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Journal articles on the topic 'Ligand/substrate identification'

Author: Grafiati

Published: 8 June 2024

Last updated: 31 July 2025

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1

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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Ruan, Ke-He. "High resolution nuclear magnetic resonance spectroscopy-guided mutagenesis for characterization of membrane-bound proteins: Experimental designs and applications." Spectroscopy 18, no. 1 (2004): 13–29. http://dx.doi.org/10.1155/2004/802728.

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High resolution Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for determining the solution structures of peptides and small proteins, and their ligand binding functions. Molecular biology mutagenesis is a widely used and powerful approach for identification of the protein functions. We have developed a strategy integrating NMR experiments with mutagenesis studies to advance and extend the approaches used for structure/function relationship studies of proteins, especially for membrane-bound proteins, which play important roles in physiopathological processes. The procedures i

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Mora Lagares, Liadys, Yunierkis Pérez-Castillo, Nikola Minovski, and Marjana Novič. "Structure–Function Relationships in the Human P-Glycoprotein (ABCB1): Insights from Molecular Dynamics Simulations." International Journal of Molecular Sciences 23, no. 1 (2021): 362. http://dx.doi.org/10.3390/ijms23010362.

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P-Glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette superfamily of transporters, and it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping compounds out of cells. P-gp contributes to a reduction in toxicity, and has broad substrate specificity. It is involved in the failure of many cancer and antiviral chemotherapies due to the phenomenon of multidrug resistance (MDR), in which the membrane transporter removes chemotherapeutic drugs from target cells. Understanding the details of the ligand–P-gp interaction is therefore critica

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Reynolds, A. B., J. Daniel, P. D. McCrea, M. J. Wheelock, J. Wu, and Z. Zhang. "Identification of a new catenin: the tyrosine kinase substrate p120cas associates with E-cadherin complexes." Molecular and Cellular Biology 14, no. 12 (1994): 8333–42. http://dx.doi.org/10.1128/mcb.14.12.8333-8342.1994.

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p120cas is a tyrosine kinase substrate implicated in ligand-induced receptor signaling through the epidermal growth factor, platelet-derived growth factor, and colony-stimulating factor receptors and in cell transformation by Src. Here we report that p120 associates with a complex containing E-cadherin, alpha-catenin, beta-catenin, and plakoglobin. Furthermore, p120 precisely colocalizes with E-cadherin and catenins in vivo in both normal and Src-transformed MDCK cells. Unlike beta-catenin and plakoglobin, p120 has at least four isoforms which are differentially expressed in a variety of cell

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Reynolds, A. B., J. Daniel, P. D. McCrea, M. J. Wheelock, J. Wu, and Z. Zhang. "Identification of a new catenin: the tyrosine kinase substrate p120cas associates with E-cadherin complexes." Molecular and Cellular Biology 14, no. 12 (1994): 8333–42. http://dx.doi.org/10.1128/mcb.14.12.8333.

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p120cas is a tyrosine kinase substrate implicated in ligand-induced receptor signaling through the epidermal growth factor, platelet-derived growth factor, and colony-stimulating factor receptors and in cell transformation by Src. Here we report that p120 associates with a complex containing E-cadherin, alpha-catenin, beta-catenin, and plakoglobin. Furthermore, p120 precisely colocalizes with E-cadherin and catenins in vivo in both normal and Src-transformed MDCK cells. Unlike beta-catenin and plakoglobin, p120 has at least four isoforms which are differentially expressed in a variety of cell

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Adams, James, Benjamin P. Thornton, and Lydia Tabernero. "A New Paradigm for KIM-PTP Drug Discovery: Identification of Allosteric Sites with Potential for Selective Inhibition Using Virtual Screening and LEI Analysis." International Journal of Molecular Sciences 22, no. 22 (2021): 12206. http://dx.doi.org/10.3390/ijms222212206.

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The kinase interaction motif protein tyrosine phosphatases (KIM-PTPs), HePTP, PTPSL and STEP, are involved in the negative regulation of mitogen-activated protein kinase (MAPK) signalling pathways and are important therapeutic targets for a number of diseases. We have used VSpipe, a virtual screening pipeline, to identify a ligand cluster distribution that is unique to this subfamily of PTPs. Several clusters map onto KIM-PTP specific sequence motifs in contrast to the cluster distribution obtained for PTP1B, a classic PTP that mapped to general PTP motifs. Importantly, the ligand clusters coi

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Duan, Huaichuan, Quanshan Shi, Xinru Yue, et al. "Identification of core therapeutic targets for Monkeypox virus and repurposing potential of drugs: A WEB prediction approach." PLOS ONE 19, no. 12 (2024): e0303501. https://doi.org/10.1371/journal.pone.0303501.

