Relevant bibliographies by topics / Ligand/substrate identification

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Ligand/substrate identification'

Author: Grafiati
Published: 8 June 2024
Last updated: 31 July 2025

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Journal articles on the topic "Ligand/substrate identification"

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Singh, Manvi, Priya Kempanna, and Kavitha Bharatham. "Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches." Molecules 27, no. 9 (2022): 2805. http://dx.doi.org/10.3390/molecules27092805.

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Targeting enzymes that play a role in the biosynthesis of the bacterial cell wall has long been a strategy for antibacterial discovery. In particular, the cell wall of Mycobacterium tuberculosis (Mtb) is a complex of three layers, one of which is Peptidoglycan, an essential component providing rigidity and strength. UDP-GlcNAc, a precursor for the synthesis of peptidoglycan, is formed by GlmU, a bi-functional enzyme. Inhibiting GlmU Uridyltransferase activity has been proven to be an effective anti-bacterial, but its similarity with human enzymes has been a deterrent to drug development. To de
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Fernández, Rico-Jiménez, Ortega, et al. "Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins." International Journal of Molecular Sciences 20, no. 20 (2019): 5156. http://dx.doi.org/10.3390/ijms20205156.

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Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomonas aeruginosa PAO1 that is composed of 98 proteins. Bioinformatic predictions indicate that many of these proteins have a redundant ligand profile such as 27 SBPs for proteinogenic amino acids, 13 proteins for spermidine/putrescine, or 9 proteins for quaternary amines. To assess the precision of these bioinformatic predictions, we have purified 17
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Rothweiler, Elisabeth M., Paul E. Brennan, and Kilian V. M. Huber. "Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators." Biological Chemistry 403, no. 4 (2022): 391–402. http://dx.doi.org/10.1515/hsz-2021-0396.

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Abstract Ubiquitination is a key regulatory mechanism vital for maintenance of cellular homeostasis. Protein degradation is induced by E3 ligases via attachment of ubiquitin chains to substrates. Pharmacological exploitation of this phenomenon via targeted protein degradation (TPD) can be achieved with molecular glues or bifunctional molecules facilitating the formation of ternary complexes between an E3 ligase and a given protein of interest (POI), resulting in ubiquitination of the substrate and subsequent proteolysis by the proteasome. Recently, the development of novel covalent fragment sc
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Wang, Wenyuan, Junli Zhu, Qi Huang, et al. "DFT Exploration of Metal Ion–Ligand Binding: Toward Rational Design of Chelating Agent in Semiconductor Manufacturing." Molecules 29, no. 2 (2024): 308. http://dx.doi.org/10.3390/molecules29020308.

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Chelating agents are commonly employed in microelectronic processes to prevent metal ion contamination. The ligand fragments of a chelating agent largely determine its binding strength to metal ions. Identification of ligands with suitable characteristics will facilitate the design of chelating agents to enhance the capture and removal of metal ions from the substrate in microelectronic processes. This study employed quantum chemical calculations to simulate the binding process between eleven ligands and the hydrated forms of Ni2+, Cu2+, Al3+, and Fe3+ ions. The binding strength between the me
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Weng, Z., S. M. Thomas, R. J. Rickles, et al. "Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains." Molecular and Cellular Biology 14, no. 7 (1994): 4509–21. http://dx.doi.org/10.1128/mcb.14.7.4509-4521.1994.

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Src homology 3 (SH3) domains mediate protein-protein interactions necessary for the coupling of cellular proteins involved in intracellular signal transduction. We previously established solution-binding conditions that allow affinity isolation of Src SH3-binding proteins from cellular extracts (Z. Weng, J. A. Taylor, C. E. Turner, J. S. Brugge, and C. Seidel-Dugan, J. Biol. Chem. 268:14956-14963, 1993). In this report, we identified three of these proteins: Shc, a signaling protein that couples membrane tyrosine kinases with Ras; p62, a protein which can bind to p21rasGAP; and heterogeneous n
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Weng, Z., S. M. Thomas, R. J. Rickles, et al. "Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains." Molecular and Cellular Biology 14, no. 7 (1994): 4509–21. http://dx.doi.org/10.1128/mcb.14.7.4509.

