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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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2
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Manska S, Octaviano R, Rossetto CC. 5-Ethynyl-2'-deoxycytidine and 5-ethynyl-2'-deoxyuridine are differentially incorporated in cells infected with HSV-1, HCMV, and KSHV viruses. J Biol Chem 2020; 295:5871-5890. [PMID: 32205447 PMCID: PMC7196651 DOI: 10.1074/jbc.ra119.012378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/18/2020] [Indexed: 11/06/2022] Open
Abstract
Nucleoside analogues are a valuable experimental tool. Incorporation of these molecules into newly synthesized DNA (i.e. pulse-labeling) is used to monitor cell proliferation or to isolate nascent DNA. Some of the most common nucleoside analogues used for pulse-labeling of DNA in cells are the deoxypyrimidine analogues 5-ethynyl-2'-deoxyuridine (EdU) and 5-ethynyl-2'-deoxycytidine (EdC). Click chemistry enables conjugation of an azide molecule tagged with a fluorescent dye or biotin to the alkyne of the analog, which can then be used to detect incorporation of EdU and EdC into DNA. The use of EdC is often recommended because of the potential cytotoxicity associated with EdU during longer incubations. Here, by comparing the relative incorporation efficiencies of EdU and EdC during short 30-min pulses, we demonstrate significantly lower incorporation of EdC than of EdU in noninfected human fibroblast cells or in cells infected with either human cytomegalovirus or Kaposi's sarcoma-associated herpesvirus. Interestingly, cells infected with herpes simplex virus type-1 (HSV-1) incorporated EdC and EdU at similar levels during short pulses. Of note, exogenous expression of HSV-1 thymidine kinase increased the incorporation efficiency of EdC. These results highlight the limitations when using substituted pyrimidine analogues in pulse-labeling and suggest that EdU is the preferable nucleoside analogue for short pulse-labeling experiments, resulting in increased recovery and sensitivity for downstream applications. This is an important discovery that may help to better characterize the biochemical properties of different nucleoside analogues with a given kinase, ultimately leading to significant differences in labeling efficiency of nascent DNA.
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Affiliation(s)
- Salomé Manska
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557
| | - Rionna Octaviano
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557
| | - Cyprian C Rossetto
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557.
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3
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Glowacki RWP, Pudlo NA, Tuncil Y, Luis AS, Sajjakulnukit P, Terekhov AI, Lyssiotis CA, Hamaker BR, Martens EC. A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner. Cell Host Microbe 2019; 27:79-92.e9. [PMID: 31901520 DOI: 10.1016/j.chom.2019.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/03/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Efficient nutrient acquisition in the human gut is essential for microbial persistence. Although polysaccharides have been well-studied nutrients for the gut microbiome, other resources such as nucleic acids and nucleosides are less studied. We describe several ribose-utilization systems (RUSs) that are broadly represented in Bacteroidetes and appear to have diversified to access ribose from a variety of substrates. One Bacteroides thetaiotaomicron RUS variant is critical for competitive gut colonization in a diet-specific fashion. We used molecular genetics to probe the required functions of the system and the nature of the nutrient source(s) underlying this phenotype. Two RUS-encoded ribokinases were the only components required for this effect, presumably because they generate ribose-phosphate derivatives from products of an unlinked but essential nucleoside phosphorylase. Our results underscore the extensive mechanisms that gut symbionts have evolved to access nutrients and the potential for unexpected dependencies among systems that mediate colonization and persistence.