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A new round of monkeypox virus has emerged in the United Kingdom since July 2022 and rapidly swept the world. Currently, despite numerous research groups are studying this virus and seeking effective treatments, the information on the open reading frame, inhibitors, and potential targets of monkeypox has not been updated in time, and the comprehension of monkeypox target ligand interactions remains a key challenge. Here, we first summarized and improved the open reading frame information of monkeypox, constructed the monkeypox inhibitor library and potential targets library by database researc

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Yadav, Rolly, Anwesh Pandey, Nidhi Awasthi, and Anamika Shukla. "Molecular Docking Studies of Enzyme Binding Drugs on Family of Cytochrome P450." Advanced Science, Engineering and Medicine 12, no. 1 (2020): 83–87. http://dx.doi.org/10.1166/asem.2020.2520.

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The combination of experimental and computational strategies has been of great value in the identification and development of metabolism of drugs. Nowadays modern drug design, molecular docking methods are helpful in exploring the ligand conformations adopted within the binding sites of macro-molecular targets such as DNA, proteins, and enzymes, there by reducing cost, time and wayward efforts of chemist. Since the development of the algorithms in the 1980s, molecular docking became an important tool in drug discovery like investigation of crucial molecular events, including ligand binding mod

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BARNETT, Stanley F., Deborah DEFEO-JONES, Sheng FU, et al. "Identification and characterization of pleckstrin-homology-domain-dependent and isoenzyme-specific Akt inhibitors." Biochemical Journal 385, no. 2 (2005): 399–408. http://dx.doi.org/10.1042/bj20041140.

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We developed a high-throughput HTRF (homogeneous time-resolved fluorescence) assay for Akt kinase activity and screened approx. 270000 compounds for their ability to inhibit the three isoforms of Akt. Two Akt inhibitors were identified that exhibited isoenzyme specificity. The first compound (Akt-I-1) inhibited only Akt1 (IC50 4.6 μM) while the second compound (Akt-I-1,2) inhibited both Akt1 and Akt2 with IC50 values of 2.7 and 21 μM respectively. Neither compound inhibited Akt3 nor mutants lacking the PH (pleckstrin homology) domain at concentrations up to 250 μM. These compounds were reversi

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Wei, Min, Richard Wynn, Gregory Hollis, et al. "High-Throughput Determination of Mode of Inhibition in Lead Identification and Optimization." Journal of Biomolecular Screening 12, no. 2 (2007): 220–28. http://dx.doi.org/10.1177/1087057106296679.

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After finishing the primary high-throughput screening, the screening team is often faced with thousands of hits to be evaluated further. Effective filtering of these hits is crucial in identifying leads. Mode of inhibition (MOI) study is extremely useful in validating whether the observed compound activity is specific to the biological target. In this article, the authors describe a high-throughput MOI determination method for evaluating thousands of compounds using an existing screening infrastructure. Based on enzyme or receptor kinetics theory, the authors developed the method by measuring

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D’Arrigo, Giulia, Ida Autiero, Eleonora Gianquinto, et al. "Exploring Ligand Binding Domain Dynamics in the NRs Superfamily." International Journal of Molecular Sciences 23, no. 15 (2022): 8732. http://dx.doi.org/10.3390/ijms23158732.

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Nuclear receptors (NRs) are transcription factors that play an important role in multiple diseases, such as cancer, inflammation, and metabolic disorders. They share a common structural organization composed of five domains, of which the ligand-binding domain (LBD) can adopt different conformations in response to substrate, agonist, and antagonist binding, leading to distinct transcription effects. A key feature of NRs is, indeed, their intrinsic dynamics that make them a challenging target in drug discovery. This work aims to provide a meaningful investigation of NR structural variability to

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Takeuchi, Hajime, Daniel J. Rigden, Bahram Ebrahimi, Philip C. Turner, and Huw H. Rees. "Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration." Biochemical Journal 389, no. 3 (2005): 637–45. http://dx.doi.org/10.1042/bj20050498.

