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110 results for “Hydroxylase”
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 dimer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation starting from 21 dimer conformations simulation</p> <p>Simulation setup files are also included in each folder.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Molecular dynamics simulation data of regulatory ACT domain monomer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 monomer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from monomer with bound Phe ligand</p> <p><strong>monomer_only.zip</strong>: simulation starting from 21 monomer conformations simulation</p> <p>Simulation setup files are also included in each folder. Adaptive sampling data are also included in <strong>monomer </strong>and <strong>binding</strong> simulations.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
All-atom molecular dynamics simulations of phenylalanine-4-hydroxylase (PAH) tetramer to investigate the impact of two novel heterozygous mutations, p.Y198N and p.Y204F, observed in a classical phenylketonuria patient
<p>Phenylalanine-4-hydroxylase (PAH) tetramer system (Robetta modelling to complete the structure with template PDB ID: 6hyc) with parametrised BH<sub>4</sub> ligand (parameters are available in the dataset) and Fe(II) metal ions in a TIP3P water box ionised with 0.15 M KCl were presented as wild-type and carrying two novel mutations as Y198N on dimeric chains A and B, and Y204F on dimeric chains C and D. In addition, E353 and E422 are protonated as predicted by PROPKA. BH<sub>4</sub> molecule parametrization was performed by using GAFF, Antechamber and “amb2chm_par.py” program of Amber2018.</p> <p>5,000-step minimization and 1 ns equilibration were performed by fixing the protein to relax the system. Then, another 5,000-step minimization and 1 ns equilibration were performed without any constraints, except the SHAKE algorithm on water molecules, to relax the protein and system. The production simulations were performed along 100 ns trajectory at 310 K collected under NpT ensemble.</p> <p>All system preparation and simulation details for this dataset is available with the related background, results and conclusions in the following article:</p> <p>Tolga Aslan, Aslı Yenenler-Kutlu, Umut Gerlevik, Ayşe Çiğdem Aktuğlu Zeybek, Ertuğrul Kıykım, Osman Uğur Sezerman & Necla Birgul Iyison (2021) Identifying and elucidating the roles of Y198N and Y204F mutations in the PAH enzyme through molecular dynamic simulations, Journal of Biomolecular Structure and Dynamics, DOI: <a href="https://doi.org/10.1080/07391102.2021.1921619">10.1080/07391102.2021.1921619</a></p>
Fig. 2 in Tyrosine hydroxylase, a potential target for the RNAi-mediated management of diamondback moth (Lepidoptera: Plutellidae)
Fig. 2. Larval feeding rate in treatments with various concentrations of dsRNA. Here, T1, T2, and T3 are 3 concentrations of TH dsRNA. The initial leaf disc area was 19.16 cm2.
Fig. 1 in Tyrosine hydroxylase, a potential target for the RNAi-mediated management of diamondback moth (Lepidoptera: Plutellidae)
Fig. 1. Extent of TH silencing in the larvae treated with various concentrations of dsRNA. The expression levels of TH were analyzed on the 3rd day of feeding on various concentrations of cognate TH dsRNA and 3.12 μg/cm2 non-target DREB1A (control) dsRNA. Error bars indicate the standard error of the mean of 3 replicates.
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (dimer only)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper:</p> <p>Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Data from: HIF prolyl hydroxylase 2/3 deletion disrupts astrocytic integrity and exacerbates neuroinflammation
<p><span>Astrocytes constitute the parenchymal border of the blood-brain barrier (BBB), modulate the exchange of soluble and cellular elements, and are essential for neuronal metabolic support. Thus, astrocytes critically influence neuronal network integrity. In hypoxia, astrocytes upregulate a transcriptional program that has been shown to boost neuroprotection in several models of neurological diseases. We investigated transgenic mice with astrocyte-specific activation of the hypoxia-response program by deleting the oxygen sensors, HIF prolyl-hydroxylase domains 2 and 3 (Phd2/3). We induced Phd2/3 deletion in experimental autoimmune encephalomyelitis (EAE) in a therapeutic approach that led to an exacerbation of the disease mediated by massive immune cell infiltration. We found that Phd2/3-ko astrocytes, though expressing a neuroprotective signature, exhibited a gradual loss of gap-junctional Connexin-43 (Cx43), which was induced by vascular endothelial growth factor-alpha (Vegf-a) expression. These results provide mechanistic insights into astrocyte biology, their critical role in hypoxic states, and in chronic inflammatory CNS diseases.</span></p>
Anemia Studies in Chronic Kidney Disease: Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor Daprodustat-Non-Dialysis (ASCEND-ND)
ClinicalTrials.gov study NCT02876835. IPD Sharing: YES. Countries: 39. Publications: 5.
Anemia Studies in Chronic Kidney Disease (CKD): Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor (PHI) Daprodustat-in Incident Dialysis (ASCEND-ID)
ClinicalTrials.gov study NCT03029208. IPD Sharing: YES. Countries: 15. Publications: 2.
