Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Post translational modifications in spider major ampullate silk influence structural conformation and N-terminal dimerization dynamics

ABSTRACT: Our current understanding of spider silk’s structure-function is largely based upon conclusions drawn from the comparison of amino acid sequences generated by genomics to techniques like NMR and X-ray crystallography. However, this comparison is ultimately limited to the extent that any given silk genome closely matches its proteome; with post-translational modifications (PTM) significantly influencing the structure and function of many proteins. This study utilizes phosphopeptide enrichment and mass spectrometry to produce a comprehensive PTM map across the major MaSp proteins of Trichonephila clavata, with PTMs observed in all structural domains. Solid-state NMR further confirms the presence and conformation of hydroxyproline, phosphoserine, phosphotyrosine and dityrosine, revealing phosphoserine’s roll in β-sheet inhibition. Moreover, N-terminal domain (NTD) phosphomimics where utilized to examine the impact of phosphorylation at the dimer interface, indicating that changes in charged clusters of the NTD monomers alters dimerization behavior in a manner that can possibly facilitate heterodimer formation.

ORGANISM(S): Cellular Organisms

SUBMITTER: Kazuharu Arakawa

PROVIDER: PXD039602 | JPOST Repository | Tue Jan 23 00:00:00 GMT 2024

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	201127mm_001_Jorogumo-%23PMT-1_Chymotrypsin_200ng.d.zip	Other
	201127mm_002_Jorogumo-%23PMT-2_Chymotrypsin_200ng.d.zip	Other
	201127mm_003_Jorogumo-%23PMT-3_Chymotrypsin_200ng.d.zip	Other
	201127mm_004_Jorogumo-%23PMT-4_Chymotrypsin_200ng.d.zip	Other
	201127mm_005_Jorogumo-%23PMT-5_Chymotrypsin_200ng.d.zip	Other

Items per page:

1 - 5 of 20

Similar Datasets

Trichonephila clavata

Project description:Multi-Omics Research of Trichonephila clavata spider

| PRJNA1058179 | ENA

Structure-guided development of high-performance antibodies targeting site-specific post-translational modifications

Project description:Post-translational modifications (PTMs) of proteins play critical roles in regulating many cellular events. Antibodies targeting site-specific PTMs are essential tools for detecting and enriching PTMs at sites of interest. However, fundamental difficulties in molecular recognition of both PTM and surrounding peptide sequence have hindered the efficient generation of highly specific anti-PTM antibodies. Furthermore, the widespread use of potentially inconsistent, non-renewable and molecularly undefined antibodies presents experimental challenges thought to contribute to the reproducibility crisis in biomedical research. In this study, we describe the structure-guided development of a platform that efficiently generates potent and selective recombinant antibodies to PTMs that are molecularly-defined and infinitely renewable. Our platform is built on our previous discovery of an unconventional binding mode of anti-PTM antibodies, antigen clasping, where two antigen binding sites cooperatively clasp a single antigen, creating extensive interactions with the antigen and leading to high selectivity and potency. We designed the platform that generates clasping antibodies with two distinct binding units, resulting in efficient generation of antibodies to a set of trimethylated histone H3 with high levels of specificity and affinity. Performance comparison in chromatin immunoprecipitation (ChIP), a common application in epigenomics, revealed that an anti-H3K27me3 clasping antibody exhibited superior specificity to a widely-used conventional antibody and captured symmetric and asymmetric nucleosomes in a less biased manner. We further generated clasping antibodies to phosphotyrosine antigens by using the same principle. These results suggest the broad applicability of our platform to generating high-performance clasping antibodies to diverse PTMs.

2024-12-02 | GSE270275 | GEO

Multivalent histone and DNA engagement by a PHD/BRD/PWWP triple reader cassette recruits ZMYND8 to K14ac-rich chromatin

Project description:Elucidation of interactions involving DNA and histone post-translational-modifications (PTMs) is essential for providing insight into complex biological functions. Reader assemblies connected via flexible linkages facilitate avidity and increase affinity, however little is known of the contribution to the recognition process of multiple PTMs due to rigidity in the absence of conformational flexibility. We report here the high resolution crystal structure of the triple-reader module (PHD-Bromo-PWWP) of ZMYND8 which forms a stable unit capable of simultaneously recognizing multiple histone PTMs, while presenting a charged platform for association with DNA. Single domain disruptions destroy the functional network of interactions initiated by ZMYND8, impairing recruitment to sites of DNA damage. Our data establish proof-of-principle that rigidity can be compensated by concomitant DNA and histone PTM interactions, maintaining multivalent engagement of transient chromatin states, thus identifying an important underappreciated role for rigid multivalent reader modules in nucleosome binding and chromatin function.

2016-11-23 | GSE81696 | GEO

Orb-weaver spider (Trichonephila inaurata madagascariensis) dragline silk proteome

Project description:Proteome analysis for a dragline silk in orb-weaver spider (Trichonephila inaurata madagascariensis).

2021-07-21 | PXD024372 | JPOST Repository

Detect the shared protein components between spider dragline silk and silkworm cocoon by Label free quantitative proteomics

Project description:The spider major ampullate gland and silkworm silk gland have similar morphological structure and function, so we explored whether there are some common protein components on silks, with three biological replicates for each sample. Dragline silk samples from mature female Trichonephila clavata spider and cocoon samples are from silkworm Bombyx mori chain. The dragline silk of the spider T. clavata and cocoon silk of the silkworm B. mori were cut with scissors. First, silk samples (20 mg of each sample) were dissolved in 500 μL of 9 M LiSCN, and the supernatant was collected after centrifugation (10,000 × g, 10 min). Protein concentrations were measured via the Bradford protein assay (Beyotime, China). Then, the samples were diluted 10-fold in an 8 M urea solution, mixed with 5 × SDS–PAGE buffer, and separated using a NuPAGE 4–12% Bis-Tris protein gel (Thermo Fisher Scientific, USA). The samples were subsequently digested using trypsin, and peptides were measured via LC–MS/MS on a Q Exactive HF-X column.

2022-12-09 | PXD038734 |

Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A

Project description:Comparison of overall tRNA level and fraction of charged tRNAs of different variants

2021-08-19 | GSE137567 | GEO

Barley transcriptional responses to specialist and generalist spider mite herbivores

Project description:Spider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, sorghum and barley. Historically, studies of plant-herbivore interactions have focused largely on insects. However, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalists and specialists. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from barley (Hordeum vulgare L.) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included.

2016-06-24 | GSE83676 | GEO

Maize transcriptional responses to specialist and generalist spider mite herbivores

Project description:Spider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, and sorghum. Historically, studies of plant-herbivore interactions have focused largely on insects. As such, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalist and specialist mites. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from maize (Zea mays) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included. In total, four biological samples were generated per treatment.

2017-06-17 | GSE100121 | GEO

Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (expression data)

Project description:Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA. Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states. Comparison of Brd2 and HP1b shRNA knockdown HEK293 cells to control knockdown HEK293 cells.

2012-07-30 | E-GEOD-39580 | biostudies-arrayexpress

Total tRNA level and tRNA charged fraction in DLD-1 cells treated with 4-hydroxytamoxefen and compared to untreated cells

Project description:Comparison of overall tRNA level and fraction of charged tRNAs upon treatment with 4-hydroxytamoxefen and compared to untreated cells

2019-04-20 | GSE116812 | GEO