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1,744 results for “peptide”
Genetic and transcriptomic datasets characterizing gene drive mosquitoes expressing antimicrobial peptides that retard Plasmodium sporogonic development
<p><span>Gene drives hold promise for the genetic control of malaria vectors. The development of vector population modification strategies hinges on the availability of effector mechanisms impeding parasite development in transgenic mosquitoes. We augmented a midgut gene of the malaria mosquito <em>Anopheles gambiae</em> to secrete two exogenous antimicrobial peptides, Magainin 2 and Melittin. This small genetic modification, capable of efficient non-autonomous gene</span> drive, hampers oocyst development in both <em>Plasmodium falciparum</em> and <em>Plasmodium berghei</em>. It delays the release of infectious sporozoites while it simultaneously reduces the lifespan <span>of homozygous female transgenic mosquitoes. Modeling the spread of this modification using a large-scale agent-based model of malaria epidemiology reveals that it can break the cycle of disease transmission across a range of transmission intensities.</span></p>
Cytosolic peptides encoding CaV1 C-termini downregulate the calcium channel activity-neuritogenesis coupling
<p><span>L-type Ca<sup>2+</sup> (Ca<sub>V</sub>1) channels transduce channel activities into nuclear signals critical to neuritogenesis. Also, standalone peptides encoded by </span><span><span>Ca<sub>V</sub>1</span> DCT (distal carboxyl-terminus) act as nuclear transcription factors reportedly promoting neuritogenesis. Here, by focusing on exemplary </span><span><span>Ca<sub>V</sub>1</span>.3 and cortical neurons under basal conditions, we discover that cytosolic DCT peptides downregulate neurite outgrowth by the interactions with </span><span><span>Ca<sub>V</sub>1</span>'s apo-calmodulin binding motif. Distinct from nuclear DCT, various cytosolic peptides exert a gradient of inhibitory effects on </span><span>Ca<sup>2+</sup></span><span> influx via CaV1 channels and neurite extension and arborization, and also the intermediate events including CREB activation and c-Fos expression. The inhibition efficacies of DCT are quantitatively correlated with its binding affinities. Meanwhile, c</span><span>ytosolic inhibition tends to facilitate neuritogenesis indirectly by favoring </span><span>Ca<sup>2+</sup>-sensitive nuclear retention of DCT. In summary, DCT peptides as a class of </span><span><span>Ca<sub>V</sub>1</span> inhibitors specifically regulate the channel activity-neuritogenesis coupling in a variant-, affinity-, and localization-dependent manner.</span></p>
Peptide flip coordinates for qFit 2 paper
<p>Peptide flip coordinates for qFit 2 paper (https://doi.org/10.1371/journal.pcbi.1004507)</p>
Interaction of the inhibitory peptides ShK and HmK with the voltage-gated potassium channel KV1.3: Role of conformational dynamics
<p><strong>ABSTRACT: </strong>Peptide toxins that adopt the ShK fold can inhibit the voltage-gated potassium channel K<sub>V</sub>1.3 with IC<sub>50</sub> values in the pM range, and are therefore potential leads for drugs targeting autoimmune and neuroinflammatory diseases. NMR relaxation measurements and pressure-dependent NMR have shown that, despite being cross-linked by disulfide bonds, ShK itself is flexible in solution. This flexibility affects the local structure around the pharmacophore for K<sub>V</sub>1.3 channel blockade and, in particular, the relative orientation of the key Lys and Tyr side chains (Lys22 and Tyr23 in ShK), and has implications for the design of K<sub>V</sub>1.3 inhibitors. In this study, we have performed molecular dynamics (MD) simulations on ShK and a close homolog, HmK, in order to probe the conformational space occupied by the Lys and Tyr residues, and docked the different conformations with a recently determined cryo-EM structure of the K<sub>V</sub>1.3 channel. Although ShK and HmK have 60% sequence identity, their dynamic behaviors are quite different, with ShK sampling a broad range of conformations over the course of a 5 μs MD simulation, while HmK is relatively rigid. We also investigated the importance of conformational dynamics, in particular the distance between the side chains of the key dyad Lys22 and Tyr23, for binding to K<sub>V</sub>1.3. Although these peptides have quite different dynamics, the dyad in both adopts a similar configuration upon binding, revealing a conformational selection upon binding to K<sub>V</sub>1.3 in the case of ShK. Intriguingly, the more flexible peptide, ShK, binds with nearly 300-fold higher affinity than HmK.</p>
