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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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Yang K, Greenberg MM. Histone Tail Sequences Balance Their Role in Genetic Regulation and the Need To Protect DNA against Destruction in Nucleosome Core Particles Containing Abasic Sites. Chembiochem 2018; 20:78-82. [PMID: 30307690 DOI: 10.1002/cbic.201800559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/14/2022]
Abstract
Abasic sites (AP) are produced 10 000 times per day in a single cell. Strand cleavage at AP is accelerated ≈100-fold within a nucleosome core particle (NCP) compared to free DNA. The lysine-rich N-terminal tails of histone proteins catalyze single-strand breaks through a mechanism used by base-excision-repair enzymes, despite the general dearth of glutamic acid, aspartic acid, and histidine-the amino acids that are typically responsible for deprotonation of Schiff base intermediates. Incorporating glutamic acid, aspartic acid, or histidine proximal to lysine residues in histone N-terminal tails increases AP reactivity as much as sixfold. The rate acceleration is due to more facile DNA cleavage of Schiff-base intermediates. These observations raise the possibility that histone proteins could have evolved to minimize the presence of histidine, glutamic acid, and aspartic acid in their lysine-rich N-terminal tails to guard against enhancing the toxic effects of DNA damage.
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Affiliation(s)
- Kun Yang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
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3
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Behrendt R, White P, Offer J. Advances in Fmoc solid-phase peptide synthesis. J Pept Sci 2016; 22:4-27. [PMID: 26785684 PMCID: PMC4745034 DOI: 10.1002/psc.2836] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]
Abstract
Today, Fmoc SPPS is the method of choice for peptide synthesis. Very-high-quality Fmoc building blocks are available at low cost because of the economies of scale arising from current multiton production of therapeutic peptides by Fmoc SPPS. Many modified derivatives are commercially available as Fmoc building blocks, making synthetic access to a broad range of peptide derivatives straightforward. The number of synthetic peptides entering clinical trials has grown continuously over the last decade, and recent advances in the Fmoc SPPS technology are a response to the growing demand from medicinal chemistry and pharmacology. Improvements are being continually reported for peptide quality, synthesis time and novel synthetic targets. Topical peptide research has contributed to a continuous improvement and expansion of Fmoc SPPS applications.
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Affiliation(s)
- Raymond Behrendt
- Novabiochem, Merck & CieIm Laternenacker 58200SchaffhausenSwitzerland
| | - Peter White
- Novabiochem, Merck Chemicals LtdPadge RoadBeestonNG9 2JRUK
| | - John Offer
- The Francis Crick Institute215 Euston RoadLondonNW1 2BEUK
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Tveen-Jensen K, Gesellchen F, Wilson R, Spickett CM, Cooper JM, Pitt AR. Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples. Sci Rep 2015; 5:9736. [PMID: 25978651 PMCID: PMC4432867 DOI: 10.1038/srep09736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/10/2015] [Indexed: 01/29/2023] Open
Abstract
Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid, and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.
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Affiliation(s)
- Karina Tveen-Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Frank Gesellchen
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Rab Wilson
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Jonathan M Cooper
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
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Nguyen HTH, Shaffer CJ, Tureček F. Probing peptide cation-radicals by near-UV photodissociation in the gas phase. Structure elucidation of histidine radical chromophores formed by electron transfer reduction. J Phys Chem B 2015; 119:3948-61. [PMID: 25688483 DOI: 10.1021/jp511717c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ωB97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase.
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Affiliation(s)
- Huong T H Nguyen
- Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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Newman RH, Zhang J, Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front Genet 2014; 5:263. [PMID: 25177341 PMCID: PMC4133750 DOI: 10.3389/fgene.2014.00263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/16/2014] [Indexed: 11/13/2022] Open
Abstract
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks.
