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Barneda D, Janardan V, Niewczas I, Collins DM, Cosulich S, Clark J, Stephens LR, Hawkins PT. Acyl chain selection couples the consumption and synthesis of phosphoinositides. EMBO J 2022; 41:e110038. [PMID: 35771169 PMCID: PMC9475507 DOI: 10.15252/embj.2021110038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Phosphoinositides (PIPn) in mammalian tissues are enriched in the stearoyl/arachidonoyl acyl chain species ("C38:4"), but its functional significance is unclear. We have used metabolic tracers (isotopologues of inositol, glucose and water) to study PIPn synthesis in cell lines in which this enrichment is preserved to differing relative extents. We show that PIs synthesised from glucose are initially enriched in shorter/more saturated acyl chains, but then rapidly remodelled towards the C38:4 species. PIs are also synthesised by a distinct 're-cycling pathway', which utilises existing precursors and exhibits substantial selectivity for the synthesis of C38:4-PA and -PI. This re-cycling pathway is rapidly stimulated during receptor activation of phospholipase-C, both allowing the retention of the C38:4 backbone and the close coupling of PIPn consumption to its resynthesis, thus maintaining pool sizes. These results suggest that one property of the specific acyl chain composition of PIPn is that of a molecular code, to facilitate 'metabolic channelling' from PIP2 to PI via pools of intermediates (DG, PA and CDP-DG) common to other lipid metabolic pathways.
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Affiliation(s)
- David Barneda
- Signalling Programme, Babraham Institute, Cambridge, UK.,Projects, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Vishnu Janardan
- Cellular Organization and Signalling, National Centre for Biological Sciences, Bangalore, India
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2
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Lawson CD, Hornigold K, Pan D, Niewczas I, Andrews S, Clark J, Welch HCE. Small-molecule inhibitors of P-Rex guanine-nucleotide exchange factors. Small GTPases 2022; 13:307-326. [PMID: 36342857 PMCID: PMC9645260 DOI: 10.1080/21541248.2022.2131313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
P-Rex1 and P-Rex2 are guanine-nucleotide exchange factors (GEFs) that activate Rac small GTPases in response to the stimulation of G protein-coupled receptors and phosphoinositide 3-kinase. P-Rex Rac-GEFs regulate the morphology, adhesion and migration of various cell types, as well as reactive oxygen species production and cell cycle progression. P-Rex Rac-GEFs also have pathogenic roles in the initiation, progression or metastasis of several types of cancer. With one exception, all P-Rex functions are known or assumed to be mediated through their catalytic Rac-GEF activity. Thus, inhibitors of P-Rex Rac-GEF activity would be valuable research tools. We have generated a panel of small-molecule P-Rex inhibitors that target the interface between the catalytic DH domain of P-Rex Rac-GEFs and Rac. Our best-characterized compound, P-Rex inhibitor 1 (PREX-in1), blocks the Rac-GEF activity of full-length P-Rex1 and P-Rex2, and of their isolated catalytic domains, in vitro at low-micromolar concentration, without affecting the activities of several other Rho-GEFs. PREX-in1 blocks the P-Rex1 dependent spreading of PDGF-stimulated endothelial cells and the production of reactive oxygen species in fMLP-stimulated mouse neutrophils. Structure-function analysis revealed critical structural elements of PREX-in1, allowing us to develop derivatives with increased efficacy, the best with an IC50 of 2 µM. In summary, we have developed PREX-in1 and derivative small-molecule compounds that will be useful laboratory research tools for the study of P-Rex function. These compounds may also be a good starting point for the future development of more sophisticated drug-like inhibitors aimed at targeting P-Rex Rac-GEFs in cancer.
