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Dubrovskii Y, Murashko E, Chuprina O, Beltyukov P, Radilov A, Solovyev N, Babakov V. Mass spectrometry based proteomic approach for the screening of butyrylcholinesterase adduct formation with organophosphates. Talanta 2019; 197:374-382. [DOI: 10.1016/j.talanta.2019.01.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/13/2019] [Accepted: 01/15/2019] [Indexed: 11/29/2022]
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2
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Zhang H, Chingin K, Zhu L, Chen H. Molecular Characterization of Ongoing Enzymatic Reactions in Raw Garlic Cloves Using Extractive Electrospray Ionization Mass Spectrometry. Anal Chem 2015; 87:2878-83. [DOI: 10.1021/ac504371z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hua Zhang
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
| | - Konstantin Chingin
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
| | - Liang Zhu
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
| | - Huanwen Chen
- Jiangxi Key Laboratory for
Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang 330013 P.R. China
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3
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Robbins MD, Yoon OK, Barbula GK, Zare RN. Stopped-flow kinetic analysis using Hadamard transform time-of-flight mass spectrometry. Anal Chem 2010; 82:8650-7. [PMID: 20843011 DOI: 10.1021/ac101899n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A home-built stopped-flow apparatus is interfaced to a Hadamard transform time-of-flight mass spectrometer, which permits study of reaction kinetics with a time between reaction initiation and observation as short as about 100 ms and a sampling rate of chemical change that can approach 1 ms. This technique is applied to the trypsin-catalyzed hydrolysis of several peptides and is validated by comparing the results with literature values as well as to optical data obtained with the present stopped-flow apparatus. In addition, we report a kinetic study of the action of trypsin on a peptide having more than one cleavage site.
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Affiliation(s)
- Matthew D Robbins
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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4
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Roberts A, Furdui C, Anderson KS. Observation of a chemically labile, noncovalent enzyme intermediate in the reaction of metal-dependent Aquifex pyrophilus KDO8PS by time-resolved mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1919-1924. [PMID: 20533322 PMCID: PMC3381509 DOI: 10.1002/rcm.4594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The direct detection of intermediates in enzymatic reactions can yield important mechanistic insights but may be difficult due to short intermediate lifetimes and chemical instability. Using a rapid-mixing device coupled with electrospray ionization time-of-flight mass spectrometry, the noncovalent hemiketal intermediate in the reaction of metal-dependent 3-deoxy-D-manno-octulosonate-8-phosphate (KDO8P) synthase from Aquifex pyrophilus was observed in the millisecond time range. Using single turnover conditions, the noncovalent complexes of enzyme with Cd(2+):phosphoenolpyruvate, Cd(2+):phosphate, Cd(2+):KDO8P, and Cd(2+):intermediate complexes were resolved. The intermediate complex is present during times ranging from 50-630 ms, indicating that the intermediate builds up at the ambient temperatures of the experiment. This represents the first direct detection of the intermediate with a native metal-dependent KDO8PS, and further demonstrates that time-resolved mass spectrometry is a useful tool in mechanistic studies of enzymatic reactions.
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Affiliation(s)
- Anne Roberts
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Cristina Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
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5
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Zhang H, Wang L, Gao P. Use of the contour approach for visualizing the dynamic behavior of intermediates during O-nitrophenyl-β-d-galactoside hydrolysis by β-galactosidase. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Leib RD, Flick TG, Williams ER. Direct quantitation of peptide mixtures without standards using clusters formed by electrospray ionization mass spectrometry. Anal Chem 2009; 81:3965-72. [PMID: 19354265 DOI: 10.1021/ac900294r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In electrospray ionization mass spectrometry, ion abundances depend on a number of different factors, including analyte surface activity, competition between analytes for charge, analyte concentration, as well as instrumental factors, including mass-dependent ion transmission and detection. Here, a novel method for obtaining quantitative information about solution-phase concentrations of peptide mixtures is described and demonstrated for five different peptide mixtures with relative concentrations ranging from 0.05% to 50%. In this method, the abundances of large clusters containing anywhere from 0 to 13 impurity molecules are measured and directly related to the relative solution-phase concentration of the peptides. For clusters containing approximately 15 or more peptides, the composition of the clusters approaches the statistical value indicating that these clusters are formed nonspecifically and that any differences in ion detection or ionization efficiency are negligible at these large cluster sizes. This method is accurate to within approximately 20% or better, even when the relative ion intensities of the protonated monomers can differ by over an order of magnitude compared to their solution-phase concentrations. Although less accurate than other quantitation methods that employ internal standards, this method does have the key advantages of speed, simplicity, and the ability to quantitate components in solution even when the identities of the components are unknown.