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The steroidal moulting hormones (ecdysteroids) mediate developmental transitions in insects, and their regulation is mainly controlled by the production and inactivation of these steroid hormones at the appropriate developmental times. One route of metabolism of ecdysteroids in insects involves EO (ecdysone oxidase)-catalysed conversion into 3-dehydroecdysteroid, which undergoes reduction to the corresponding 3-epiecdysteroid. By a twin-stranded bioinformatics approach, employing both phylogenomics and model structure-based analysis, we first predicted that DmEO (the EO of Drosophila melanogas

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Astegno, Alessandra, Alejandro Giorgetti, Alessandra Allegrini, Barbara Cellini, and Paola Dominici. "Characterization of C-S Lyase fromC. diphtheriae: A Possible Target for New Antimicrobial Drugs." BioMed Research International 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/701536.

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The emergence of antibiotic resistance in microbial pathogens requires the identification of new antibacterial drugs. The biosynthesis of methionine is an attractive target because of its central importance in cellular metabolism. Moreover, most of the steps in methionine biosynthesis pathway are absent in mammals, lowering the probability of unwanted side effects. Herein, detailed biochemical characterization of one enzyme required for methionine biosynthesis, a pyridoxal-5′-phosphate (PLP-) dependent C-S lyase fromCorynebacterium diphtheriae, a pathogenic bacterium that causes diphtheria, ha

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Basu, Nirmalya, Rashna Bhandari, Vivek T. Natarajan, and Sandhya S. Visweswariah. "Cross Talk between Receptor Guanylyl Cyclase C and c-src Tyrosine Kinase Regulates Colon Cancer Cell Cytostasis." Molecular and Cellular Biology 29, no. 19 (2009): 5277–89. http://dx.doi.org/10.1128/mcb.00001-09.

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ABSTRACT Increased activation of c-src seen in colorectal cancer is an indicator of a poor clinical prognosis, suggesting that identification of downstream effectors of c-src may lead to new avenues of therapy. Guanylyl cyclase C (GC-C) is a receptor for the gastrointestinal hormones guanylin and uroguanylin and the bacterial heat-stable enterotoxin. Though activation of GC-C by its ligands elevates intracellular cyclic GMP (cGMP) levels and inhibits cell proliferation, its persistent expression in colorectal carcinomas and occult metastases makes it a marker for malignancy. We show here that

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Sanguinetti, Manuel, Lucianna Helene Silva Santos, Juliette Dourron, et al. "Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter." International Journal of Molecular Sciences 23, no. 24 (2022): 16039. http://dx.doi.org/10.3390/ijms232416039.

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Through a combination of comparative modeling, site-directed and classical random mutagenesis approaches, we previously identified critical residues for binding, recognition, and translocation of urea, and its inhibition by 2-thiourea and acetamide in the Aspergillus nidulans urea transporter, UreA. To deepen the structural characterization of UreA, we employed the artificial intelligence (AI) based AlphaFold2 (AF2) program. In this analysis, the resulting AF2 models lacked inward- and outward-facing cavities, suggesting a structural intermediate state of UreA. Moreover, the orientation of the

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Thakur, Priti, Jowad Atway, Patrick A. Limbach, and Balasubrahmanyam Addepalli. "RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site." International Journal of Molecular Sciences 23, no. 13 (2022): 7021. http://dx.doi.org/10.3390/ijms23137021.

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Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. Here, we detail the cleavage specificity and efficiency of ribonuclease MC1 and cusativin using a customized RNA sequence that contained all dinucleotide combinations and homopolymer sequences. The sequencing of the oligonucleotide digestion products by a semi-quantitative liquid chromatography coupled with mass spectrometry (LC-MS) analysis documented as little as 0.5–1% cleavage levels for a given dinucleotide sequence combination. While RNase M

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Xia, Daosong, Renwen Zheng, Jianhua Huang, Sihan Lu, and Qingfeng Tang. "Identification and Functional Analysis of Glutathione S-Transferases from Sitophilus zeamais in Olfactory Organ." Insects 13, no. 3 (2022): 259. http://dx.doi.org/10.3390/insects13030259.