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Affiliation(s)
- CD Lawson
- Signalling Programme, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK
| | - K Hornigold
- Signalling Programme, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK
| | - D Pan
- Signalling Programme, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK
| | - I Niewczas
- Biological Chemistry Facility, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK
| | - S Andrews
- Bioinformatics Facility, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK
| | - J Clark
- Biological Chemistry Facility, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK
| | - HCE Welch
- Signalling Programme, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, UK,CONTACT HCE Welch Signalling Programme, The Babraham Institute, Babraham Research Campus, CambridgeCB22 3ATUK
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Ohashi Y, Tremel S, Masson GR, McGinney L, Boulanger J, Rostislavleva K, Johnson CM, Niewczas I, Clark J, Williams RL. Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes. eLife 2020; 9:58281. [PMID: 32602837 PMCID: PMC7326497 DOI: 10.7554/elife.58281] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022] Open
Abstract
The lipid kinase VPS34 orchestrates diverse processes, including autophagy, endocytic sorting, phagocytosis, anabolic responses and cell division. VPS34 forms various complexes that help adapt it to specific pathways, with complexes I and II being the most prominent ones. We found that physicochemical properties of membranes strongly modulate VPS34 activity. Greater unsaturation of both substrate and non-substrate lipids, negative charge and curvature activate VPS34 complexes, adapting them to their cellular compartments. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) of complexes I and II on membranes elucidated structural determinants that enable them to bind membranes. Among these are the Barkor/ATG14L autophagosome targeting sequence (BATS), which makes autophagy-specific complex I more active than the endocytic complex II, and the Beclin1 BARA domain. Interestingly, even though Beclin1 BARA is common to both complexes, its membrane-interacting loops are critical for complex II, but have only a minor role for complex I.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Shirley Tremel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Glenn Robert Masson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Lauren McGinney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Ksenia Rostislavleva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | | | | | - Roger L Williams
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
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Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VY, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Clark J, Hawkins PT, Stephens LR. PTEN Regulates PI(3,4)P 2 Signaling Downstream of Class I PI3K. Mol Cell 2017; 68:566-580.e10. [PMID: 29056325 PMCID: PMC5678281 DOI: 10.1016/j.molcel.2017.09.024] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/09/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022]
Abstract
The PI3K signaling pathway regulates cell growth and movement and is heavily mutated in cancer. Class I PI3Ks synthesize the lipid messenger PI(3,4,5)P3. PI(3,4,5)P3 can be dephosphorylated by 3- or 5-phosphatases, the latter producing PI(3,4)P2. The PTEN tumor suppressor is thought to function primarily as a PI(3,4,5)P3 3-phosphatase, limiting activation of this pathway. Here we show that PTEN also functions as a PI(3,4)P2 3-phosphatase, both in vitro and in vivo. PTEN is a major PI(3,4)P2 phosphatase in Mcf10a cytosol, and loss of PTEN and INPP4B, a known PI(3,4)P2 4-phosphatase, leads to synergistic accumulation of PI(3,4)P2, which correlated with increased invadopodia in epidermal growth factor (EGF)-stimulated cells. PTEN deletion increased PI(3,4)P2 levels in a mouse model of prostate cancer, and it inversely correlated with PI(3,4)P2 levels across several EGF-stimulated prostate and breast cancer lines. These results point to a role for PI(3,4)P2 in the phenotype caused by loss-of-function mutations or deletions in PTEN. PTEN is a PI(3,4)P2 3-phosphatase PTEN and INPP4B regulate PI(3,4)P2 accumulation downstream of class I PI3K PTEN regulates PI(3,4)P2-dependent activation of Akt and formation of invadopodia PI(3,4)P2 signaling may play a role in the tumor suppressor function of PTEN
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Affiliation(s)
| | | | - Tamara Chessa
- Signalling Programme, Babraham Institute, Cambridge, UK
| | | | - David Barneda
- Signalling Programme, Babraham Institute, Cambridge, UK; AstraZeneca R&D Cambridge, CRUK Cambridge Institute, Cambridge, UK
| | - Pınar Pir
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Hiroki Nakanishi
- Department of Medical Biology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Japan
| | - Satoshi Eguchi
- Department of Medical Biology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Japan
| | - Atsushi Koizumi
- Department of Urology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Japan
| | - Junko Sasaki
- Department of Medical Biology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Japan
| | | | | | | | - Alexander Gray
- School of Life Sciences, University of Dundee, Dow St., Dundee, UK
| | | | | | - Marine Imbert
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Sergio Felisbino
- Department of Morphology, Institute of Biosciences of Botucatu, Sao Paulo State University - UNESP, Botucatu, Sao Paulo, Brazil
| | - Tomonori Habuchi
- Department of Urology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Japan
| | - Soren Beinke
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Sabina Cosulich
- AstraZeneca R&D Cambridge, CRUK Cambridge Institute, Cambridge, UK
| | | | - Takehiko Sasaki
- Department of Medical Biology, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Japan
| | | | | | - Len R Stephens
- Signalling Programme, Babraham Institute, Cambridge, UK.