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Affiliation(s)
- Ryan D Leib
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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7
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Abstract
A major scientific challenge at the present time for cancer research is the determination of the underlying biological basis for cancer development. It is further complicated by the heterogeneity of cancer's origin. Understanding the molecular basis of cancer requires studying the dynamic and spatial interactions among proteins in cells, signaling events among cancer cells, and interactions between the cancer cells and the tumor microenvironment. Recently, it has been proposed that large-scale protein expression analysis of cancer cell proteomes promises to be valuable for investigating mechanisms of cancer transformation. Advances in mass spectrometry technologies and bioinformatics tools provide a tremendous opportunity to qualitatively and quantitatively interrogate dynamic protein-protein interactions and differential regulation of cellular signaling pathways associated with tumor development. In this review, progress in shotgun proteomics technologies for examining the molecular basis of cancer development will be presented and discussed.
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Affiliation(s)
- Emily I Chen
- Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037, USA
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8
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Clarke DJ, Mackay CL, Campopiano DJ, Langridge-Smith P, Brown AR. Interrogating the Molecular Details of the Peroxiredoxin Activity of the Escherichia coli Bacterioferritin Comigratory Protein Using High-Resolution Mass Spectrometry. Biochemistry 2009; 48:3904-14. [PMID: 19298085 DOI: 10.1021/bi900189e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- David J. Clarke
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - C. Logan Mackay
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - Dominic J. Campopiano
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - Pat Langridge-Smith
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - Alan R. Brown
- Department of Medical Microbiology, Centre for Infectious Diseases, University of Edinburgh, 49 Little France Crescent, Edinburgh, EH16 4SB, U.K
- Current address: School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
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9
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Bumpus SB, Kelleher NL. Accessing natural product biosynthetic processes by mass spectrometry. Curr Opin Chem Biol 2009; 12:475-82. [PMID: 18706516 DOI: 10.1016/j.cbpa.2008.07.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/23/2008] [Accepted: 07/17/2008] [Indexed: 11/16/2022]
Abstract
Two important classes of natural products are made by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). With most biosynthetic intermediates covalently tethered during biogenesis, protein mass spectrometry (MS) has proven invaluable for their interrogation. New mass spectrometric assay formats (such as selective cofactor ejection and proteomics style LC-MS) are showcased here in the context of functional insights into new breeds of NRPS/PKS enzymes, including the first characterization of an 'iterative' PKS, the biosynthesis of the enediyne antitumor antibiotics, the study of a new strategy for PKS initiation via a GNAT-like mechanism, and the analysis of branching strategies in the so-called 'AT-less' NRPS/PKS hybrid systems. The future of MS analysis of NRPS and PKS biosynthetic pathways lies in adoption and development of methods that continue bridging enzymology with proteomics as both fields continue their post-genomic acceleration.