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Odorant-degrading enzymes (ODEs) play an important role in rapidly degrading and inactivating odorant molecules that have completed information transmission, as well as in maintaining the stability and sensitivity of insect olfactory sensing systems. Glutathione S-transferases (GSTs), as a group of ODEs, supposedly bear the ability to catalyze the conjugation of glutathione (GSH) and xenobiotic odorant molecules in the degrading process. However, there are few reports regarding the role of the GST genes of Sitophilus zeamais in the degrading process. Thus, we characterized 13 full-length genes

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Milot, Marie-Michelle, and Adrian Hofmann. "Shikimate kinase-like 1 plays an integral role in chloroplast biogenesis." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C452. http://dx.doi.org/10.1107/s2053273314095473.

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The shikimate pathway is found in plants, fungi, and microbes, but not mammals which makes it an attractive target for antimicrobials and herbicide development. In plants, the shikimate pathway produces precursors of compounds that are crucial for growth, defense and, survival. We focused on the enzyme shikimate kinase (SK) which catalyzes the phosphorylation of shikimate; the fifth reaction of the pathway. Plant SK underwent a gene duplication event yielding shikimate kinase-like genes (SKL1 and SKL2) roughly 400 MYA. Despite the overall similarity in sequence between SK and SKL1, a previous

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N'Diaye, Elsa-Noah, Aylin C. Hanyaloglu, Kimberly K. Kajihara, et al. "The Ubiquitin-like Protein PLIC-2 Is a Negative Regulator of G Protein-coupled Receptor Endocytosis." Molecular Biology of the Cell 19, no. 3 (2008): 1252–60. http://dx.doi.org/10.1091/mbc.e07-08-0775.

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The activity of many signaling receptors is regulated by their endocytosis via clathrin-coated pits (CCPs). For G protein-coupled receptors (GPCRs), recruitment of the adaptor protein arrestin to activated receptors is thought to be sufficient to drive GPCR clustering in CCPs and subsequent endocytosis. We have identified an unprecedented role for the ubiquitin-like protein PLIC-2 as a negative regulator of GPCR endocytosis. Protein Linking IAP to Cytoskeleton (PLIC)-2 overexpression delayed ligand-induced endocytosis of two GPCRs: the V2 vasopressin receptor and β-2 adrenergic receptor, witho

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Venkatraman, Janani, Jyothi Bhat, Suresh M. Solapure, et al. "Screening, Identification, and Characterization of Mechanistically Diverse Inhibitors of the Mycobacterium Tuberculosis Enzyme, Pantothenate Kinase (CoaA)." Journal of Biomolecular Screening 17, no. 3 (2011): 293–302. http://dx.doi.org/10.1177/1087057111423069.

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The authors describe the discovery of anti-mycobacterial compounds through identifying mechanistically diverse inhibitors of the essential Mycobacterium tuberculosis ( Mtb) enzyme, pantothenate kinase (CoaA). Target-driven drug discovery technologies often work with purified enzymes, and inhibitors thus discovered may not optimally inhibit the form of the target enzyme predominant in the bacterial cell or may not be available at the desired concentration. Therefore, in addition to addressing entry or efflux issues, inhibitors with diverse mechanisms of inhibition (MoI) could be prioritized bef

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Pallen, C. J., D. S. Y. Lai, H. P. Chia, I. Boulet, and P. H. Tong. "Purification and characterization of a higher-molecular-mass form of protein phosphotyrosine phosphatase (PTP 1B) from placental membranes." Biochemical Journal 276, no. 2 (1991): 315–23. http://dx.doi.org/10.1042/bj2760315.

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Purification of a major placental membrane protein phosphotyrosine phosphatase (PTP-I) through the use of a nonhydrolysable phosphotyrosine analogue affinity ligand has enabled identification of the enzyme as a single polypeptide of at least 46 kDa. This phosphatase specifically dephosphorylates phosphotyrosine-containing substrates, including the src peptide, the epidermal-growth-factor receptor tyrosine kinase and the non-receptor tyrosine kinase p56lck. The p56lck can be dephosphorylated by PTP-I at two tyrosine residues (Tyr-394 and Tyr-505), which are differentially phosphorylated in vitr

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Jahn, Dieter, and Martina Johanna Jahn. "Heme Biosynthesis and Degradation in Bacteria." ECS Meeting Abstracts MA2025-01, no. 17 (2025): 1248. https://doi.org/10.1149/ma2025-01171248mtgabs.

