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90 results for “Alanine”
Proline and β-alanine influence bumblebee nectar consumption without affecting survival
<p>These files (.txt) contain the dataset used for analyses of bumblebee aminoacid consumption and survival in the article "Proline and β-alanine influence bumblebee nectar consumption without affecting survival" by Bogo G. et al., accepted for publication in Apidologie (2024, xx:xxx-xxx, DOI: xxx).</p>
Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"
<p>Native mass spectrometry dataset used in: <strong>Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants.</strong> Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)</p> <p><strong>Description:</strong></p> <p>Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.</p> <p><strong>Sample processing:</strong></p> <p>AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, <em>Sartorius</em>). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<em>World Precision Instruments</em>). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.</p> <p><strong>Data processing:</strong></p> <p>Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.</p>
Alanine dipeptide in an implicit solvent at 300K
<p>This dataset has been introduced in the article <a href="https://arxiv.org/abs/2208.01893">Midgley, et al.: Flow Annealed Importance Sampling Bootstrap, 2022</a>.</p> <p>It contains samples from the Boltzmann distribution of alanine dipeptide in an implicit solvent, which have been generated with a Replica Exchange Molecular Dynamics (REMD) simulation. The ff96 with an OBC GBSA implicit solvent was used.</p> <p>The REMD uses 21 replicas starting at a temperature of 300K and increasing the temperature by an increment of 50K. The replicas are exchanged every 200 iterations and use the state at each multiple of 1000 time steps as samples. Many of these simulations were in parallel with different seeds. We let the system equilibrate for <span class="math-tex">\(2\times10^5\)</span> iterations and run the simulation subsequently for <span class="math-tex">\(2\times10^6\)</span> iterations.</p> <p>The data is split into a training set, which consists of <span class="math-tex">\(10^6\)</span> samples; a validation set consisting of <span class="math-tex">\(10^6\)</span> samples as well; and a test set with <span class="math-tex">\(10^7\)</span> samples.</p> <p>The data is provided as raw <span class="math-tex">\((x,y,z)\)</span>-coordinates, stored as *.h5 files, and transformed to internal coordinates, stored as *.pt files.</p> <p>More details about the data and how to use it are given in our <a href="https://github.com/lollcat/fab-torch">GitHub repository</a> and <a href="https://arxiv.org/abs/2208.01893">paper</a>.</p>
AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes
<p>Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2 that combines<span> randomized</span> <span><span> </span>alanine<span> </span>sequence masking<span> </span>with shallow multiple sequence alignment<span> </span>subsampling to expand the conformational diversity of the predicted structural<span> </span>ensembles and<span> </span>capture conformational changes between apo and holo protein forms. Using several well-established datasets of<span> </span>structurally diverse apo-holo protein pairs, the proposed approach </span><span>enables<span> </span>robust predictions of apo and holo structures and conformational ensembles, while also displaying notably similar dynamics distributions. These observations are consistent with<span> </span>the view </span><span> </span>that the intrinsic dynamics of allosteric proteins is defined by the structural topology of the fold and favors conserved conformational motions driven by soft modes among orthologs. We also found<span> </span>a significant <span>correlation </span>between conformational flexibility and <span> </span>AlphaFold2 metric of statistical significance pLDDT for the apo-holo pairs in which ligand binding induced local moderate conformational changes. For apo-holo pairs exhibiting larger structural changes, this relationship<span> </span>becomes nonlinear, reflecting inability of AlphaFold2 confidence metrics to identify high energy functional conformations. Our findings support the notion that AlphaFold2 approaches can yield reasonable accuracy in predicting minor conformational adjustments between apo and holo states, especially for proteins with <span> </span>moderate localized changes upon ligand binding. However, for large, hinge-like domain movements, AF2 tends to predict the most stable domain orientation which is typically the apo form rather than the full range of functional conformations characteristic of the holo ensemble. These results indicate that modeling of multiple functional states of proteins may require more accurate detection of flexible region conformations and cannot solely rely on the pLDDT metric as the major determinant of the prediction accuracy in reproducing functional conformational ensembles.<span> </span></p>
Single crystal X-ray diffraction data for Rhizobium radiobacter N-carbamoyl-beta-alanine amidohydrolase
<p>Single crystal X-ray diffraction data for Rhizobium radiobacter N-carbamoyl-beta-alanine amidohydrolase collected from crystals produced as below:</p> <p>Purified recombinant RrCβAA was concentrated to 15 mg/mL using a 10 kDa MWCO centrifugal concentrator (Vivaspin) and subjected to sitting drop vapor diffusion crystallization screening with commercial screens from Molecular Dimensions and Hampton Research. Drops of 100 nL protein plus 100 nL well solution were set up against wells containing 70 L of crystallisation solutions. After two weeks crystals were found in xxx condition. An optimisation screen based on this condition was set up in 24 well plates by varying the PEG1500 concentration and MMT buffer pH. Drops of 1 μL protein and 1 μL well solution were set up on plastic cover slips over wells containing 1 ml crystallisation solution. Crystals grew in a well solution containing 23 % (w/v) PEG1500 and 100 mM MMT pH 6.0. Crystals were harvested with a LithoLoop (Molecular Dimensions Limited) and transferred to a cryoprotection solution of well solution supplemented with 50 % PEG400. Cryoprotected crystals were flash cooled in liquid nitrogen. </p>