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Src homology 3 (SH3) domains mediate protein-protein interactions necessary for the coupling of cellular proteins involved in intracellular signal transduction. We previously established solution-binding conditions that allow affinity isolation of Src SH3-binding proteins from cellular extracts (Z. Weng, J. A. Taylor, C. E. Turner, J. S. Brugge, and C. Seidel-Dugan, J. Biol. Chem. 268:14956-14963, 1993). In this report, we identified three of these proteins: Shc, a signaling protein that couples membrane tyrosine kinases with Ras; p62, a protein which can bind to p21rasGAP; and heterogeneous n
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Evans, S. W., D. Rennick, and W. L. Farrar. "Identification of a signal-transduction pathway shared by haematopoietic growth factors with diverse biological specificity." Biochemical Journal 244, no. 3 (1987): 683–91. http://dx.doi.org/10.1042/bj2440683.

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The haematopoietic growth factors multi-colony-stimulating factor, granulocyte/macrophage colony-stimulating factor, granulocyte colony-stimulating factor and interleukin 2 specifically control the production and proliferation of distinct leucocyte series. Each growth factor acts on a unique surface receptor associated with an appropriate signal-transduction apparatus. In this report we identify a 68 kDa substrate which is phosphorylated after stimulation of different cell types with multi-colony-stimulating factor, granulocyte colony-stimulating factor and interleukin 2. The 68 kDa substrate
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Duarte Filho, Luiz Antonio Miranda de Souza, Cintia Emi Yanaguibashi Leal, Pierre-Edouard Bodet, et al. "The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy." Marine Drugs 22, no. 6 (2024): 244. http://dx.doi.org/10.3390/md22060244.

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Brown seaweeds of the Fucus genus represent a rich source of natural antiviral products. In this study, a Fucus ceranoides hydroalcoholic extract (FCHE) was found to inhibit 74.2 ± 1.3% of the proteolytic activity of the free SARS-CoV-2 3CL protease (3CLpro), an enzyme that plays a pivotal role in polyprotein processing during coronavirus replication and has been identified as a relevant drug discovery target for SARS- and MERS-CoVs infections. To purify and identify 3CLpro ligands with potential inhibitory activity using a one-step approach, we immobilized the enzyme onto magnetic microbeads
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Lamaze, C., and S. L. Schmid. "Recruitment of epidermal growth factor receptors into coated pits requires their activated tyrosine kinase." Journal of Cell Biology 129, no. 1 (1995): 47–54. http://dx.doi.org/10.1083/jcb.129.1.47.

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EGF-receptor (EGF-R) tyrosine kinase is required for the down-regulation of activated EGF-R. However, controversy exists as to whether ligand-induced activation of the EGF-R tyrosine kinase is required for internalization or for lysosomal targeting. We have addressed this issue using a cell-free assay that selectively measures the recruitment of EGF-R into coated pits. Here we show that EGF bound to wild-type receptors is efficiently sequestered in coated pits. In contrast, sequestration of kinase-deficient receptors occurs inefficiently and at the same basal rate of endocytosis of unoccupied
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Drexler, Hannes C. A., Matthias Vockel, Christian Polaschegg, Maike Frye, Kevin Peters, and Dietmar Vestweber. "Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2." Molecular & Cellular Proteomics 18, no. 10 (2019): 2058–77. http://dx.doi.org/10.1074/mcp.ra119.001716.

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Vascular endothelial protein tyrosine phosphatase (VE-PTP, PTPRB) is a receptor type phosphatase that is crucial for the regulation of endothelial junctions and blood vessel development. We and others have shown recently that VE-PTP regulates vascular integrity by dephosphorylating substrates that are key players in endothelial junction stability, such as the angiopoietin receptor TIE2, the endothelial adherens junction protein VE-cadherin and the vascular endothelial growth factor receptor VEGFR2. Here, we have systematically searched for novel substrates of VE-PTP in endothelial cells by uti
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Dissertations / Theses on the topic "Ligand/substrate identification"

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Sylvestre-Gonon, Elodie. "Caractérisation biochimique et structurale de quelques glutathion transférases de la classe Tau d'arabette (Arabidopsis thaliana) et de peuplier (Populus trichocarpa)." Electronic Thesis or Diss., Université de Lorraine, 2020. http://www.theses.fr/2020LORR0253.

