Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1089143 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28385520.fastq.gz | Fastqsanger.gz | |||
| SRR28385521.fastq.gz | Fastqsanger.gz | |||
| SRR28385522.fastq.gz | Fastqsanger.gz | |||
| SRR28385523.fastq.gz | Fastqsanger.gz | |||
| SRR28385524.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and also functions as a cell entry receptor for several henipaviruses, which are zoonotic viruses with pandemic potential. Two such viruses, Nipah (NiV) and Hendra (HeV), are highly pathogenic in humans yet do not have any widely approved virus-specific therapeutics or vaccines. Soluble Fc-fusions of EFNB2 (sEFNB2-Fc) are known to bind the attachment glycoprotein G of both viruses and inhibit viral infection of cells. However, the potential of sEFNB2-Fc as a neutralizing agent in vivo is hindered by its binding activity to native Eph receptors. Therefore, using deep mutagenesis, variants of EFNB2 at cell surface are identified with increased binding to the soluble head domain of NiV-G over soluble Fc-fusions of the extracellular domains of Eph receptors. Specificity mutations for NiV-G are found primarily at the binding interface, especially around the G-H binding loop. The mutational landscape offers a preliminary blueprint for engineering sEFNB2-Fc variants with high specificity and affinity for potent neutralization of henipaviruses.
2023-06-12 | GSE234213 | GEO
Project description:Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and also functions as a cell entry receptor for several henipaviruses, which are zoonotic viruses with pandemic potential. Two such viruses, Nipah (NiV) and Hendra (HeV), are highly pathogenic in humans yet do not have any widely approved virus-specific therapeutics or vaccines. Soluble Fc-fusions of EFNB2 (sEFNB2-Fc) are known to bind the attachment glycoprotein G of both viruses and inhibit viral infection of cells. However, the potential of sEFNB2-Fc as a neutralizing agent in vivo is hindered by its binding activity to native Eph receptors. Therefore, using deep mutagenesis, variants of EFNB2 at cell surface are identified with increased binding to the soluble head domain of NiV-G over soluble Fc-fusions of the extracellular domains of Eph receptors. Specificity mutations for NiV-G are found primarily at the binding interface, especially around the G-H binding loop. The mutational landscape offers a preliminary blueprint for engineering sEFNB2-Fc variants with high specificity and affinity for potent neutralization of henipaviruses.
2023-06-12 | GSE234214 | GEO
Project description:Immunoglobulins G (IgG) and their Fc gamma receptors (FcγRs) play important roles in our immune system. The conserved N-glycan in the Fc region of IgG1 impacts interaction of IgG with FcγRs and the resulting effector functions, which has led to design of antibody therapeutics with greatly improved antibody-dependent cell cytotoxicity (ADCC) activities. Studies have suggested that also N-glycosylation of the FcγRIII affects receptor inteactions with IgG, but detailed studies of the interaction of IgG1 and FcγRIIIa with distinct N-glycans have been hindered by the natural heterogeneity in N-glycosylation. In this study, we employed comprehensive genetic engineering of the N-glycosylation capacities in mammalian cell lines to express IgG1 and FcγRIIIa with different N-glycan structures to more generally explore the role of N-glycosylation in IgG1:FcRIIIa binding interactions. We included FcRIIIa variants of both the 158F and 158V allotypes and investigated the key N-glycan features that affected binding affinity. Our study confirms that afucosylated IgG1 has the highest binding affinity to oligomannose FcγRIIIa, a glycan structure commonly found on FcγRIIIa expressed by NK cells but not monocytes or recombinantly expressed FcγRIIIa.
2022-08-30 | PXD035846 | Pride
Project description:Engineering of the ligand specificity of transcriptional regulator XylS by deep mutational scanning
| PRJDB12536 | ENA
Project description:Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, facilitates their characterization and optimization. Here, we developed a robust anti-CRISPR deep mutational scanning pipeline in Escherichia coli that combines synthetic gene circuits based on CRISPR interference with flow cytometry coupled sequencing and mathematical modeling. Using this pipeline, we characterized comprehensive single point mutation libraries for AcrIIA4 and AcrIIA5, two potent inhibitors of CRISPR-Cas9. The resulting mutational fitness landscapes revealed considerable mutational tolerance for both Acrs, suggesting an intrinsic redundancy with respect to Cas9 inhibitory features, and – for AcrIIA5 – indicated mutations that boost Cas9 inhibition. Subsequent in vitro characterization suggested that the observed differences in inhibitory potency between mutant inhibitors were mostly due to changes in binding affinity rather than protein expression levels. Finally, to demonstrate that our pipeline can inform Acrs-based genome editing applications, we employed a selected subset of mutant inhibitors to increase CRISPR-Cas9 target specificity by modulating Cas9 activity. Taken together, our work establishes deep mutational scanning as a powerful method for anti-CRISPR protein characterization and optimization.
2024-03-01 | GSE254101 | GEO
Project description:Platelet-derived growth factors (PDGF) are disulfide-bonded dimers that act on PDGF receptors (PDGFR) to stimulate cell proliferation, differentiation, migration, and/or function. There are multiple isoforms of both the ligand and receptor, which combined with the potential for heterodimerization, gives the system great complexity. Different ligands may be promiscuous or specific for receptor partners. To better understand how ligand sequence relates to receptor recognition, the mutational landscape of PDGF-B for binding to the high affinity receptor PDGFRbeta was experimentally determined by deep mutational scanning. A PDGF-B library containing all possible single amino acid substitutions was displayed on the surface of yeast and sorted for binding to the PDGFRbeta ectodomain. Following deep sequencing, the enrichment or depletion of all mutations was calculated as a proxy for relative activity. All PDGF-B cysteines forming three intra- and two interchain disulfides are highly conserved, indicating that PDGF-B is correctly folding into disulfide-linked dimers on the yeast surface. Indeed, several mutations at the ligand dimer interface are enriched and may enhance dimerization through increased hydrophobic packing or reduced electrostatic repulsion. Residues from the protruding PDGF-B subunit in contact with the receptor are tightly conserved, whereas interfacial residues from the receding subunit are mutationally tolerant. There are multiple enriched mutations at the receptor interface that the scan predicts increase PDGF-BB–PDGFRbeta affinity. The data may prove insightful for engineering PDGF ligands biased towards forming homodimers with increased receptor affinity.
2024-11-11 | GSE129019 | GEO
Project description:Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning
| PRJNA391469 | ENA
Project description:Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff
| PRJNA1023263 | ENA