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Nature utilizes three distinct pathways to synthesise the essential enzyme cofactor heme. An overview of the pathways will be given. The coproporphyrin III-dependent pathway, predominantly present in Bacillaceae,employs an oxygen-dependent coproporphyrinogen III oxidase (CgoX) that converts coproporphyrinogen III into coproporphyrin III. We report the bioinformatic-based identification of a gene called ytpQ, encoding the oxygen-independent counterpart, which we propose to term CgoN, from Priestia (Bacillus) megaterium. The recombinantly produced, purified, and monomeric YtpQ (CgoN) protein is

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Powell, David W., Madhavi J. Rane, Brian A. Joughin та ін. "Proteomic Identification of 14-3-3ζ as a Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 Substrate: Role in Dimer Formation and Ligand Binding". Molecular and Cellular Biology 23, № 15 (2003): 5376–87. http://dx.doi.org/10.1128/mcb.23.15.5376-5387.2003.

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ABSTRACT Mitogen-activated protein kinase (MAPK)-activated protein kinase 2 (MAPKAPK2) mediates multiple p38 MAPK-dependent inflammatory responses. To define the signal transduction pathways activated by MAPKAPK2, we identified potential MAPKAPK2 substrates by using a functional proteomic approach consisting of in vitro phosphorylation of neutrophil lysate by active recombinant MAPKAPK2, protein separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and phosphoprotein identification by peptide mass fingerprinting with matrix-assisted laser desorption ionization mas

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Dryuchko, Oleksandr, Natalia Bunyakina, Bogdan Korobko, Oleksandr Shefer, Kateryna Kytaihora, and Iryna Ivanytska. "SEARCH FOR WAYS OF CONTROLLED MODIFICATION OF CHARACTERISTICS OF FUNCTIONAL UNITS OF ADAPTIVE AIR PURIFICATION SYSTEMS." Bulletin of the National Technical University "KhPI". Series: Chemistry, Chemical Technology and Ecology, no. 2(6) (December 23, 2021): 34–51. http://dx.doi.org/10.20998/2079-0821.2021.02.06.

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Information on alkaline coordination nitrates of rare-earth elements of the cerium subgroup - precursors of promising modern multifunctional materials - on the conditions of their formation and existence, the nature of the chemical bond, the composition, structure, shape of the Ln coordination polyhedra, the type of ligand coordination, and the existence of isotypic series in stoichiometry are generalized. composition, structure, characteristic properties. The data obtained (as primary information) is the basis for the detection, identification, and control of the phase state of processing obj

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Byrne, Dominic P., Yong Li, Pawin Ngamlert, et al. "New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors." Biochemical Journal 475, no. 15 (2018): 2435–55. http://dx.doi.org/10.1042/bcj20180266.

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Protein tyrosine sulfation is a post-translational modification best known for regulating extracellular protein–protein interactions. Tyrosine sulfation is catalysed by two Golgi-resident enzymes termed tyrosylprotein sulfotransferases (TPSTs) 1 and 2, which transfer sulfate from the cofactor PAPS (3′-phosphoadenosine 5′-phosphosulfate) to a context-dependent tyrosine in a protein substrate. A lack of quantitative tyrosine sulfation assays has hampered the development of chemical biology approaches for the identification of small-molecule inhibitors of tyrosine sulfation. In the present paper,

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Aytenfisu, Asaminew H., Daniel Deredge, Erik H. Klontz, Jonathan Du, Eric J. Sundberg, and Alexander D. MacKerell. "Insights into substrate recognition and specificity for IgG by Endoglycosidase S2." PLOS Computational Biology 17, no. 7 (2021): e1009103. http://dx.doi.org/10.1371/journal.pcbi.1009103.

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Antibodies bind foreign antigens with high affinity and specificity leading to their neutralization and/or clearance by the immune system. The conserved N-glycan on IgG has significant impact on antibody effector function, with the endoglycosidases of Streptococcus pyogenes deglycosylating the IgG to evade the immune system, a process catalyzed by the endoglycosidase EndoS2. Studies have shown that two of the four domains of EndoS2, the carbohydrate binding module (CBM) and the glycoside hydrolase (GH) domain are critical for catalytic activity. To yield structural insights into contributions

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Lobell, Robert B., Joseph P. Davide, Nancy E. Kohl, H. Donald Burns, Wai-Si Eng, and Raymond E. Gibson. "A Cell-Based Radioligand Binding Assay for Farnesyl: Protein Transferase Inhibitors." Journal of Biomolecular Screening 8, no. 4 (2003): 430–38. http://dx.doi.org/10.1177/1087057103256153.

