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1,204 results for “Enzyme”
Deep sequencing datasets from: Witnessing the structural evolution of an RNA enzyme
<p>An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.</p> <p> </p>
Comprehensive Chromatome Profiling Reveals Hundreds of Metabolic Enzymes in the Nucleus
<p>Data behind figures for <span>Comprehensive Chromatome Profiling Reveals </span><span>Hundreds of</span><span> Metabolic Enzymes in the Nucleus </span>paper</p>
EvoMining genomic and enzyme databases for Actinobacteria, Cyanobacteria, Pseudomonas and Archaea
<p>Databases for EvoMining 2.0</p> <p>Genomic DB is a collection of genomes of a certain taxonomical group, functionally annotated by RAST.</p> <p>Enzyme-DB</p> <p>Actinobacteria</p> <p>Cyanobacteria</p> <p>Pseudomonas</p> <p>Archaea</p> <p>SampleData</p>
Dataset for Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria
<p>Dataset includes: </p> <p>1. Analysed source data for figures</p> <p>2. Raw time-lapse images and tracking data that were used to generate the analysis</p>
Imprint of tree species mycorrhizal association on microbial-mediated enzyme activity and stoichiometry
<p>1. Understanding the effects of tree species and their mycorrhizal association on soil processes is critical for predicting the ecosystem consequences of species shifts owing to global change and forest management decisions. While it is well established that forests dominated by different mycorrhizal types can vary in how they cycle carbon (C), nitrogen (N) and phosphorus (P), the degree to which these patterns are driven by microbial-mediated enzyme activity (EA) and ecoenzymatic stoichiometry (ES) remain elusive.</p> <p>2. Here, we synthesized the effects of mycorrhizal association on seven soil enzymes involved in microbial C, N and P acquisition and ES using data from 56 peer-reviewed papers.</p> <p>3. We found that relative to soil in ectomycorrhizal (EcM) trees, soil in arbuscular mycorrhizal (AM) trees exhibited greater activity of some C acquisition enzymes (e.g., beta-glucosidase; BG) and higher ecoenzymatic ratios of BG/NAG (N-acetyl-glucosaminidase) and BG/AP (acid phosphatase). These results supported that AM trees had rapid C and nutrient turnover rates, inorganic nutrient economics and high soil microbial C limitation. We also found evidence for an organic nutrient economy and greater soil microbial demand for nutrients in EcM trees compared to AM trees. In addition, the effect of mycorrhizal association on the activity of certain soil enzymes and enzymatic stoichiometry (i.e., BG and BG/NAG ratio) appeared to be associated with the differences in soil pH, phylogenetic group (i.e., conifers and broadleaves) and leaf habit (i.e., evergreen and deciduous) between AM and EcM trees.</p> <p>4. The results from the global meta-analysis suggested that soil EA and ES appear to play critical roles in shaping the differences in the nutrient economy between AM and EcM tree species, but leaf morphology and soil conditions should be considered in evaluations of soil processes in forests of different mycorrhizal associations. Given that most of the studies in the database were from the temperate and subtropical regions, further research in other biomes is needed to elucidate the underlying mechanisms driving the mycorrhizal effect at the global scale. </p>
Datasets for Application of particle swarm optimization to understand the mechanism of action of allosteric inhibitors of the enzyme HSD17ß13
<p>Datasets used in the publication '</p> <p>Application of particle swarm optimization to understand the</p> <p>mechanism of action of allosteric inhibitors of the enzyme HSD17ß13'</p>
Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
<p>Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)</p>
Data Set "Protein network centralities as descriptor for QM region construction in QM/MM simulations of enzymes"
<p>This data set accompanies the publication "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis" by Felix Brandt and Christoph R. Jacob (TU Braunschweig, Germany) </p> <p>It contains:</p> <p>- PDB files of the starting structures</p> <p>- modified AMBER95 force field file</p> <p>- AMS fragment files for the substrates and ions</p> <p>- AMS input files for all geometry optimizations and single point calculations</p> <p>- Python script for WISP and centrality analysis</p>
Information regarding the particulate methane monooxygenase enzyme of known methanotrophs