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Les glutathion transférases (GSTs) constituent une famille multigénique d’enzymes ubiquitaires impliquées notamment dans la détoxication des xénobiotiques et le métabolisme secondaire. Les GSTs canoniques sont constituées d’un domaine N-terminal de type thiorédoxine et d’un domaine C-terminal formé d’hélices α. Chez les plantes terrestres, les GSTs peuvent être regroupées en 14 classes et selon le résidu conservé au sein de leur motif catalytique en GSTs à cystéine (Cys-GSTs) ou à sérine (Ser-GSTs). Les Ser-GSTs présentent des activités de réduction des peroxydes et/ou de conjugaison de glutat
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Williams, Jamie John Lewis. "Identification of substrates for the EPAC1-inducible E3 ubiquitin ligase component SOCS3." Thesis, University of Glasgow, 2012. http://theses.gla.ac.uk/4013/.

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It is now accepted that there is a link between obesity and several diseases such as cardiovascular disease (CVD), diabetes, rheumatoid arthritis (RA), and atherosclerosis with the common initiating factor in pathogenesis being a state of low grade, chronic inflammation. This state, characterised by elevated levels of pro-inflammatory cytokines such as interleukin (IL) 6, leads to sustained activation of inflammatory signalling pathways such as the Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway and subsequently pathogenesis. Suppressor of cytokine signalling
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Burande, Clara. "Identification des substracts d'ASB2alpha, la sous-unité de spécificité d'une E3 ubiquitine ligase impliquée dans la différenciation hématopoïétique." Toulouse 3, 2010. http://thesesups.ups-tlse.fr/1639/.

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La dégradation des protéines dépendante de l'ubiquitine est une voie de protéolyse contrôlée cruciale chez les Eucaryotes dont la spécificité est apportée par les E3 ubiquitine ligases impliquées dans la reconnaissance des protéines à polyubiquitinyler et donc dégradées par le protéasome. Au cours de ma thèse, j'ai développé une nouvelle stratégie d'identification de substrats d'E3 ubiquitine ligases par protéomique quantitative sans marquage, appliquée à l'étude d'ASB2alpha. La protéine ASB2alpha est la sous-unité de spécificité d'une E3 ubiquitine ligase exprimée dans les cellules hématopoïé
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Book chapters on the topic "Ligand/substrate identification"

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Cox, Eric, Ijeoma Uzoma, Catherine Guzzo, et al. "Identification of SUMO E3 Ligase-Specific Substrates Using the HuProt Human Proteome Microarray." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2550-6_32.

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Jing, Lei, Xin Huo, Yufeng Li, Yuyin Li, and Aipo Diao. "Identification of the Binding Domains of Nedd4 E3 Ubiquitin Ligase with Its Substrate Protein TMEPAI." In Lecture Notes in Electrical Engineering. Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-45657-6_6.

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Ayad, Nagi G., Susannah Rankin, Danny Ooi, Michael Rape, and Marc W. Kirschner. "Identification of Ubiquitin Ligase Substrates by In Vitro Expression Cloning." In Methods in Enzymology. Elsevier, 2005. http://dx.doi.org/10.1016/s0076-6879(05)99028-9.

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Conference papers on the topic "Ligand/substrate identification"

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Geddes, V. A., G. V. Louie, G. D. Brayer, and R. T. A. MacGillivray. "MOLECULAR BASIS OF HEMOPHILIA B: IDENTIFICATION OF THE DEFECT IN FACTOR IX VANCOUVER." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643872.

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Factor IX Vancouver (fIX-V) is the cause of a moderate form of hemophilia B. An individual presenting with this disorder had 2.6% of normal procoagulant activity in his plasma but had 62% of the normal factor IX antigen level. Specific antibodies showed that fIX-V contains epitopes for both the heavy and light chains of factor IXa. To identify the defect involved, DNA was isolated from the lymphocytes of the male hemophiliac. Southern blot analysis using a full-length factor IX cDNA as a hybridization probe showed no gross differences between the fIX-V gene and the normal factor IX gene. The D
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Journal articles
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