DESIGN, SYNTHESIS AND STUDY OF BIOLOGICAL ACTIVITY OF PEPTIDES WITH NEUROPROTECTIVE PROPERTIES
<p>The main purpose of this project is to search for novel compounds that will protect neurons against oxidative stress (6-hydroxydopamine, 6-OHDA) and glucocorticoids (corticosterone, CORT) in a human neuroblastoma cell line (SH-SY5Y) and elucidate the mechanism by which attenuated the physiological changes induced by these neurotoxins. We will explore whether this protective role of tested compounds will be involved also in the regulation of apoptosis, maintaining oxidoreductive balance, and stabilization of mitochondrial membrane potential. Furthermore, the involvement of the BDNF/TrkB-ERK-CREB/mTOR signalling pathway in neuronal survival will be examined.</p>
Fig. 1 in Antimicrobial activity of the crude peptide extracts from Blackfin sea catfish Arius jella Day, 1877
Fig. 1 — Photograph of experimental species Arius jella
Supplementary material of "The A1/A2 β-casein genotype of cows, but not their horn status, influences peptide generation during simulated digestion of milk"
<p>Supplementary tables and figures of the research article "The A1/A2 β-casein genotype of cows, but not their horn status, influences peptide generation during simulated digestion of milk"</p>
Reactions of cold argon plasma with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation - ESI
<p>ESI data for the paper 'Reactions of cold argon plasma with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation'.</p>
HLApollo: Towards designing improved cancer immunotherapy targets with a superior peptide-MHC-I presentation model
<p><strong>Based on the success of cancer immunotherapy, personalized cancer vaccines have recently emerged as the vanguard of oncology treatment. Because antigen presentation on MHC class I (MHC-I) is key to the adaptive immune response to cancerous cells, it is critical to have highly predictive computational methods to model which peptides are presented on MHC-I. Here, we introduce HLApollo, a transformer-based model with end-to-end treatment of MHC-I sequence, deconvolution of multi-allelic data, and ligand-flanking sequences. We develop negative-set switching, a novel training strategy that greatly reduces overfitting, which is key to HLApollo’s performance, leading to increases of 20.19% and 4.1% in average precision (AP) vs. next best model on MHC-I presentation and immunogenicity, respectively. Incorporating protein features derived from protein language models yielded further gains and reduced the need for gene expression measurements. We achieve excellent pan-allelic generalization, and create a framework for estimating performance on untrained alleles. This guides the clinical use of HLApollo, where rare alleles may be observed – particularly for individuals from underrepresented ancestries. Our work uses all facets of available MHC-I data to develop a highly accurate MHC-I presentation predictor that meaningfully improves immunogenicity prediction and allelic coverage, important for clinical applications of personalized neoantigen vaccines.</strong></p>
Screen of A6 TCR against a library of HLA-A*02:01 MHC-I peptides from the human exome
<p>T2 cells expressing a library of off targets (derived from A6 and B7 binding motifs in Hausmann 1999) are co-cultured with A6, DMF5 or 1G4 expressing T cells (from a non-A2 donor) and minigenes from surviving cells are amplified.</p>
Screen of Pr20 TCR mimic antibody against a library of HLA-A*02:01 MHC-I peptides
<p>Minigene sequencing of T2 cells sorted for high and low binding to the TCR mimic antibody "Pr20."</p>
Screen of A6 and B7 TCR against a library of HLA-A*02:01 MHC-I peptides from the human exome
<p>T2 cells expressing a library of off targets (derived from A6 and B7 binding motifs in Hausmann 1999) are co-cultured with A6, B7. DMF5 or 1G4 expressing T cells (from a non-A2 donor) and minigenes from surviving cells are amplified.</p>