Comparison of heterologous β-alanine-responsive biosensors in Escherichia coli
<p>This dataset contains the raw data that lie at the basis of the results discussed in <strong>Chapter 6: Comparison of heterologous β-alanine-responsive biosensors in <em>Escherichia coli</em> </strong>of the PhD thesis of Amber Bernauw. The README.txt file provides more information on the different data files.</p>
Input files and data for path generation of alanine dipeptide isomerization in virtual reality
<p>The input files and resulting data for the accelerated sampling of the isomerization of alanine dipeptide used in the thesis:</p> <p>"Accelerated Sampling Methods for High Dimensional Molecular Systems", Mike O'Connor, University of Bristol. </p> <p> </p> <p> </p>
Unbiased simulation of Alanine Dipeptide in gas phase
<p>87 microsecond long unbiased Molecular Dynamics (MD) trajectory of alanine dipeptide in gas phase (traj_comp.xtc). Temperature = 300 K. Force Field: AMBER99SB-ILDN. There are 30+ back and forth transitions between the C_7eq and the C_7ax state. Simulations were performed using GROMACS 2021.4. The .tpr file is provided for reproduction. Details of the simulation parameters are accessible from the md.log file. The phi and psi torsion angles and the internal energy is printed in the COLVAR file at 2 ps interval. </p> <p>Alanine dipeptide is often used as a model system to test new simulation methods. We hope that sharing our long unbiased trajectory will help other research groups to compare the accuracy of the results obtained from new methods. </p> <p>This trajectory was generated as a part of our recent publication below. Please cite the following paper when using this trajectory: </p> <p>1. Ray, Dhiman, Narjes Ansari, Valerio Rizzi, Michele Invernizzi, and Michele Parrinello. "Rare event kinetics from adaptive bias enhanced sampling." Journal of Chemical Theory and Computation (2022). https://doi.org/10.1021/acs.jctc.2c00806 </p>
Behavior and brain size of larval zebrafish exposed to environmentally relevant concentrations of betamethylamino- L-alanine (BMAA)
<p>Harmful algal blooms (HABs) release toxic compounds in water and are increasing in frequency worldwide. The neurotoxin β-methylamino-L-alanine (BMAA) is released by HABs and has garnered much attention over the past twenty years due to its association with human neurodegenerative disorders, but its effects on wildlife are still largely unknown. This study characterized the effects of chronic exposure to environmentally relevant concentrations of BMAA on the behavior and brain size of developing zebrafish (<em>Danio</em> <em>rerio</em>). Zebrafish were continuously exposed to 0, 1, 10, or 100 μg/L waterborne BMAA between 0- and 5-days post-fertilization (dpf) before the onset of exogenous feeding. At 5 dpf, locomotion and responses to vibrational and visual stimuli were assessed. Following behavioral testing, larvae body and brain size were measured. Survival between 0 and 5 dpf did not differ between treatments. Moreover, BMAA exposure did not affect thigmotaxis, startle response magnitude, habituation to repeated presentation of vibrational startling stimuli, or relative brain size. A moderate increase in overall activity was observed in larvae exposed to 10 ug/L BMAA under light, but this effect was not seen in dark conditions, indicating that visual processing may have been affected by chronic BMAA exposure. Thus, our results show that passive continuous exposure to environmentally relevant concentrations of BMAA prior to first feeding in zebrafish does not affect overall brain development, locomotion, anxiety, and motor neuron-mediated reflexes, but suggest targeted neurotoxicity within the visual system.</p>
Effects of β-alanine and Sodium Bicarbonate Supplementation on Physical Capacity and Biochemical Markers Concentrations
ClinicalTrials.gov study NCT07092930. IPD Sharing: YES. Countries: 1. Publications: 2.
Brivanib Alaninate in Treating Patients With Persistent or Recurrent Cervical Cancer
ClinicalTrials.gov study NCT01267253. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Behavior and brain size of larval zebrafish exposed to environmentally relevant concentrations of betamethylamino- L-alanine (BMAA)
Open the record for dataset details and reuse information.
The effects of dietary proline, β-alanine, and γ-aminobutyric acid (GABA) on the nest construction behavior in the Oriental hornet
<p>Dataset for "The effects of dietary proline, β-alanine, and γ-aminobutyric acid (GABA) on the nest construction behavior in the Oriental hornet "</p>
Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins"
<p>Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins"</p> <p>The README files contain a description of all files and scripts in this repo.</p>
Datasets: Absorbed-dose-to-water measurement using alanine in ultra-high-pulse-dose-rate electron beams
<p>Open access datasets for:</p> <p>Absorbed-dose-to-water measurement using alanine in ultra-high-pulse-dose-rate electron beams</p> <p>doi: 10.1088/1361-6560/ac950b</p>
Efficacy, Safety and Tolerability of Telbivudine in HBeAg Positive Chronic Hepatitis B Pregnant Women With Elevated Alanine Aminotransferase Levels
ClinicalTrials.gov study NCT01337791. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effects of Alanine in Patients With Nonalcoholic Steatohepatitis
ClinicalTrials.gov study NCT00586885. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Measurement of Alanine Aminotransaminase (ALT) Following Initiation of Antidiabetic Agents in Patients With Type 2 Diabetes in a Real-world Clinical Setting: a Retrospective Cohort Study
ClinicalTrials.gov study NCT03233178. IPD Sharing: NO. Countries: 1. Publications: 1.
The Efficacy β-Alanine Supplementation in Performance Outcomes of Road Professional Endurance Cyclists
ClinicalTrials.gov study NCT04427319. IPD Sharing: NO. Countries: 1. Publications: 1.
Acute Supplementation With Beta-Alanine Improves Performance in Aerobic-anaerobic Transition Zones in Endurance Athletes
ClinicalTrials.gov study NCT05096793. IPD Sharing: NO. Countries: 1. Publications: 28.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.