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Farnesyl:protein transferase (FPTase) catalyzes the covalent addition of the isoprenyl moiety of farnesylpyrophosphate to the C-terminus of the Ras oncoprotein and other cellular proteins. Inhibitors of FPTase (FTIs) have been developed as potential anticancer agents, and several compounds have been evaluated in clinical trials. To facilitate the identification of cell-active FTIs with high potency, the authors developed a method that uses a radiolabeled FTI that serves as a ligand in competitive displacement assays. Using high-affinity [3H]-labeled or [125I]-labeled FTI radioligands, they sho

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Vargas-Pérez, María de los Ángeles, Damien Paul Devos, and Guillermo López-Lluch. "An AlphaFold Structure Analysis of COQ2 as Key a Component of the Coenzyme Q Synthesis Complex." Antioxidants 13, no. 4 (2024): 496. http://dx.doi.org/10.3390/antiox13040496.

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Coenzyme Q (CoQ) is a lipidic compound that is widely distributed in nature, with crucial functions in metabolism, protection against oxidative damage and ferroptosis and other processes. CoQ biosynthesis is a conserved and complex pathway involving several proteins. COQ2 is a member of the UbiA family of transmembrane prenyltransferases that catalyzes the condensation of the head and tail precursors of CoQ, which is a key step in the process, because its product is the first intermediate that will be modified in the head by the next components of the synthesis process. Mutations in this prote

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Ma, Peilin, Raghuveer Mali, Li-Fan Zeng, et al. "KIT Induced Myeloproliferative Disease Is Dependent on PI3Kinase and SHP2 Phosphatase: Identification of SHP2 As a Druggable Target for Treating MPD and AML." Blood 118, no. 21 (2011): 868. http://dx.doi.org/10.1182/blood.v118.21.868.868.

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Abstract Abstract 868 Gain-of-function mutations in KIT receptor in humans are associated with gastrointestinal stromal tumors (GIST), systemic mastocytosis (SM), and acute myelogenous leukemia (AML). An activating KIT receptor mutation of aspartic acid to valine at codon 814 in mice (KITD814V) or codon 816 in humans (KITD816V) results in altered substrate recognition and constitutive tyrosine autophosphorylation leading to promiscuous signaling. Consequently, cells bearing oncogenic form of KIT (KITD814V) demonstrate ligand independent proliferation in vitro and MPD in vivo. However, the intr

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Wang, Xingdong, Jie Pei, Pengjia Bao, et al. "Identification of Yak’s TLR4 Alternative Spliceosomes and Bioinformatic Analysis of TLR4 Protein Structure and Function." Animals 11, no. 1 (2020): 32. http://dx.doi.org/10.3390/ani11010032.

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In this study, the yak’s TLR4 gene alternative spliceosomes were investigated using PCR amplification and cloning to improve disease-resistance in yak and promote efficient utilization of yak’s resources. qRT-PCR was used to determine the expression levels of two alternatively spliced transcripts of the TLR4 gene in seven distinct tissues. To predict the function of proteins expressed by each TLR4 spliceosome, bioinformatic analysis of yak’s TLR4 protein structure and function was performed, which led to the identification of two alternative spliceosomes of yak’s TLR4 gene. The TLR4-X1 sequenc

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Perduca, Massimiliano, Michele Bovi, Mattia Bertinelli, et al. "High-resolution structures of mutants of residues that affect access to the ligand-binding cavity of human lipocalin-type prostaglandin D synthase." Acta Crystallographica Section D Biological Crystallography 70, no. 8 (2014): 2125–38. http://dx.doi.org/10.1107/s1399004714012462.