ROS-Specific Huntingtin Interactions: Peptide poly ADP ribose overlay assay
<p>In vitro testing of peptides representing potential poly ADP ribose binding motifs within the huntingtin sequence.</p>
Research data supporting "Residue-Specific Solvation Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection"
<p>Experimental research raw data supporting the publication by Lin, Y. et al, 2019, "Residue-Specific Solvation Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection", ACS Nano. DOI: 10.1021/acsnano.8b08117.</p> <p>Molecular simulation data is available upon reasonable request from irene.yarovsky@rmit.edu.au.</p>
Raw diffraction images of prokaryotic peptide transporter PepTSo2
<p>Diffraction images of prokaryotic peptide transporter PepTSo2. In Nagamura et al. (<a href="https://doi.org/10.1107/S2053230X19003546">Acta Cryst. F, 2019</a>), the crystal form A (PDB code: <a href="http://www.rcsb.org/structure/6JKD">6JKD</a>, space group I4, 3.9 Å resolution) and the form B (PDB code: <a href="http://www.rcsb.org/structure/6JKC">6JKC</a>, space group P42<sub>1</sub>2, 3.5 Å resolution) were reported.</p> <p>Small-wedge (5 or 10°/crystal) datasets collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8.</p> <p>PepT-So2_171220_BL32XU_{1..4}.tar.xz contains directories 01, 07-1, 07-2, 09, 10, 11. PepT-So2_180215_BL32XU.tar.xz contains directories 01, 02, 03, 04, 05, 14. Different directories are from different crystallization conditions. It seems they have different space groups even though they may share the same reduced cells. In the literature for form A data (I4, a=b=115, c=110 Å) from 07-2 and 11 of 171220_BL32XU were used while for form B data (P42<sub>1</sub>2, a=b=119, c=104.3 Å) from 04 and 05 of 180215_BL32XU were used.<br> <br> Note that master.h5 files were modified; see <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</a>.</p>
Dataset CMKLR1-targeting peptide tracers for PET/MR imaging of breast cancer
<p>Dataset for the menuscript CMKLR1-targeting peptide tracers for PET/MR imaging of breast cancer</p>
NGS data produced in 'Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide-coding libraries'; Nature Communications (2019)
<p>Sharma, G et al. Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide-coding libraries. <em>Nature Communications</em>. Accepted (August 2019)</p> <p><strong>Abstract:</strong></p> <p>Cytotoxic CD8+ T-cells recognize and eliminate infected or malignant cells that present, at their cell surfaces, short peptide epitopes derived from intracellularly processed antigens. However, broadly searching for specific major histocompatibility complex (MHC)-bound peptide epitopes that are naturally processed and capable of eliciting a functional T-cell response has been challenging. Here, we report a method for deep and unbiased T-cell epitope profiling, which is done by using <em>in vitro</em> co-culture of CD8+ T-cells and target cells transduced with high-complexity epitope-encoding minigene libraries. Target cells that are subject to cytotoxic attack from T-cells in co-culture are isolated, before they are lost to apoptosis, by fluorescence-activated cell sorting and characterized by sequencing the minigenes encoded within. In the present study, we validate this highly parallelized method using known murine T-cell receptor/peptide-MHC pairs and diverse minigene-encoded epitope libraries to identify naturally processed and MHC-presented peptide epitopes unambiguously and with high sensitivity.</p>
ROS-Specific Huntingtin Interactions: PAR overlay assay with PBM3 peptide mutant
<p>Poly-ADP ribose overlay assay with huntingtin PBM peptides to test ability of a PBM3 alanine mutant to bind poly-ADP ribose.</p>
Bioprospecting for bioactive peptide production by lactic acid bacteria isolated from fermented dairy food
<p>Table S1 of the review article "Bioprospecting for bioactive peptide production by lactic acid bacteria isolated from fermented dairy food"</p> <p>by Davide Tagliazucchi, Serena Martini and Lisa Solieri</p>
ROS-Specific Huntingtin Interactions: Competition of huntingtin PAR binding by PBM3 peptide
<p>Attempts to use the PBM3 peptide in a competition assay to measure the on-off rates of huntingtin PAR binding.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.