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Affiliation(s)
- Robert W P Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yunus Tuncil
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
| | - Ana S Luis
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Sajjakulnukit
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anton I Terekhov
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Bruce R Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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4
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Mueller P, Gauttam R, Raab N, Handrick R, Wahl C, Leptihn S, Zorn M, Kussmaul M, Scheffold M, Eikmanns B, Elling L, Gaisser S. High level in vivo mucin-type glycosylation in Escherichia coli. Microb Cell Fact 2018; 17:168. [PMID: 30367634 PMCID: PMC6202839 DOI: 10.1186/s12934-018-1013-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/19/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Increasing efforts have been made to assess the potential of Escherichia coli strains for the production of complex recombinant proteins. Since a considerable part of therapeutic proteins are glycoproteins, the lack of the post-translational attachment of sugar moieties in standard E. coli expression strains represents a major caveat, thus limiting the use of E. coli based cell factories. The establishment of an E. coli expression system capable of protein glycosylation could potentially facilitate the production of therapeutics with a putative concomitant reduction of production costs. RESULTS The previously established E. coli strain expressing the soluble form of the functional human-derived glycosyltransferase polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2) was further modified by co-expressing the UDP-GlcNAc 4-epimerase WbgU derived from Plesiomonas shigelloides. This enables the conversion of uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) to the sugar donor uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) in the bacterial cytoplasm. Initially, the codon-optimised gene wbgU was inserted into a pET-derived vector and a Tobacco Etch Virus (TEV) protease cleavable polyhistidine-tag was translationally fused to the C- terminus of the amino acid sequence. The 4-epimerase was subsequently expressed and purified. Following the removal of the polyhistidine-tag, WbgU was analysed by circular dichroism spectroscopy to determine folding state and thermal transitions of the protein. The in vitro activity of WbgU was validated by employing a modified glycosyltransferase assay. The conversion of UDP-GlcNAc to UDP-GalNAc was shown by capillary electrophoresis analysis. Using a previously established chaperone pre-/co- expression platform, the in vivo activity of both glycosyltransferase GalNAc-T2 and 4-epimerase WbgU was assessed in E. coli, in combination with a mucin 10-derived target protein. Monitoring glycosylation by liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS), the results clearly indicated the in vivo glycosylation of the mucin-derived acceptor peptide. CONCLUSION In the present work, the previously established E. coli- based expression system was further optimized and the potential for in vivo O-glycosylation was shown by demonstrating the transfer of sugar moieties to a mucin-derived acceptor protein. The results offer the possibility to assess the practical use of the described expression platform for in vivo glycosylations of important biopharmaceutical compounds in E. coli.
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Affiliation(s)
- Phillipp Mueller
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Rahul Gauttam
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Nadja Raab
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - René Handrick
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Claudia Wahl
- Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Sebastian Leptihn
- Zhejiang University-Edinburgh University Institute, School of Medicine, Zhejiang University, Zhejiang, China
| | - Michael Zorn
- Boehringer Ingelheim Pharma GmbH and Co.KG, Analytical Development Biologics, Biberach, Germany
| | - Michaela Kussmaul
- Boehringer Ingelheim Pharma GmbH and Co.KG, Analytical Development Biologics, Biberach, Germany
| | - Marianne Scheffold
- Boehringer Ingelheim Pharma GmbH and Co.KG, Analytical Development Biologics, Biberach, Germany
| | - Bernhard Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Lothar Elling
- Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Sabine Gaisser
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
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Härmä H, Tong-Ochoa N, van Adrichem AJ, Jelesarov I, Wennerberg K, Kopra K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb) 2018; 54:2910-2913. [PMID: 29498735 DOI: 10.1039/c7cc09575a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Post-translational modification (PTM) of proteins plays essential regulatory roles in a variety of pathological conditions. Reliable and practical assays are required to accelerate the discovery of inhibitors and activators for PTM related diseases. Today, methodologies are based on specific or group-specific PTM recognition of e.g. phosphate for kinase activity without extending to other type of PTMs. Here we have established a universal time-resolved luminescence assay on a peptide-break platform for the direct detection of wide variety of PTMs. The developed assay is based on the leucine zipper concept wherein a europium-chelate labeled detection peptide and a non-labeled peptide substrate form a highly luminescent dimer. As an active PTM enzyme at sub or low nanomolar concentration modifies the substrate peptide, the luminescent signal of the detached detection peptide is quenched in the presence of soluble quenchers. The functionality of this universal assay technique has been demonstrated for the monitoring of phosphorylation, dephosphorylation, deacetylation, and citrullination with high applicability also to other PTMs in a high throughput format.
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Affiliation(s)
- Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Turku, Finland.