<p>A collection of information with regard to the particulate methane monooxygenase (pmmo) enzyme of known methanotrophs which was extracted from NCBI is published in this database. </p>
Slow soil enzyme recovery following invasive tree removal through gradual changes in bacterial and fungal communities
<p><span>Biological invasions of plants have profound effects on ecosystem functioning by directly and indirectly altering soil microbiota, especially when invasive plants co-invade with their associated microbiomes. Ecosystem functions may recover slowly following invader removal, with implications for restoration. </span></p> <p><span>We investigated the recovery of soil ecosystem function (measured as soil enzymes) following the removal, at different densities and times, of invasive <em>Pinus</em> spp. in New Zealand, and how different enzymatic activities responded to pine legacies. </span></p> <p><span>Enzymatic activities were driven by pine legacies via both abiotic (soil nutrients) and biotic (fungi and bacteria) soil properties, with different enzymes showing distinct patterns. The activity of the enzymes cellobiohydrolase (cellulose degrading), β-glucosidase (cellulose degrading), N-acetyl-glucosaminidase (chitin degrading), laccase (lignin oxidising) and acid phosphatase (organic phosphate hydrolysing) were influenced by time since pine removal and by pine density at removal via effects on biotic communities. In comparison, Mn-peroxidase (lignin oxidising) was positively correlated with density of pines at removal and was negatively correlated with time since removal and was only influenced by fungal communities. </span></p> <p><em><span>Synthesis</span></em><span>. The recovery of soil enzymatic function following invasive species removal is slow, and dependent on pine legacies through the gradual changes in fungal and bacterial communities. The cascading effects of these changes suggest potential implications for the success of future plant establishment and restoration of co-invaded ecosystems.</span></p>
Understanding Activity-Stability Tradeoffs in Biocatalysts by Enzyme Proximity Sequencing
<p>Data and scripts of the manuscript "<strong>Understanding Activity-Stability Tradeoffs in Biocatalysts by Enzyme Proximity Sequencing</strong>" by Rosario Vanella, Christoph Küng, Alexandre A. Schoepfer, Vanni Doffini, Jin Ren and Michael A. Nash.</p>
A Study of Eliglustat Tartrate (Genz-112638) in Patients With Gaucher Disease Who Have Reached Therapeutic Goals With Enzyme Replacement Therapy (ENCORE)
ClinicalTrials.gov study NCT00943111. IPD Sharing: Not stated. Countries: 12. Publications: 7.
A Multicenter Open-Label Treatment Protocol to Observe the Safety of Replagal (Agalsidase Alfa) Enzyme Replacement Therapy in Canadian Patients With Fabry Disease
ClinicalTrials.gov study NCT01298141. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pancreatic Enzyme Supplementation for Celiac Disease
ClinicalTrials.gov study NCT02475369. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Study to Compare the Efficacy and Safety of Oral AT1001 and Enzyme Replacement Therapy in Patients With Fabry Disease
ClinicalTrials.gov study NCT01218659. IPD Sharing: Not stated. Countries: 10. Publications: 6.
A Phase 3 Study of UX003 Recombinant Human Betaglucuronidase (rhGUS) Enzyme Replacement Therapy in Patients With Mucopolysaccharidosis Type 7 (MPS 7)
ClinicalTrials.gov study NCT02230566. IPD Sharing: Not stated. Countries: 1. Publications: 5.
An Open-Label Phase 1/2 Study to Assess the Safety, Efficacy and Dose of Study Drug UX003 Recombinant Human Beta-glucuronidase (rhGUS) Enzyme Replacement Therapy in Patients With Mucopolysaccharidosis
ClinicalTrials.gov study NCT01856218. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Angiotensin Converting Enzyme (ACE) Inhibition and Cardiac Allograft Vasculopathy
ClinicalTrials.gov study NCT01078363. IPD Sharing: Not stated. Countries: 1. Publications: 3.
A Study to Describe the Experience of Both Patients and Their Clinicians in the Treatment of Fabry Disease With Enzyme Replacement Therapy.
ClinicalTrials.gov study NCT04281537. IPD Sharing: Not stated. Countries: 5. Publications: 1.
Recombinant Human Angiotensin-converting Enzyme 2 (rhACE2) as a Treatment for Patients With COVID-19
ClinicalTrials.gov study NCT04335136. IPD Sharing: Not stated. Countries: 5. Publications: 2.
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