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Lipocalin-type prostaglandin D synthase (L-PGDS) catalyzes the isomerization of the 9,11-endoperoxide group of PGH2(prostaglandin H2) to produce PGD2(prostaglandin D2) with 9-hydroxy and 11-keto groups. The product of the reaction, PGD2, is the precursor of several metabolites involved in many regulatory events. L-PGDS, the first member of the important lipocalin family to be recognized as an enzyme, is also able to bind and transport small hydrophobic molecules and was formerly known as β-trace protein, the second most abundant protein in human cerebrospinal fluid. Previous structural work on

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ZECHEL, David L., Shouming HE, Claude DUPONT, and Stephen G. WITHERS. "Identification of Glu-120 as the catalytic nucleophile in Streptomyces lividans endoglucanase CelB." Biochemical Journal 336, no. 1 (1998): 139–45. http://dx.doi.org/10.1042/bj3360139.

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Streptomyces lividans CelB is a family-12 endoglucanase that hydrolyses cellulose with retention of anomeric configuration. A recent X-ray structure of the catalytic domain at 1.75 Å resolution has led to the preliminary assignment of Glu-120 and Glu-203 as the catalytic nucleophile and general acid–base respectively [Sulzenbacher, Shareck, Morosoli, Dupont and Davies (1997) Biochemistry 36, 16032–16039]. The present study confirms the identity of the nucleophile by trapping the glycosyl-enzyme intermediate with the mechanism-based inactivator 2´,4´-dinitrophenyl 2-deoxy-2-fluoro-β-d-cellobios

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Harith-Fadzilah, Nazmi, Mohammad Nihad, Mohammed Ali AlSaleh, et al. "Genome-Wide Identification and Expression Profiling of Glycosidases, Lipases, and Proteases from Invasive Asian Palm Weevil, Rhynchophorus ferrugineus." Insects 16, no. 4 (2025): 421. https://doi.org/10.3390/insects16040421.

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The red palm weevil, Rhynchophorus ferrugineus, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening natural small-molecule inhibitors that specifically target R. ferrugineus proteins critical to its life processes can pave the way for developing novel bioinsecticides. Digestive enzymes (DEs), which impair feeding on plants (herbivory), are promising targets. We generated de novo transcriptomes,

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Cooper, William C., Yi Jin, and Trevor M. Penning. "Elucidation of a Complete Kinetic Mechanism for a Mammalian Hydroxysteroid Dehydrogenase (HSD) and Identification of All Enzyme Forms on the Reaction Coordinate." Journal of Biological Chemistry 282, no. 46 (2007): 33484–93. http://dx.doi.org/10.1074/jbc.m703414200.

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Hydroxysteroid dehydrogenases (HSDs) are essential for the biosynthesis and mechanism of action of all steroid hormones. We report the complete kinetic mechanism of a mammalian HSD using rat 3α-HSD of the aldo-keto reductase superfamily (AKR1C9) with the substrate pairs androstane-3,17-dione and NADPH (reduction) and androsterone and NADP+ (oxidation). Steady-state, transient state kinetics, and kinetic isotope effects reconciled the ordered bi-bi mechanism, which contained 9 enzyme forms and permitted the estimation of 16 kinetic constants. In both reactions, loose association of the NADP(H)

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Purushotham, K. R., Y. Nakagawa, M. G. Humphreys-Beher, N. Maeda, and C. A. Schneyer. "Rat Parotid Gland Acinar Cell Proliferation: Signal Transduction at the Plasma Membrane." Critical Reviews in Oral Biology & Medicine 4, no. 3 (1993): 537–43. http://dx.doi.org/10.1177/10454411930040034001.

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Galactosyltransferase (Gal Tase) is involved in a "receptor-ligand-type" interaction at the cell surface that mediates signal transduction following isoproterenol (ISO) treatment leading to acinar cell proliferation. Evidence is presented herein for the identification of the cell-surface glycoprotein signaling component. Using intact cells or isolated plasma membranes, the EGF-receptor (EGF-R) was specifically radiolabeled with [14C]-Galactose following ISO treatment. Injection of a polyclonal antibody monospecific for rat EGF-R also inhibited proliferation in a dose-dependent manner. The immu

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Diaz-Bárcena, Alba, Luis Fernandez-Pacios, and Patricia Giraldo. "Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L." Biomolecules 14, no. 1 (2023): 2. http://dx.doi.org/10.3390/biom14010002.