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Irague R, Topham CM, Martineau N, Baylac A, Auriol C, Walther T, François JM, André I, Remaud-Siméon M. A generic HTS assay for kinase screening: Validation for the isolation of an engineered malate kinase. PLoS One 2018; 13:e0193036. [PMID: 29462203 PMCID: PMC5819781 DOI: 10.1371/journal.pone.0193036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/03/2018] [Indexed: 01/17/2023] Open
Abstract
An end-point ADP/NAD+ acid/alkali assay procedure, directly applicable to library screening of any type of ATP-utilising/ADP producing enzyme activity, was implemented. Typically, ADP production is coupled to NAD+ co-enzyme formation by the conventional addition of pyruvate kinase and lactate dehydrogenase. Transformation of enzymatically generated NAD+ into a photometrically active alkali derivative product is then achieved through the successive application of acidic/alkali treatment steps. The assay was successfully miniaturized to search for malate kinase activity in a structurally-guided library of LysC aspartate kinase variants comprising 6,700 clones. The screening procedure enabled the isolation of nine positive variants showing novel kinase activity on (L)-malate, the best mutant, LysC V115A:E119S:E434V exhibited strong substrate selectivity for (L)-malate compared to (L)-aspartate with a (kcat/Km)malate/(kcat/Km)aspartate ratio of 86. Double mutants V115A:E119S, V115A:E119C and E119S:E434V were constructed to further probe the origins of stabilising substrate binding energy gains for (L)-malate due to mutation. The introduction of less sterically hindering side-chains in engineered enzymes carrying E119S and V115A mutations increases the effective volume available for substrate binding in the catalytic pocket. Improved binding of the (L)-malate substrate may be assisted by less hindered movement of the Phe184 aromatic side-chain. Additional favourable long-range electostatic effects on binding arising from the E434V surface mutation are conditionally dependent upon the presence of the V115A mutation close to Phe184 in the active-site.
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Affiliation(s)
- Romain Irague
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Christopher M. Topham
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Nelly Martineau
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Audrey Baylac
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Clément Auriol
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Thomas Walther
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Jean-Marie François
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
| | - Magali Remaud-Siméon
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Toulouse White Biotechnology, Parc technologique du canal, Bâtiment NAPA CENTER B, Toulouse, France
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7
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Dutta D, Das R, Mandal C, Mandal C. Structure-Based Kinase Profiling To Understand the Polypharmacological Behavior of Therapeutic Molecules. J Chem Inf Model 2017; 58:68-89. [PMID: 29243930 DOI: 10.1021/acs.jcim.7b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Several drugs elicit their therapeutic efficacy by modulating multiple cellular targets and possess varied polypharmacological actions. The identification of the molecular targets of a potent bioactive molecule is essential in determining its overall polypharmacological profile. Experimental procedures are expensive and time-consuming. Therefore, computational approaches are actively implemented in rational drug discovery. Here, we demonstrate a computational pipeline, based on reverse virtual screening technique using several consensus scoring strategies, and perform structure-based kinase profiling of 12 FDA-approved drugs. This target prediction showed an overall good performance, with an average AU-ROC greater than 0.85 for most drugs, and identified the true targets even at the top 2% cutoff. In contrast, 10 non-kinase binder drugs exhibited lower binding efficiency and appeared in the bottom of ranking list. Subsequently, we validated this pipeline on a potent therapeutic molecule, mahanine, whose polypharmacological profile related to targeting kinases is unknown. Our target-prediction method identified different kinases. Furthermore, we have experimentally validated that mahanine is able to modulate multiple kinases that are involved in cross-talk with different signaling molecules, which thereby exhibits its polypharmacological action. More importantly, in vitro kinase assay exhibited the inhibitory effect of mahanine on two such predicted kinases' (mTOR and VEGFR2) activity, with IC50 values being ∼12 and ∼22 μM, respectively. Next, we generated a comprehensive drug-protein interaction fingerprint that explained the basis of their target selectivity. We observed that it is controlled by variations in kinase conformations followed by significant differences in crucial hydrogen-bond and van der Waals interactions. Such structure-based kinase profiling could provide useful information in revealing the unknown targets of therapeutic molecules from their polypharmacological behavior and would assist in drug discovery.