Anemia Studies in CKD: Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor (PHI) Daprodustat- Iron (ASCEND: Fe)
ClinicalTrials.gov study NCT03457701. IPD Sharing: YES. Countries: 1. Publications: 1.
Anemia Study in Chronic Kidney Disease (CKD): Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor (PHI) Daprodustat-Blood Pressure (ASCEND-BP)
ClinicalTrials.gov study NCT03029247. IPD Sharing: YES. Countries: 1. Publications: 1.
Anemia Studies in Chronic Kidney Disease (CKD): Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor (PHI) Daprodustat-Three-times Weekly Dosing in Dialysis (ASCEND-TD)
ClinicalTrials.gov study NCT03400033. IPD Sharing: YES. Countries: 13. Publications: 2.
A Phase 1 Positron Emission Tomography Study to Measure Cholesterol 24S-Hydroxylase Target Occupancy of TAK-935
ClinicalTrials.gov study NCT02497235. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Anemia Studies in Chronic Kidney Disease: Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor Daprodustat-Dialysis (ASCEND-D)
ClinicalTrials.gov study NCT02879305. IPD Sharing: Not stated. Countries: 35. Publications: 6.
Anemia Study in Chronic Kidney Disease (CKD) : Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor (PHI) Daprodustat -Forearm Blood Flow (ASCEND-FBF)
ClinicalTrials.gov study NCT03446612. IPD Sharing: YES. Countries: 1. Publications: 1.
Anemia Studies in Chronic Kidney Disease (CKD): Erythropoiesis Via a Novel Prolyl Hydroxylase Inhibitor (PHI) Daprodustat in Non-Dialysis Subjects Evaluating Hemoglobin (Hgb) and Quality of Life (ASCE
ClinicalTrials.gov study NCT03409107. IPD Sharing: YES. Countries: 14. Publications: 2.
Data from: HIF prolyl hydroxylase 2/3 deletion disrupts astrocytic integrity and exacerbates neuroinflammation
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Inhibition of firefly luciferase activity by a HIF prolyl hydroxylase inhibitor
<p>The three hypoxia-inducible factor (HIF) prolyl-4-hydroxylase domain (PHD) 1–3 enzymes confer oxygen sen-sitivity to the HIF pathway and are novel therapeutic targets for treatment of renal anemia. Inhibition of thePHDs may further be beneficial in other hypoxia-associated diseases, including ischemia and chronic in-flammation. Several pharmacologic PHD inhibitors (PHIs) are available, but our understanding of their selectivity and its chemical basis is limited.We here report that the PHI JNJ-42041935 (JNJ-1935) is structurally similar to the firefly luciferase substrate D-luciferin. Our results demonstrate that JNJ-1935 is a novel inhibitor of firefly luciferase enzymatic activity. In contrast, the PHIs FG-4592 (roxadustat) and FG-2216 (ICA,BIQ,IOX3,YM311) did not affect firefly luciferase. The JNJ-1935 mode of inhibition is competitive with a Ki of 1.36 μM. D-luciferin did not inhibit the PHDs, despite its structural similarity to JNJ-1935. This study provides insights into a previously unknown JNJ-1935 off-target effect as well as into the chemical requirements for firefly luciferase and PHD inhibitors and may inform the development of novel compounds targeting these enzymes.</p>
Supplementary data for "Analysis of Non-21α-hydroxylase-deficiency Primary Adrenal Insufficiency in Childhood: Data from 113 Chinese Patients"
<p>Supplementary data for "Analysis of Non-21α-hydroxylase-deficiency Primary Adrenal Insufficiency in Childhood: Data from 113 Chinese Patients"</p> <p><strong>Supplementary Table 1 </strong>Causes of Primary Adrenal Insufficiency in Children</p> <p><strong>Supplementary Table 2</strong> Mutations Detected in Subjects with non-21-OHD CAH Inherited Causes of Childhood-Onset Primary Adrenal Insufficiency</p> <p><strong>Supplementary Table 3 </strong>Clinical findings in Subjects with Non-21-OHD Inherited Causes of Childhood-Onset Primary Adrenal Insufficiency</p> <p><strong>Supplementary Table 4 </strong>Population Frequencies of Common Variants in <em>STAR</em> or <em>MC2R</em></p>
Enantioselective Hydroxylation of Benzylic C(sp3)–H Bonds by an Artificial Iron Hydroxylase Based on the Biotin–Streptavidin Technology
<p>Data underlying the figures in the publication “Enantioselective Hydroxylation of Benzylic C(sp<sup>3</sup>)–H Bonds by an Artificial Iron Hydroxylase Based on the Biotin–Streptavidin Technology”, published in <em>J. Am. Chem. Soc.,</em> <strong>2020</strong>, 142, 24, 10617–10623.</p> <p><a href="https://pubs.acs.org/doi/10.1021/jacs.0c02788">https://pubs.acs.org/doi/10.1021/jacs.0c02788</a></p> <p>Table of contents:</p> <p><strong>1. Dataset</strong>; Excel file containing the numerical data for <em>Scheme 3b)</em> and <em>3c).</em></p> <p> </p> <p> </p>
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