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68 results for “capsid”
Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery
<p>Datasets for "Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery", Eid et al., <em>Nature Communications. </em></p>
HDX-MS dataset for: "Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility"
<p>Hydrogen/deuterium exchange mass spectrometry dataset used in: <strong>Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility.</strong> Yuzhen Feng*, Dominik van Bodegraven*, Alan Kádek*, Ignacio L.B. Munguira, Laura Soria-Martinez, Sarah Nentwich, Sreedeepa Saha, Florian Chardon, Daniel Kavan, Charlotte Uetrecht#, Mario Schelhaas#, Wouter H. Roos#. <em>Nature Communications</em> 10076 (2024). doi: 10.1038/s41467-024-54373-0</p> <p>* - authors contributing equally</p> <p># - corresponding authors</p> <p><strong>Description:</strong></p> <p>Hydrogen/deuterium exchange mass spectrometry (HXMS) analysis of the effect of heparin on the conformational dynamics of human papillomavirus 16 pseudovirus (PsV).</p> <p><strong>Sample processing:</strong></p> <p>HPV16 PsV were prepared according to (Buck & Thompson: Current Protocols in Cell Biology 2007). In short, p16Shell and pClneo-EGFP were transfected into HEK293TT cells. After 48 h, cells were harvested and lysed followed by maturation of the virus particles for 24 h. For purification, the particles were purified using a CsCl step gradient (27 % w/V and 38.8 % w/V CsCl in 10 mM Tris-HCl pH 7.4, 207570 x g, 3 h 50 min, 4 °C) followed by dialysis in Float-A-Lyzer devices (1 mL, Spectra/Por) against a total of 3 L HPV virion buffer (1x PBS, 635 mM NaCl, 0.9 mM CaCl2, 0.5 mM MgCl2, 2.1 mM KCl, pH 7.4).</p> <p>PsV were pre-incubated for 1 h either with or without heparin (H4784, Sigma-Aldrich) at room temperature. To initiate deuterium labelling the samples were 6-fold diluted with the virion buffer they were obtained in, only made of 99.9% D2O (150 mM NaCl, 4.8 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, 0.9 mM CaCl2, 0.5 mM MgCl2, pD 7.2). This resulted in a final concentration of 0.5 µM L1 monomer in the form of PsV with or without 1 mg/ml heparin during deuterium labelling. The exchange reaction was left to proceed at room temperature until aliquots of 45 µl were removed at predetermined time points (1 min, 5 min, 15 min, 1 h and 4 h). In the aliquots, the exchange was immediately stopped by twofold dilution with ice-cold quench buffer (0.25 M glycine, 100 mM TCEP, 8 M urea, indicated pH 2.7), resulting in final pH 2.5. For samples with heparin, the quench buffer additionally contained 1 mg/ml protamine sulphate (P4020, Sigma-Aldrich). After 30 s incubation on ice, the samples were centrifuged at 10.000 x g for 1 min at 0 °C. Each supernatant was transferred to a fresh tube and flash frozen in liquid nitrogen. Low binding microtubes and low binding pipette tips (both Axygen) were used throughout for all handling of viral particles.</p> <p>The frozen samples were quickly thawed and injected into a refrigerated (1°C) HPLC system (Infinity 1260, Agilent Technologies), through a porcine pepsin column (≥ 3200 units/mg, Sigma-Aldrich) in-house immobilized onto POROS-20AL perfusion resin (Thermo Scientific) as described previously (Wang et al.: Molecular & Cellular Proteomics 2002), which was kept at 4°C. Pepsin digestion was performed at isocratic 200 µl/min flow rate (0.4 % formic acid in water). After the digestion, peptides were online desalted for 3 min on a peptide microtrap (OPTI-TRAP, Optimize Technologies) and then eluted on a reversed-phase analytical column (ZORBAX 300SB-C18, 0.5 x 35 mm, 3.5 µm, 300Å, Agilent Technologies). There LC separation proceeded at 25 µl/min flow rate through an 8 min gradient of 8–30% solvent B, followed by a 3 min gradient of 30-90 % solvent B (solvent A: 0.4 % formic acid in water, solvent B: 0.4 % formic acid in acetonitrile). The outlet of the HPLC system was connected to an electrospray ionization (ESI) source of an Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Scientific). The instrument was operated in positive ESI MS-only mode for deuterated samples, scan range 300-2000 m/z, using 4 microscans at resolving power setting 120,000. In a separate measurement on non-deuterated sample, the instrument was used in positive data-dependent ESI MS/MS mode with 30% HCD dissociation, 1 microscan and 240,000 resolving power setting for the identification of all peptides produced by non-specific pepsin cleavage.