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Affiliation(s)
- Devawati Dutta
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , Kolkata 700032, India
| | - Ranjita Das
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , Kolkata 700032, India
| | - Chhabinath Mandal
- National Institute of Pharmaceutical Education and Research , Kolkata 700032, India
| | - Chitra Mandal
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , Kolkata 700032, India
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8
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Chen ESW, Weng JH, Chen YH, Wang SC, Liu XX, Huang WC, Matsui T, Kawano Y, Liao JH, Lim LH, Bessho Y, Huang KF, Wu WJ, Tsai MD. Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation. Biochemistry 2017; 56:5112-5124. [PMID: 28858528 DOI: 10.1021/acs.biochem.7b00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The vast majority of in vitro structural and functional studies of the activation mechanism of protein kinases use the kinase domain alone. Well-demonstrated effects of regulatory domains or allosteric factors are scarce for serine/threonine kinases. Here we use a site-specifically phosphorylated SCD1-FHA1-kinase three-domain construct of the serine/threonine kinase Rad53 to show the effect of phospho-priming, an in vivo regulatory mechanism, on the autophosphorylation intermediate and specificity. Unphosphorylated Rad53 is a flexible monomer in solution but is captured in an asymmetric enzyme:substrate complex in crystal with the two FHA domains separated from each other. Phospho-priming induces formation of a stable dimer via intermolecular pT-FHA binding in solution. Importantly, autophosphorylation of unprimed and phospho-primed Rad53 produced predominantly inactive pS350-Rad53 and active pT354-Rad53, respectively. The latter mechanism was also demonstrated in vivo. Our results show that, while Rad53 can display active conformations under various conditions, simulation of in vivo regulatory conditions confers functionally relevant autophosphorylation.
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Affiliation(s)
- Eric Sheng-Wen Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
| | - Yu-Hou Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Xiao-Xia Liu
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Liang-Hin Lim
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
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9
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Hughes CS, Longo E, Phillips-Jones MK, Hussain R. Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci. Biochim Biophys Acta Gen Subj 2017; 1861:1951-1959. [PMID: 28511809 PMCID: PMC5482315 DOI: 10.1016/j.bbagen.2017.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 02/04/2023]
Abstract
A-type resistance towards "last-line" glycopeptide antibiotic vancomycin in the leading hospital acquired infectious agent, the enterococci, is the most common in the UK. Resistance is regulated by the VanRASA two-component system, comprising the histidine sensor kinase VanSA and the partner response regulator VanRA. The nature of the activating ligand for VanSA has not been identified, therefore this work sought to identify and characterise ligand(s) for VanSA. In vitro approaches were used to screen the structural and activity effects of a range of potential ligands with purified VanSA protein. Of the screened ligands (glycopeptide antibiotics vancomycin and teicoplanin, and peptidoglycan components N-acetylmuramic acid, D-Ala-D-Ala and Ala-D-y-Glu-Lys-D-Ala-D-Ala) only glycopeptide antibiotics vancomycin and teicoplanin were found to bind VanSA with different affinities (vancomycin 70μM; teicoplanin 30 and 170μM), and were proposed to bind via exposed aromatic residues tryptophan and tyrosine. Furthermore, binding of the antibiotics induced quicker, longer-lived phosphorylation states for VanSA, proposing them as activators of type A vancomycin resistance in the enterococci.
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Affiliation(s)
- C S Hughes
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom; Membranes, Membrane Proteins & Peptides Research Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - E Longo
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom
| | - M K Phillips-Jones
- Membranes, Membrane Proteins & Peptides Research Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom.
| | - R Hussain
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom.
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10
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ATPase activity measurement of DNA replicative helicase from Bacillus stearothermophilus by malachite green method. Anal Biochem 2016; 509:46-49. [PMID: 27372608 DOI: 10.1016/j.ab.2016.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 11/24/2022]
Abstract
The DnaB helicase from Bacillus stearothermophilus (DnaBBst) was a model protein for studying the bacterial DNA replication. In this work, a non-radioactive method for measuring ATPase activity of DnaBBst helicase was described. The working parameters and conditions were optimized. Furthermore, this method was applied to investigate effects of DnaG primase, ssDNA and helicase loader protein (DnaI) on ATPase activity of DnaBBst. Our results showed this method was sensitive and efficient. Moreover, it is suitable for the investigation of functional interaction between DnaB and related factors.