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Affiliation(s)
- Stefanie B Bumpus
- Department of Chemistry & The Institute for Genomic Biology, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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Stack D, Neville C, Doyle S. Nonribosomal peptide synthesis in Aspergillus fumigatus and other fungi. MICROBIOLOGY-SGM 2007; 153:1297-1306. [PMID: 17464044 DOI: 10.1099/mic.0.2006/006908-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In fungi, nonribosomal peptide synthetases (NRP synthetases) are large multi-functional enzymes containing adenylation, thiolation (or peptidyl carrier protein, PCP) and condensation domains. These enzymes are often encoded within gene clusters. Multiple NRP synthetase ORFs have also been identified in fungi (14 in Aspergillus fumigatus). LeaA, a methyltransferase, is involved in secondary metabolite gene cluster regulation in Aspergillus spp. The NRP synthetases GliP and FtmA respectively direct the biosynthesis of the toxic metabolites gliotoxin and brevianamide F, a precursor of bioactive prenylated alkaloids. The NRP synthetase Pes1 has been shown to mediate resistance to oxidative stress, and in plant-pathogenic ascomycetes (e.g. Cochliobolus heterostrophus) an NRP synthetase, encoded by the NPS6 gene, significantly contributes to virulence and resistance to oxidative stress. Adenylation (A) domains within NRP synthetases govern the specificity of amino acid incorporation into nonribosomally synthesized peptides. To date there have only been limited demonstrations of A domain specificity (e.g. A. fumigatus GliP and in Beauveria bassiana) in fungi. Indeed, only in silico prediction data are available on A domain specificity of NRP synthetases from most fungi. NRP synthetases are activated by 4'-phosphopantetheinylation of serine residues within PCP domains by 4'-phosphopantetheinyl transferases (4'-PPTases). Coenzyme A acts as the 4'-phosphopantetheine donor, and labelled coenzyme A can be used to affinity-label apo-NRP synthetases. Emerging fungal gene disruption and gene cluster expression strategies, allied to proteomic strategies, are poised to facilitate a greater understanding of the coding potential of NRP synthetases in fungi.
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Affiliation(s)
- Deirdre Stack
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Claire Neville
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Sean Doyle
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland
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11
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Shipovskov S, Reimann CT. Electrospray ionization mass spectrometry in enzymology: uncovering the mechanisms of two-substrate reactions. Analyst 2007; 132:397-402. [PMID: 17471382 DOI: 10.1039/b615394c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to draw attention to the use of electrospray ionization mass spectrometry (ESI-MS) for monitoring the course of enzyme-substrate interactions, in the particular case of complex systems in which two substrates participate. The determination and characterization of intra-molecular reactions, especially those that occur in the enzyme active site, is not a trivial task in chemical kinetics, typically requiring long measurement times and relatively expensive techniques such as nuclear magnetic resonance (NMR), X-ray crystallography or electron microscopy (EM). However, nowadays almost all laboratories are equipped with or else have access to the ESI-MS technique. The aim of this review is to focus on the possibilities of employing even quite simple MS equipment to tackle different applications in studies of complex enzymatic systems.
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Affiliation(s)
- Stepan Shipovskov
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UKM1 7DN.
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12
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Koeniger SL, Merenbloom SI, Sevugarajan S, Clemmer DE. Transfer of structural elements from compact to extended states in unsolvated ubiquitin. J Am Chem Soc 2006; 128:11713-9. [PMID: 16939296 PMCID: PMC2507767 DOI: 10.1021/ja062137g] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multidimensional ion mobility spectrometry techniques (IMS-IMS and IMS-IMS-IMS) combined with mass spectrometry are used to study structural transitions of ubiquitin ions in the gas phase. It is possible to select and activate narrow distributions of compact and partially folded conformation types and examine new distributions of structures that are formed. Different compact conformations unfold, producing a range of new partially folded states and three resolvable peaks associated with elongated conformers. Under gentle activation conditions, the final populations of the three elongated forms depend on the initial structures of the selected ions. This requires that some memory of the compact state (most likely secondary structure) is preserved along the unfolding pathway. Activation of selected, partially folded intermediates (formed from specific compact states) leads to elongated state populations that are consistent with the initial selected compact form-evidence that intermediates not only retain elements of initial structure but also are capable of transmitting structure to final states.