</p> <p>In total 22 pmol and 50 pmol L1 protein were injected per MS and MS/MS analysis, respectively. To minimize sample carry-over on the protease column, two washing solutions were always injected between sample injections modified from Majumdar et al. 69 (wash solution 1: 5% acetonitrile, 5% isopropanol, 20% acetic acid; wash solution 2: 4 M Urea, 1 M glycine, pH 2.5). All HDX samples were analysed in technical triplicates, except for the 15 min time point for PsV without heparin, which was measured in duplicate.</p> <p><br><strong>Data processing:</strong></p> <p>Peptides were identified from the MS/MS data by the Andromeda search algorithm implemented in MaxQuant (version 1.6.5.0) using a custom protein database containing the sequences of HPV16 L1 and L2 proteins. Deuterium uptake for the identified peptides was calculated with DeutEx (in-house developed), manually inspected and the statistical significance of the observed differences in deuteration was evaluated by applying an unpaired two-tailed Student’s T-test with single pooled variance evaluated with alpha ≤ 0.05 using the Holm-Šidák correction for multiple comparisons in Prism 8.0.1 (GraphPad Software). The processed data were visualized using MSTools (https://peterslab.org/MSTools/, Kavan & Man: International Journal of Mass Spectrometry 2011) and open-source PyMol 2.6.0a0 (Schrödinger, Inc).</p> <p>For ZENODO the datafiles were deposited as native Thermo .raw files (including instrumental parameters metadata) while all peaks in the spectra were additionally exported into plain m/z vs intensity .txt files per each scan in the LC-MS analysis as also used for the DeutEx HDX-MS processing.</p>
Data for the "Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1"
<p>Bottom-up mass spectrometry-based proteomic analysis (trypsin) was performed on four biological replicates of HIV-1 virions. These virions were isolated from HEK293T cells transfected with a HIV-1 proviral plasmid derived from the pNL4-3 molecular clone, rendered biosafe due to inactivating point mutations in both the env and vpr reading frames. There are 8 total spectra, 4 are from unlabeled aliquots of sample, and 4 are from aliquots of sample treated with glutathione to label dehydroamino acids (Spectra can be accessed on MassIVE (MSV000088220). All data was analyzed using MetaMorpheus version 0.0.319 (https://github.com/smith-chem-wisc/MetaMorpheus). Provided here are the results of this analysis.</p>
Quantitative electrostatic force tomography for virus capsids in interaction with an approaching nanoscale probe
<p>This repository contains the simulated data of a simple electrostatic model, based on the Poisson-Boltzmann equation, that quantifies the subnanometric electrostatic interactions between an AFM tip and a proteinaceous capsid (Zika Virus) from molecular snapshots. This allows us to describe the contributions of specific amino acids and atoms to the interaction force.</p> <p>The contains of this repository can be easily visualized through Jupyter Notebooks contained here:</p> <p>https://github.com/pyF4all/eTipVirusForce</p>
Fig. 2. Western blot analysis for SINV-3 capsid protein 9 d afer inoculating 6 in Solenopsis invicta virus 3: infection tests with adult honey bees (Hymenoptera: Apidae)
Fig. 2. Western blot analysis for SINV-3 capsid protein 9 d afer inoculating 6 groups of honey bees and 6 fire ant colonies. Lanes 1 and 2 show positive detection of capsid proteins in all 6 inoculated fire ant colonies (shown in 3 rows). Lanes 3 to 8 show negative tests for 18 bees (3 from each of the 6 groups inoculated with SINV-3).