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Affiliation(s)
- Robert H Newman
- Department of Biology, North Carolina Agricultural and Technical State University Greensboro, NC, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Oncology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine Baltimore, MD, USA ; High-Throughput Biology Center, Institute for Basic Biomedical Sciences, Johns Hopkins University Baltimore, MD, USA
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Piggott MJ, Attwood PV. Post-translational modifications: Panning for phosphohistidine. Nat Chem Biol 2013; 9:411-2. [PMID: 23708075 DOI: 10.1038/nchembio.1273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew J Piggott
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Australia.
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Theillet FX, Smet-Nocca C, Liokatis S, Thongwichian R, Kosten J, Yoon MK, Kriwacki RW, Landrieu I, Lippens G, Selenko P. Cell signaling, post-translational protein modifications and NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 54:217-36. [PMID: 23011410 PMCID: PMC4939263 DOI: 10.1007/s10858-012-9674-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/07/2012] [Indexed: 05/13/2023]
Abstract
Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.
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Affiliation(s)
- Francois-Xavier Theillet
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Caroline Smet-Nocca
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Stamatios Liokatis
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Rossukon Thongwichian
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Jonas Kosten
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
| | - Mi-Kyung Yoon
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Isabelle Landrieu
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Guy Lippens
- CNRS UMR 8576, Universite Lille Nord de France, 59655 Villeneuve d’Ascq, France
| | - Philipp Selenko
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), In-cell NMR Group, Robert-Roessle Strasse 10, 13125 Berlin, German
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Sidoli S, Cheng L, Jensen ON. Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics 2012; 75:3419-33. [PMID: 22234360 DOI: 10.1016/j.jprot.2011.12.029] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/18/2011] [Accepted: 12/20/2011] [Indexed: 12/11/2022]
Affiliation(s)
- Simone Sidoli
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Kee JM, Muir TW. Chasing phosphohistidine, an elusive sibling in the phosphoamino acid family. ACS Chem Biol 2012; 7:44-51. [PMID: 22148577 DOI: 10.1021/cb200445w] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This year (2012) marks the 50th anniversary of the discovery of protein histidine phosphorylation. Phosphorylation of histidine (pHis) is now widely recognized as being critical to signaling processes in prokaryotes and lower eukaryotes. However, the modification is also becoming more widely reported in mammalian cellular processes and implicated in certain human disease states such as cancer and inflammation. Nonetheless, much remains to be understood about the role and extent of the modification in mammalian cell biology. Studying the functional role of pHis in signaling, either in vitro or in vivo, has proven devilishly hard, largely due to the chemical instability of the modification. As a consequence, we are currently handicapped by a chronic lack of chemical and biochemical tools with which to study histidine phosphorylation. Here, we discuss the challenges associated with studying the chemical biology of pHis and review recent progress that offers some hope that long-awaited biochemical reagents for studying this elusive posttranslational modification (PTM) might soon be available.
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Affiliation(s)
- Jung-Min Kee
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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Dhall A, Chatterjee C. Chemical approaches to understand the language of histone modifications. ACS Chem Biol 2011; 6:987-99. [PMID: 21827195 DOI: 10.1021/cb200142c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genomic DNA in the eukaryotic cell nucleus is present in the form of chromatin. Histones are the principal protein component of chromatin, and their post-translational modifications play important roles in regulating the structure and function of chromatin and thereby in determining cell development and disease. An understanding of how histone modifications translate into downstream cellular events is important from both developmental and therapeutic perspectives. However, biochemical studies of histone modifications require access to quantities of homogenously modified histones that cannot be easily isolated from natural sources or generated by enzymatic methods. In the past decade, chemical synthesis has proven to be a powerful tool in translating the language of histone modifications by providing access to uniformly modified histones and by the development of stable analogues of thermodynamically labile modifications. This Review highlights the various synthetic and semisynthetic strategies that have enabled biochemical and biophysical characterization of site-specifically modified histones.
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Affiliation(s)
- Abhinav Dhall
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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