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11
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Leishmania donovani Aurora kinase: A promising therapeutic target against visceral leishmaniasis. Biochim Biophys Acta Gen Subj 2016; 1860:1973-88. [PMID: 27288586 DOI: 10.1016/j.bbagen.2016.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Aurora kinases are key mitotic kinases executing multiple aspects of eukaryotic cell-division. The apicomplexan homologs being essential for survival, suggest that the Leishmania homolog, annotated LdAIRK, may be equally important. METHODS Bioinformatics, stage-specific immunofluorescence microscopy, immunoblotting, RT-PCR, molecular docking, in-vitro kinase assay, anti-leishmanial activity assays, flow cytometry, fluorescence microscopy. RESULTS Ldairk expression is seen to vary as the cell-cycle progresses from G1 through S and finally G2M and cytokinesis. Kinetic studies demonstrate their enzymatic activity exhibiting a Km and Vmax of 6.12μM and 82.9pmoles·min(-1)mg(-1) respectively against ATP using recombinant Leishmania donovani H3, its physiological substrate. Due to the failure of LdAIRK-/+ knock-out parasites to survive, we adopted a chemical knock-down approach. Based on the conservation of key active site residues, three mammalian Aurora kinase inhibitors were investigated to evaluate their potential as inhibitors of LdAIRK activity. Interestingly, the cell-cycle progressed unhindered, despite treatment with GSK-1070916 or Barasertib, inhibitors with greater potencies for the ATP-binding pocket compared to Hesperadin, which at nanomolar concentrations, severely compromised viability at IC50s 105.9 and 36.4nM for promastigotes and amastigotes, respectively. Cell-cycle and morphological studies implicated their role in both mitosis and cytokinesis. CONCLUSION We identified an Aurora kinase homolog in L. donovani implicated in cell-cycle progression, whose inhibition led to aberrant changes in cell-cycle progression and reduced viability. GENERAL SIGNIFICANCE Human homologs being actively pursued drug targets and the observations with LdAIRK in both promastigotes and amastigotes suggest their potential as therapeutic-targets. Importantly, our results encourage the exploration of other proteins identified herein as potential novel drug targets.
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Roy J, Pondenis H, Fan TM, Das A. Direct Capture of Functional Proteins from Mammalian Plasma Membranes into Nanodiscs. Biochemistry 2015; 54:6299-302. [PMID: 26415091 DOI: 10.1021/acs.biochem.5b00954] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian plasma membrane proteins make up the largest class of drug targets yet are difficult to study in a cell free system because of their intransigent nature. Herein, we perform direct encapsulation of plasma membrane proteins derived from mammalian cells into a functional nanodisc library. Peptide fingerprinting was used to analyze the proteome of the incorporated proteins in nanodiscs and to further demonstrate that the lipid composition of the nanodiscs directly affects the class of protein that is incorporated. Furthermore, the functionality of the incorporated membrane proteome was evaluated by measuring the activity of membrane proteins: Na(+)/K(+)-ATPase and receptor tyrosine kinases. This work is the first report of the successful establishment and characterization of a cell free functional library of mammalian membrane proteins into nanodiscs.
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Affiliation(s)
- Jahnabi Roy
- Department of Comparative Biosciences, ‡Department of Veterinary Clinical Medicine, §Department of Chemistry, and ∥Department of Biochemistry, Department of Bioengineering, and Beckman Institute for Advanced Science and Department of Bioengineering, University of Illinois Urbana-Champaign , Urbana, Illinois 61802, United States
| | - Holly Pondenis
- Department of Comparative Biosciences, ‡Department of Veterinary Clinical Medicine, §Department of Chemistry, and ∥Department of Biochemistry, Department of Bioengineering, and Beckman Institute for Advanced Science and Department of Bioengineering, University of Illinois Urbana-Champaign , Urbana, Illinois 61802, United States
| | - Timothy M Fan
- Department of Comparative Biosciences, ‡Department of Veterinary Clinical Medicine, §Department of Chemistry, and ∥Department of Biochemistry, Department of Bioengineering, and Beckman Institute for Advanced Science and Department of Bioengineering, University of Illinois Urbana-Champaign , Urbana, Illinois 61802, United States
| | - Aditi Das
- Department of Comparative Biosciences, ‡Department of Veterinary Clinical Medicine, §Department of Chemistry, and ∥Department of Biochemistry, Department of Bioengineering, and Beckman Institute for Advanced Science and Department of Bioengineering, University of Illinois Urbana-Champaign , Urbana, Illinois 61802, United States
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Structural insights into mis-regulation of protein kinase A in human tumors. Proc Natl Acad Sci U S A 2015; 112:1374-9. [PMID: 25605907 DOI: 10.1073/pnas.1424206112] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The extensively studied cAMP-dependent protein kinase A (PKA) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of PKA signaling is implicated in tumorigenesis. Recent genomic studies have identified recurrent mutations in the catalytic subunit of PKA in tumors associated with Cushing's syndrome, a kidney disorder leading to excessive cortisol production, and also in tumors associated with fibrolamellar hepatocellular carcinoma (FL-HCC), a rare liver cancer. Expression of a L205R point mutant and a DnaJ-PKA fusion protein were found to be linked to Cushing's syndrome and FL-HCC, respectively. Here we reveal contrasting mechanisms for increased PKA signaling at the molecular level through structural determination and biochemical characterization of the aberrant enzymes. In the Cushing's syndrome disorder, we find that the L205R mutation abolishes regulatory-subunit binding, leading to constitutive, cAMP-independent signaling. In FL-HCC, the DnaJ-PKA chimera remains under regulatory subunit control; however, its overexpression from the DnaJ promoter leads to enhanced cAMP-dependent signaling. Our findings provide a structural understanding of the two distinct disease mechanisms and they offer a basis for designing effective drugs for their treatment.