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5
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Manifava M, Smith M, Rotondo S, Walker S, Niewczas I, Zoncu R, Clark J, Ktistakis NT. Dynamics of mTORC1 activation in response to amino acids. eLife 2016; 5. [PMID: 27725083 PMCID: PMC5059141 DOI: 10.7554/elife.19960] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/07/2016] [Indexed: 12/12/2022] Open
Abstract
Amino acids are essential activators of mTORC1 via a complex containing RAG GTPases, RAGULATOR and the vacuolar ATPase. Sensing of amino acids causes translocation of mTORC1 to lysosomes, an obligate step for activation. To examine the spatial and temporal dynamics of this translocation, we used live imaging of the mTORC1 component RAPTOR and a cell permeant fluorescent analogue of di-leucine methyl ester. Translocation to lysosomes is a transient event, occurring within 2 min of aa addition and peaking within 5 min. It is temporally coupled with fluorescent leucine appearance in lysosomes and is sustained in comparison to aa stimulation. Sestrin2 and the vacuolar ATPase are negative and positive regulators of mTORC1 activity in our experimental system. Of note, phosphorylation of canonical mTORC1 targets is delayed compared to lysosomal translocation suggesting a dynamic and transient passage of mTORC1 from the lysosomal surface before targetting its substrates elsewhere. DOI:http://dx.doi.org/10.7554/eLife.19960.001 Cells in all organisms must constantly measure the amount of nutrients available to them in order to be healthy and grow properly. For example, cells use a complex sensing system to measure how many amino acids – the building blocks of proteins – are available to them. One enzyme called mTOR alerts the cell to amino acid levels. When amino acids are available, mTOR springs into action and turns on the production of proteins in the cell. However, when amino acids are scarce, mTOR turns off, which slows down protein production and causes the cell to begin scavenging amino acids by digesting parts of itself. Studies of mTOR have shown that the protein cannot turn on until it visits the surface of small sacks in the cell called lysosomes. These are the major sites within cell where proteins and other molecules are broken down. Scientists know how mTOR gets to the lysosomes, but not how quickly the process occurs. Now, Manifava, Smith et al. have used microscopes to record live video of the mTOR enzyme as it interacts with amino acids revealing the whole process takes place in just a few minutes. In the experiments, a fluorescent tag was added to part of mTOR to make the protein visible under a microscope. The video showed that, in human cells supplied with amino acids, mTOR reaches the lysosomes within 2 minutes of the amino acids becoming available. Then, within 3-4 minutes the mTOR turns on and leaves the lysosome. Even though the mTOR has left the lysosome, it somehow remembers that amino acids are available and stays active. The experiments show that mTOR’s brief interaction with the lysosome switches it on and keeps it on even after mTOR leaves. Future studies will be needed to determine exactly how mTOR remembers its interaction with the lysosome and stays active afterwards. DOI:http://dx.doi.org/10.7554/eLife.19960.002
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Affiliation(s)
- Maria Manifava
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Matthew Smith
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Sergio Rotondo
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Simon Walker
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jonathan Clark
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
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Clark J, Kay RR, Kielkowska A, Niewczas I, Fets L, Oxley D, Stephens LR, Hawkins PT. Dictyostelium uses ether-linked inositol phospholipids for intracellular signalling. EMBO J 2014; 33:2188-200. [PMID: 25180230 DOI: 10.15252/embj.201488677] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Inositol phospholipids are critical regulators of membrane biology throughout eukaryotes. The general principle by which they perform these roles is conserved across species and involves binding of differentially phosphorylated inositol head groups to specific protein domains. This interaction serves to both recruit and regulate the activity of several different classes of protein which act on membrane surfaces. In mammalian cells, these phosphorylated inositol head groups are predominantly borne by a C38:4 diacylglycerol backbone. We show here that the inositol phospholipids of Dictyostelium are different, being highly enriched in an unusual C34:1e lipid backbone, 1-hexadecyl-2-(11Z-octadecenoyl)-sn-glycero-3-phospho-(1'-myo-inositol), in which the sn-1 position contains an ether-linked C16:0 chain; they are thus plasmanylinositols. These plasmanylinositols respond acutely to stimulation of cells with chemoattractants, and their levels are regulated by PIPKs, PI3Ks and PTEN. In mammals and now in Dictyostelium, the hydrocarbon chains of inositol phospholipids are a highly selected subset of those available to other phospholipids, suggesting that different molecular selectors are at play in these organisms but serve a common, evolutionarily conserved purpose.