Dataset and code for article "Explicit description of viral capsid subunit shapes by unfolding dihedrons"
<p>This repository contains data and codes used in a paper "Explicit description of viral capsid subunit shapes by expanding dihedrons" by Toyooka et al.</p> <p>- [grasshopper/] contains a GH file used in the 3D CAD Rhinoceros/Grasshopper.<br>- [docking_axes_viper/] contains notebooks for aligning the subunit coordinates with the VIPER coordinate system (Z-axis is the 2-fold axis, 3-fold axis is on the X-axis, and 5-fold axis is on the Y-axis)</p> <p>- [docking_pairwise/] contains input scipts and analysis notebooks for pairwise docking simulations for subunits<br> - [1stm_zdock_iter/df.jld2] data containing top docking scores and poses, and screw motion parameters<br> - [1stm_zdock_iter/rmsd.jld2] RMSD data of docking poses with regard to the experimental structure - [1stm_zdock_iter/run.sh] is a batch script for conducting docking simulations with ZDOCK<br> - [1stm_zdock_iter/run_each.sh] is a script for a single docking simulation with a specified random seed. Called from `run.sh`<br> - [1stm_zdock_iter/skrew_parameters.ipynb] analyzes the result of docking simulations. Sort the results accoring to docking scores and find the skrew axis of each docking pose<br> - [1stm_zdock_iter/visualize.ipynb] plots the docking score and the screw axis parameters, and also calculates and plots RMSDs from the reference structure (whole-shell structure)<br> - [1stm_zdock_iter/ref.pdb] is a sympolic link to a refrence structure (whole-shell structure)<br> - [4v4m_zdock_iter/] PDB ID: 4V4M<br> - [6s44_zdock_iter/] PDB ID: 6S44<br> - [7odw_zdock_iter/] PDB ID: 7ODW<br> - [3r0r_zdock_iter/] PDB ID: 3R0R<br> - [5zju_zdock_iter/] PDB ID: 5ZJU<br> - [1vb4_zdock_iter/] PDB ID: 1VB4<br> - [1m1c_zdock_iter/] PDB ID: 1M1C<br> - [6r7m_zdock_iter/] PDB ID: 6R7M<br> - [2m99_zdock_iter/] PDB ID: 2M99</p>
Targeting AAV vectors to the CNS via de novo engineered capsid-receptor interactions
<p>Dataset for "Targeting AAV vectors to the CNS via <em>de novo</em> engineered capsid-receptor interactions."</p>
HIV-1 capsid assembly
<p>This dataset contains all information to run HIV-1 capsid assembly simulations in the presence of IP6.</p>
Data accompanying "Identification of capsid-like proteins in venomous and parasitic animals"
<p>This data accompanies the pub "Identification of capsid-like proteins in venomous and parasitic animals". The DOI for this pub is <a href="https://doi.org/10.57844/arcadia-14b2-6f27" target="_blank" rel="noopener noreferrer">https://doi.org/10.57844/arcadia-14b2-6f27</a></p> <p> </p> <p><strong>Files and folders included: </strong></p> <p> </p> <p><strong>1.</strong> Manually annotated results of searching VOG HMMs against venom transcriptomes: Annotated_capsid_no_cutoffs_summary_with_seqs_05092024.xlsx</p> <p><strong>2.</strong> Manually annotated results of running preHGT on the genomes of venomous species: Annotated_hgt_results_venom_050924.xlsx</p> <p><strong>3. </strong>The genomes we input into preHGT: preHGT_input_genomes.csv</p> <p><strong>4.</strong> Genbank files of the genomic neighborhood of putatively horizontally transferred viral genes in the tick genome. There are seven GenBank files, one for each contig. Named with protein name.</p> <p><strong>5.</strong> BLAST results from searching putatively endogenized viral proteins against tick salivary transcriptomes: TSA_blast_results.csv</p> <p><strong>6.</strong> Results from searching the putatively endogenized viral capsid proteins against AlphaFold/UniProt50 version 4, AlphaFold/Swiss-Prot version 4, and AlphaFold/Proteome version 4 using the Foldseek webserver: Foldseek_capsid_followup_05092024.xlsx</p> <p><strong>7.</strong> Newick files of the three trees displayed in Figure 3 and Figure 5 . </p>
ProteinCartograhpy data accompanying "Identification of capsid-like proteins in venomous and parasitic animals"