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Lauber J, Handrick R, Leptihn S, Dürre P, Gaisser S. Expression of the functional recombinant human glycosyltransferase GalNAcT2 in Escherichia coli. Microb Cell Fact 2015; 14:3. [PMID: 25582753 PMCID: PMC4299809 DOI: 10.1186/s12934-014-0186-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recombinant protein-based therapeutics have become indispensable for the treatment of many diseases. They are produced using well-established expression systems based on bacteria, yeast, insect and mammalian cells. The majority of therapeutic proteins are glycoproteins and therefore the post-translational attachment of sugar residues is required. The development of an engineered Escherichia coli-based expression system for production of human glycoproteins could potentially lead to increased yields, as well as significant decreases in processing time and costs. RESULTS This work describes the expression of functional human-derived glycosyltransferase UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAcT2) in a recombinant E. coli strain. For expression, a codon-optimised gene encoding amino acids 52-571 of GalNAcT2 lacking the transmembrane N-terminal domain was inserted into a pET-23 derived vector encoding a polyhistidine-tag which was translationally fused to the N-terminus of the glycosyltransferase (HisDapGalNAcT2). The glycosyltransferase was produced in E. coli using a recently published expression system. Soluble HisDapGalNAcT2 produced in SHuffle® T7 host cells was purified using nickel affinity chromatography and was subsequently analysed by size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS) and circular dichroism spectroscopy to determine molecular mass, folding state and thermal transitions of the protein. The activity of purified HisDapGalNAcT2 was monitored using a colorimetric assay based on the release of phosphate during transfer of glycosyl residues to a model acceptor peptide or, alternatively, to the granulocyte-colony stimulating growth factor (G-CSF). Modifications were assessed by Matrix Assisted Laser Desorption Ionization Time-of-flight Mass Spectrometry analysis (MALDI-TOF-MS) and Electrospray Mass Spectrometry analysis (ESI-MS). The results clearly indicate the glycosylation of the acceptor peptide and of G-CSF. CONCLUSION In the present work, we isolated a human-derived glycosyltransferase by expressing soluble HisDapGalNAcT2 in E. coli. The functional activity of the enzyme was shown in vitro. Further investigations are needed to assess the potential of in vivo glycosylation in E. coli.
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Affiliation(s)
- Jennifer Lauber
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany.
| | - René Handrick
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany.
| | - Sebastian Leptihn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany.
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
| | - Sabine Gaisser
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany.
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Guo B, Gurel PS, Shu R, Higgs HN, Pellegrini M, Mierke DF. Monitoring ATP hydrolysis and ATPase inhibitor screening using (1)H NMR. Chem Commun (Camb) 2014; 50:12037-9. [PMID: 25170530 PMCID: PMC4262093 DOI: 10.1039/c4cc04399e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a versatile method to characterize ATPase and kinase activities and discover new inhibitors of these proteins. The proton NMR-based assay directly monitors ATP turnover and is easy to implement, requires no additional reagents and can potentially be applied to GTP. We validated the method's accuracy, applied it to the monitoring of ATP turnover by actin and to the screening of ATPase inhibitors, and showed that it is also applicable for the monitoring of GTP hydrolysis.
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Affiliation(s)
- Bingqian Guo
- Department of Chemistry, Dartmouth College, Hanover 03755, USA
| | - Pinar S. Gurel
- Department of Biochemistry, Geisel School of Medicine, Dartmouth College, Hanover 03755, USA
| | - Rui Shu
- Department of Biochemistry, Geisel School of Medicine, Dartmouth College, Hanover 03755, USA
| | - Henry N. Higgs
- Department of Biochemistry, Geisel School of Medicine, Dartmouth College, Hanover 03755, USA
| | | | - Dale F. Mierke
- Department of Chemistry, Dartmouth College, Hanover 03755, USA
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Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases. MethodsX 2014; 1:187-96. [PMID: 26150952 PMCID: PMC4472957 DOI: 10.1016/j.mex.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/15/2014] [Indexed: 11/21/2022] Open
Abstract
Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.
