO7e cells leads to apoptosis and decreased mRNA expression, growth arrest without the induction of apoptosis of MO7e cells also leads to down-regulation of mRNA expression, suggesting an association with cell proliferation and not suppression of apoptosis. Nuclear localization of this SNF2-like putative helicase is dependent on a nuclear localization sequence located in the NH2-terminal region. Based on sequence homology to other SNF2-like helicases, the pattern of tissue expression, and the association of expression with cell proliferation, we refer to the protein product as proliferation-associated SNF2-like gene product [PASG (D. W. Lee et al., Blood, 94: 594a, 1999)]. Examination of acute myelogenous leukemia and acute lymphoblastic leukemia samples revealed a high frequency of a PASG transcript containing an in-frame 75-nucleotide deletion, which codes for a conserved motif known to be critical for the transactivation activity of a related yeast SWI/SNF polypeptide. These results extend our knowledge of this SNF2-like family member and suggest a role for PASG in leukemogenesis.
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Affiliation(s)
- D W Lee
- Division of Hematology/Oncology, Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
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Garry AB, Midgley JM, Whalley WB, Wilkins BJ. Unsaturated steroids. Part 3. Synthesis of steroidal 22,24(28)-dienes, erogosta-5,7,22,24(28)-tetraen-3beta-ol, and cholesta-5,7,22-trien-3beta-ol. J Chem Soc Perkin 1 1977:809-12. [PMID: 558995 DOI: 10.1039/p19770000809] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
Abstract
The human metabolism of 5-allyl-5-neopentylbarbituric acid (nealbarbitone, Censedal), taken orally, has been studied. Comparison of the gas chromatography—mass spectra of extracts from urine with the spectra of model compounds showed nealbarbitone diol (III) to be the only urinary metabolite present in significant amount (about 30–40% of dose); the rate of excretion of diol reached a maximum about 36 h after ingestion of a single 300 mg dose. Treatment of nealbarbitone with a model oxidase of the Udenfriend type resulted only in oxidation of the allyl side-chain to the 2-oxopropyl derivative, in low yield.
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