<p>This is the data for the <a href="https://github.com/Arcadia-Science/ProteinCartography/releases/tag/v0.4.2">ProteinCartography</a> analysis in the pub "<a href="https://doi.org/10.57844/arcadia-14b2-6f27">Identification of capsid-like proteins in venomous and parastic animals.</a>" Note that ProteinCartography (v0.4.2) was run in "Cluster" mode or "From-folder" mode using the parameters set in the <code>config_ff.yml</code> and the <em>Ornithodoros turicata </em>proteins. Notebooks used to fetch data and prepare custom plots can be found in the capsids GitHub <a href="https://github.com/Arcadia-Science/capsids">repository</a>.</p> <p> </p> <p><strong>Files in this data repository include: </strong></p> <p><code>output.zip</code> is a folder containing all of the output files for the <em>Ornithodoros</em> ProteinCartography run, including the maps, aggregated features files, and the all-v-all similarity matrix.</p> <p><code>structures.zip</code> is a folder containing all the structures used in the ProteinCartography analysis. Structures beginning with "VOG" are viral capsid proteins folded using <a href="https://doi.org/10.1126/science.ade2574">ESMFold</a>.</p> <p><code>ornithodoros_aggregated_features.tsv</code> is a file containing all the metadata gathered for each protein in the analysis from either <a href="https://www.uniprot.org">UniProt</a> or the <a href="https://vogdb.org">VOG database</a>.</p> <p><code>ornithodoros_aggregated_features_pca_umap.html</code> is the final map of the capsid proteins with the <em>Ornithodoros</em> proteins with metadata overlays.</p> <p><code>ornithodoros_aggregated_features_pca_umap.tsv</code> is a file containing all of the metadata gathered for each protein in the analysis, as well as the coordinates for the map.</p> <p><code>ornithodoros_leiden_similarity.html</code> is a heatmap showing the average between-cluster and within-cluster similarity between every cluster in the analysis.</p> <p><code>tick_or_virus_umap.html</code> is a version of the final map that specifically highlights which proteins are from capsids and which proteins are from <em>Ornithodoros</em>. </p> <p><code>uniprot_features1.tsv</code> is a file containing all of the UniProt metadata fetched for the <em>Ornithodoros</em> proteins, as well as the viral capsid VOG identifiers. This file is used as an input for the ProteinCartography analysis.</p> <p><code>ornithodoros.txt</code> us a file containing all of the <em>Ornithodoros</em> proteins fetched from the <a href="https://doi.org/10.1038/s41586-021-03819-2">AlphaFold</a> <a href="https://doi.org/10.1093/nar/gkab1061">database.</a></p> <p><code>config_ff.yml</code> is the configuration file for the ProteinCartography run. </p>
Simulation input files: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or Pore Formation
<p>Simulation input files, and code for modification to simulation software for article:</p> <p>Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or PoreFormation</p> <p>Lukáš Sukeník,†,‡</p> <p>Liya Mukhamedova,†</p> <p>Michaela Procházková,†</p> <p>Karel Škubník,†</p> <p>Pavel Plevka,†</p> <p>and Robert Vácha∗,†,‡,¶</p> <p>†CEITEC – Central European Institute of Technology, Masaryk University, Kamenice753/5, 625 00 Brno, Czech Republic</p> <p>‡Department of Condensed Matter Physics, Faculty of Science, Masaryk University,Kotl ́aˇrsk ́a 267/2, 611 37 Brno, Czech Republic</p> <p>¶National Centre for Biomolecular Research, Faculty of Science, Masaryk University,Kamenice 5, 625 00 Brno, Czech Republic</p> <p>E-mail: robert.vacha@mail.muni.cz</p>
Data from: HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes