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Affiliation(s)
- Jonathan Clark
- Babraham Biosciences Technology Babraham Research Campus, Cambridge, UK
| | - Robert R Kay
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Anna Kielkowska
- Babraham Biosciences Technology Babraham Research Campus, Cambridge, UK
| | - Izabella Niewczas
- Babraham Biosciences Technology Babraham Research Campus, Cambridge, UK
| | - Louise Fets
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - David Oxley
- Signalling Programme Babraham Research Campus, Cambridge, UK
| | - Len R Stephens
- Signalling Programme Babraham Research Campus, Cambridge, UK
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Kielkowska A, Niewczas I, Anderson KE, Durrant TN, Clark J, Stephens LR, Hawkins PT. A new approach to measuring phosphoinositides in cells by mass spectrometry. Adv Biol Regul 2014; 54:131-141. [PMID: 24120934 DOI: 10.1016/j.jbior.2013.09.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The phosphoinositide family of phospholipids, defined here as PtdIns, PtdIns3P, PtdIns4P, PtdIns5P, PtdIns(3,4)P2, PtdIns(3,5)P2, PtdIns(4,5)P2 and PtdIns(3,4,5)P3, play pivotal roles in organising the location and activity of many different proteins acting on biological membranes, including those involved in vesicle and protein trafficking through the endolysosomal system and receptor signal transduction at the plasma membrane. Accurate measurement of the cellular levels of these lipids, particularly the more highly phosphorylated species, is hampered by their high polarity and low cellular concentrations. Recently, much progress has been made in using mass spectrometry to measure many different lipid classes in parallel, an approach generally referred to as 'lipidomics'. Unfortunately, the acidic nature of highly phosphorylated phosphoinositides makes them difficult to measure using these methods, because they yield low levels of useful ions; this is particularly the case with PtdIns(3,4,5)P3. We have solved some of these problems by methylating the phosphate groups of these lipids with TMS-diazomethane and describe a simple, integrated approach to measuring PtdIns, PtdInsP, PtdInsP2 and PtdInsP3 classes of lipids, in parallel with other phospholipid species, in cell and tissue extracts. This methodology is sensitive, accurate and robust, and also yields fatty-acyl compositions, suggesting it can be used to further our understanding of both the normal and pathophysiological roles of these important lipids.
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Affiliation(s)
- Anna Kielkowska
- Babraham Bioscience Technologies Ltd, Babraham Research Campus, Cambridge, UK
| | - Izabella Niewczas
- Babraham Bioscience Technologies Ltd, Babraham Research Campus, Cambridge, UK
| | | | - Tom N Durrant
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Jonathan Clark
- Babraham Bioscience Technologies Ltd, Babraham Research Campus, Cambridge, UK
| | - Len R Stephens
- Babraham Institute, Babraham Research Campus, Cambridge, UK
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Newton M, Niewczas I, Clark J, Bellamy TC. A real-time fluorescent assay of the purified nitric oxide receptor, guanylyl cyclase. Anal Biochem 2010; 402:129-36. [PMID: 20371357 DOI: 10.1016/j.ab.2010.03.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 11/30/2022]
Abstract
Nitric oxide (NO) mediates intercellular signaling through activation of its receptor, soluble guanylyl cyclase (sGC), leading to elevation of intracellular guanosine 3',5'-cyclic monophosphate (cGMP) levels. Through this signal transduction pathway, NO regulates a diverse range of physiological effects, from vasodilatation and platelet disaggregation to synaptic plasticity. Measurement of sGC activity has traditionally been carried out using end-point assays of cGMP accumulation or by transfection of cells with "detector" proteins such as fluorescent proteins coupled to cGMP binding domains or cyclic nucleotide gated channels. Here we report a simpler approach: the use of a fluorescently labeled substrate analog, mant-GTP (2'-O-(N-methylanthraniloyl) guanosine 5'-triphosphate), which gives an increase in emission intensity after enzymatic cyclization to mant-cGMP. Activation of purified recombinant sGC by NO led to a rapid rise in fluorescence intensity within seconds, reaching a maximal 1.6- to 1.8-fold increase above basal levels. The sGC inhibitor, ODQ (1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one), eliminated the fluorescence increase due to NO, and the synergistic activator of sGC, BAY 41-2272 (3-(4-amino-5-cyclopropylpyrimidin-2-yl)-1-(2-fluorobenzyl)-1H-pyrazolo[3,4-b]pyridine), increased the rate at which the maximal fluorescence increase was attained. High-performance liquid chromatography (HPLC) confirmed the formation of mant-cGMP product. This real-time assay allows the progress of purified sGC activation to be quantified precisely and, with refinement, could be optimized for use in a cellular environment.
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Palyam N, Niewczas I, Majewski M. Building carbohydrates on the dioxanone scaffold: stereoselective synthesis of d-glycero-d-manno-2-octulose. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.10.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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