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Kumar PS, Kumar YN, Prasad UV, Yeswanth S, Swarupa V, Vasu D, Venkatesh K, Srikanth L, Rao VK, Sarma PVGK. Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases. Indian J Pharm Sci 2014; 76:430-6. [PMID: 25425757 PMCID: PMC4243260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/16/2022] Open
Abstract
Glucokinase is classified in bacteria based upon having ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif, the sequence of glucokinase gene (JN645812) of Staphylococcus aureus ATCC12600 showed presence of ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif. We have earlier observed glucokinase of S. aureus has higher affinity towards the substrate compared to other bacterial glucokinase and under anaerobic condition with increased glucose concentration S. aureus exhibited higher rate of biofilm formation. To establish this, 3D structure of glucokinase was built using homology modeling method, the PROCHECK and ProSA-Web analysis indicated this built glucokinase structure was close to the crystal structure. This structure was superimposed with different bacterial glucokinase structures and from the root-mean-square deviation values, it is concluded that S. aureus glucokinase exhibited very close homology with Enterococcus faecalis and Clostridium difficle while with other bacteria it showed high degree of variations both in domain and nondomain regions. Glucose docking results indicated -12.3697 kcal/mol for S. aureus glucokinase compared with other bacterial glucokinase suggesting higher affinity of glucose which correlates with enzyme kinetics and higher rate of biofilm formation.
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Affiliation(s)
- P. S. Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - Y. N. Kumar
- Department of Zoology, Sri Venkateswara University, Tirupati-517 502, India
| | - U. V. Prasad
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - S. Yeswanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - V. Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - D. Vasu
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - K. Venkatesh
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - L. Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
| | - V. K. Rao
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS 66047, USA
| | - P. V. G. K. Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati-517 507, India
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Auger C, Appanna V, Castonguay Z, Han S, Appanna VD. A facile electrophoretic technique to monitor phosphoenolpyruvate-dependent kinases. Electrophoresis 2012; 33:1095-101. [PMID: 22539312 DOI: 10.1002/elps.201100517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoenolpyruvate (PEP)-dependent kinases are central to numerous metabolic processes and mediate the production of adenosine triphosphate (ATP) by substrate-level phosphorylation (SLP). While pyruvate kinase (PK, EC: 2.7.1.40), the final enzyme of the glycolytic pathway is critical in the anaerobic synthesis of ATP from ADP, pyruvate phosphate dikinase (PPDK, EC: 2.7.9.1), and phosphoenolpyruvate synthase (PEPS, EC: 2.7.9.2) help generate ATP from AMP coupled to PEP as a substrate. Here we demonstrate an inexpensive and effective electrophoretic technology to determine the activities of these enzymes by blue-native polyacrylamide gel electrophoresis (BN-PAGE). The generation of pyruvate is linked to exogenous lactate dehydrogenase (LDH), and the oxidation of reduced nicotinamide adenine dinucleotide (NADH) coupled to 2,6-dichloroindophenol (DCIP) and iodonitrotetrazolium chloride (INT) results in a formazan precipitate which is easily quantifiable. The selectivity of the enzymes is ensured by including either AMP or ADP and pyrophosphate (PP(i) ) or inorganic phosphate (P(i) ). Activity bands were readily obtained after incubation in the respective reaction mixtures for 20-30 min. Cell-free extract concentrations as low as 20 μg protein equivalent yielded activity bands and substrate levels were manipulated to optimize sensitivity of this analytical technique. High-pressure liquid chromatography (HPLC), two-dimensional (2-D) SDS-PAGE (where SDS is sodium dodecyl sulfate), and immunoblot studies of the excised activity band help further characterize these PEP-dependent kinases. Furthermore, these enzymes were readily identified on the same gel by incubating it sequentially in the respective reaction mixtures. This technique provides a facile method to elucidate these kinases in biological systems.
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Affiliation(s)
- Christopher Auger
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
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Golgi-resident PAP-specific 3′-phosphatase-coupled sulfotransferase assays. Anal Biochem 2012; 423:86-92. [DOI: 10.1016/j.ab.2012.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 11/23/2022]
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