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Affiliation(s)
- Stormy L Koeniger
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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13
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Hassa PO, Haenni SS, Elser M, Hottiger MO. Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev 2006; 70:789-829. [PMID: 16959969 PMCID: PMC1594587 DOI: 10.1128/mmbr.00040-05] [Citation(s) in RCA: 508] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Since poly-ADP ribose was discovered over 40 years ago, there has been significant progress in research into the biology of mono- and poly-ADP-ribosylation reactions. During the last decade, it became clear that ADP-ribosylation reactions play important roles in a wide range of physiological and pathophysiological processes, including inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis. ADP-ribosylation reactions are phylogenetically ancient and can be classified into four major groups: mono-ADP-ribosylation, poly-ADP-ribosylation, ADP-ribose cyclization, and formation of O-acetyl-ADP-ribose. In the human genome, more than 30 different genes coding for enzymes associated with distinct ADP-ribosylation activities have been identified. This review highlights the recent advances in the rapidly growing field of nuclear mono-ADP-ribosylation and poly-ADP-ribosylation reactions and the distinct ADP-ribosylating enzyme families involved in these processes, including the proposed family of novel poly-ADP-ribose polymerase-like mono-ADP-ribose transferases and the potential mono-ADP-ribosylation activities of the sirtuin family of NAD(+)-dependent histone deacetylases. A special focus is placed on the known roles of distinct mono- and poly-ADP-ribosylation reactions in physiological processes, such as mitosis, cellular differentiation and proliferation, telomere dynamics, and aging, as well as "programmed necrosis" (i.e., high-mobility-group protein B1 release) and apoptosis (i.e., apoptosis-inducing factor shuttling). The proposed molecular mechanisms involved in these processes, such as signaling, chromatin modification (i.e., "histone code"), and remodeling of chromatin structure (i.e., DNA damage response, transcriptional regulation, and insulator function), are described. A potential cross talk between nuclear ADP-ribosylation processes and other NAD(+)-dependent pathways is discussed.
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Affiliation(s)
- Paul O Hassa
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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14
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Fischbach MA, Walsh CT. Assembly-Line Enzymology for Polyketide and Nonribosomal Peptide Antibiotics: Logic, Machinery, and Mechanisms. Chem Rev 2006; 106:3468-96. [PMID: 16895337 DOI: 10.1021/cr0503097] [Citation(s) in RCA: 1066] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael A Fischbach
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Hicks LM, Mazur MT, Miller LM, Dorrestein PC, Schnarr NA, Khosla C, Kelleher NL. Investigating Nonribosomal Peptide and Polyketide Biosynthesis by Direct Detection of Intermediates on >70 kDa Polypeptides by Using Fourier-Transform Mass Spectrometry. Chembiochem 2006; 7:904-7. [PMID: 16642537 DOI: 10.1002/cbic.200500416] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Leslie M Hicks
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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16
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Hicks LM, Moffitt MC, Beer LL, Moore BS, Kelleher NL. Structural characterization of in vitro and in vivo intermediates on the loading module of microcystin synthetase. ACS Chem Biol 2006; 1:93-102. [PMID: 17163649 DOI: 10.1021/cb500007v] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microcystin family of toxins is the most common cause of hepatotoxicity associated with water blooms of cyanobacterial genera. The biosynthetic assembly line producing the toxic cyclic peptide, microcystin, contains an adenylation-peptidyl carrier protein didomain (A-PCP) at the N-terminus of the initiator module McyG (295 kDa) that has been postulated to activate and load the starter unit phenylacetate for formation of the unusual aromatic beta-amino acid residue, Adda, before subsequent extension. Characterization of the McyG A-PCP didomain (78 kDa) using ATP-PP i exchange assays and mass spectrometry revealed that assorted phenylpropanoids are preferentially activated and loaded onto the PCP carrier domain rather than phenylacetate itself. For the first time, thioesters formed in vivo were detected directly using large molecule mass spectrometry. Additionally substrates were cleaved using a type II thioesterase for structural elucidation by small molecule mass spectrometry. Unprecedented features of the McyG A-PCP didomain include the in vivo acylation of the holo PCP with exogenous and endogenous substrates, along with the ability of the apo protein to retain the acyl-AMP intermediate during affinity purification. These results imply that phenylpropanoids are preferentially loaded onto the McyG PCP; however one carbon must be excised following extension of the starter unit with malonyl-CoA in order to generate the expected polyketide chain which leads us to ponder the novel biochemistry by which this occurs.
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Affiliation(s)
- Leslie M Hicks
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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