<p>The mature HIV-1 capsid is stabilized by host and viral determinants. The capsid protein CA binds to the cellular metabolites inositol hexakisphosphate (IP6) and its precursor inositol (1, 3, 4, 5, 6) pentakisphosphate (IP5) to stabilize the mature capsid. In target cells, capsid destabilization by the antiviral compounds lenacapavir and PF74 reveals an HIV-1 infectivity defect due to IP5/IP6 (IP5/6) depletion. To test whether intrinsic HIV-1 capsid stability and/ or host factor binding determines HIV-1 insensitivity to IP5/6 depletion, a panel of CA mutants was assayed for infection of IP5/6-depleted T cells and wildtype cells. Four CA mutants with unstable capsids exhibited dependence on host IP5/6 for infection and reverse transcription (RTN). Adaptation of one such mutant, Q219A, by spread in culture resulted in Vpu truncation and a capsid three-fold interface mutation, T200I. T200I increased intrinsic capsid stability as determined by <em>in vitro</em> uncoating of purified cores and partially reversed the IP5/6-dependence in target cells for each of the four CA mutants. T200I further rescued the changes to lenacapavir sensitivity associated with the parental mutation. The premature dissolution of the capsid caused by the IP5/6-dependent mutations imparted a unique defect in integration targeting that was rescued by T200I. Collectively, these results demonstrate that T200I restored other capsid functions after RTN for the panel of mutants. Thus, the hyperstable T200I mutation stabilized the instability defects imparted by the parental IP5/6-dependent CA mutation. The contribution of Vpu truncation to mutant adaptation was linked to BST-2 antagonization, suggesting that cell-to-cell transfer promoted replication of the mutants. We conclude that interactions at the three-fold interface are adaptable, key mediators of capsid stability in target cells and are able to antagonize even severe capsid instability to promote infection.</p>
Data from: Significant differences in capsid properties and potency between AAV vectors produced in Sf9 and HEK293 cells
<p>For successful vector-based gene therapy manufacturing, the selected adeno-associated virus (AAV) vector production system must produce vector at sufficient scale. However, concerns have arisen regarding the quality of vector produced using different systems. In this study, we compared AAV serotypes 1, 8, and 9 produced by two different systems (Sf9/baculovirus and HEK293/transfection) and purified by two separate processes. We evaluated capsid properties including protein composition, post-translational modification, particle content profiles, and in vitro and in vivo vector potency. Vectors produced in the Sf9/baculovirus system displayed reduced incorporation of viral protein 1 and 2 into the capsid, increased capsid protein deamidation, increased empty and partially packaged particles in vector preparations, and an overall reduced potency. The differences observed were largely independent of the harvest method and purification process. These findings illustrate the need for careful consideration when choosing an AAV vector production system for clinical production.</p>
All-atom models of SU10 and P68 viral genomes. Supplementary to the "Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses".
<p>The dataset contains mmCIF formatted all-atom models of SU10 and P68 viral genomes and the python script used for refinement of the initial MMB-generated coordinates.</p>
A Study of Teropavimab and Zinlirvimab in Combination With Capsid Inhibitor Lenacapavir in Virologically Suppressed Adults With HIV-1 Infection
ClinicalTrials.gov study NCT05729568. IPD Sharing: NO. Countries: 4. Publications: 0.
Data from: Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure
Open the record for dataset details and reuse information.
Data from: HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes
Open the record for dataset details and reuse information.
Data from: Significant differences in capsid properties and potency between AAV vectors produced in Sf9 and HEK293 cells
Open the record for dataset details and reuse information.
Data from: The HIV capsid mimics karyopherin engagement of FG-nucleoporins
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Data from: Development of an adipose-tropic AAV capsid ablating liver tropism
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