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REPI is a pivotal point enzyme in plant benzylisoquinoline alkaloid metabolism as it promotes the evolution of the biosynthetic branch of morphinan alkaloids. Experimental studies of its activity led to the identification of two modules (DRS and DRR) that catalyze two sequential steps of the epimerization of (S)- to (R)-reticuline. Recently, special attention has been paid to its genetic characterization and evolutionary history, but no structural analyses of the REPI protein have been conducted to date. We present here a computational structural characterization of REPI with heme and NADP cof

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Vepuri, S. B., S. Anbazhagan, and Rajendra Prasad Y. "Human Aldose Reductase Inhibition By (2E)-1-(5-bromothiophen-2-yl)-3- (2-bromophenyl)prop-2-en-1-one – Structure Based Lead Identification By Induced Fit Docking (IFD) Study of the Ligand Crystal Structure Conformation." International Journal of Drug Design and Discovery 3, no. 4 (2025): 955–63. https://doi.org/10.37285/ijddd.3.4.10.

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Solid state structure information for (2E)-1-(5-bromothiophen-2-yl)-3-(2-bromophenyl)prop-2-en-1-one is revealed by using single crystal x-ray diffraction study. The conformation of the molecule in solid state is used to carry out the drug design studies like structure optimization by Density Functional Theory (DFT) and Induced Fit Docking (IFD) study on human aldose reductase. Docking experiments were conducted for the crystal structure conformation inside AR active site using Maestro 9.1v. from Schrödinger Suite 2009. GLIDE scoring function was used to calculate the dock score. The co-crysta

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Gómez-Melero, Sara, Fé Isabel García-Maceira, Tania García-Maceira, et al. "Development of a High-Throughput Calcium Mobilization Assay for CCR6 Receptor Coupled to Hydrolase Activity Readout." Biomedicines 10, no. 2 (2022): 422. http://dx.doi.org/10.3390/biomedicines10020422.

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CCR6 is a chemokine receptor highly implicated in inflammatory diseases and could be a potential therapeutic target; however, no therapeutic agents targeting CCR6 have progressed into clinical evaluation. Development of a high-throughput screening assay for CCR6 should facilitate the identification of novel compounds against CCR6. To develop a cell-based assay, RBL-2H3 cells were transfected with plasmids encoding β-hexosaminidase and CCR6. Intracellular calcium mobilization of transfected cells was measured with a fluorescent substrate using the activity of released hexosaminidase as readout

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Chao, Nan, Wen-Ting Jiang, Xue-Chun Wang, Xiang-Ning Jiang, and Ying Gai. "Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants." Tree Physiology 39, no. 12 (2019): 2019–26. http://dx.doi.org/10.1093/treephys/tpz098.

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Abstract Cinnamoyl-coenzyme A reductases (CCRs) have been reported as key enzymes involved in monolignol biosynthesis. In this study, a motif-aware workflow based on a new signature motif effectively distinguished CCRs from CCR-like proteins. The divergence of CCRs and CCR-like sequences in Populus tomentosa Carr, Panicum virgatum L, Oryza sativa L and Selaginella moellendorffii Hieron suggests that NWYCY is not efficient for CCR recognition. The novel motif H202(X)2K205 (CCR-SBM or CCR substrate binding motif) was introduced to distinguish between CCRs and CCR-like proteins. The site-directed

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Zhao, Yi, Eliud Morales Morales Dávila, Xue Li, et al. "Identification of Molecular Determinants in iRhoms1 and 2 That Contribute to the Substrate Selectivity of Stimulated ADAM17." International Journal of Molecular Sciences 23, no. 21 (2022): 12796. http://dx.doi.org/10.3390/ijms232112796.

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The metalloprotease ADAM17 is a key regulator of the TNFα, IL-6R and EGFR signaling pathways. The maturation and function of ADAM17 is controlled by the seven-membrane-spanning proteins iRhoms1 and 2. The functional properties of the ADAM17/iRhom1 and ADAM17/iRhom2 complexes differ, in that stimulated shedding of most ADAM17 substrates tested to date can be supported by iRhom2, whereas iRhom1 can only support stimulated shedding of very few ADAM17 substrates, such as TGFα. The first transmembrane domain (TMD1) of iRhom2 and the sole TMD of ADAM17 are important for the stimulated shedding of AD

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Alves, Krisnna M. A., Fábio José Bonfim Cardoso, Kathia M. Honorio, and Fábio A. de Molfetta. "Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of Leishmania mexicana." Medicinal Chemistry 16, no. 6 (2020): 784–95. http://dx.doi.org/10.2174/1573406415666190712111139.

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Background:: Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. Objective:: The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). Methods: A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular dock

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