Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
59
datasets available to search
ShareScore release 0.9.0
Dataset results
59 results for “Post-translational modifications”
Curated dataset on protein's properties and post-translational modification protein properties
<p>Proteins perform essential cellular functions, which range from cell division and metabolism to DNA replication. Thus, decoding the mechanism of action of cells, requires understanding of the functioning and physicochemical properties of proteins [1]. While the genetic code encodes the primary structure of proteins, they undergo various modifications as part of their normal functioning including addition of modifying groups, such as acetyl, phosphoryl, glycosyl, and methyl, to one or more amino acids after translation, which is known as post-translational modification (PTM) [2, 3]. PTMs play an essential role in regulating protein functions by altering their physicochemical properties and understanding these reactions provides valuable insights regarding cell function. Advances in proteomics research have significantly deepened our understanding of PTMs and their impact on cellular functions and disease mechanisms. The study of PTMs is now at the forefront of research in molecular biology and biochemistry.</p> <p>Many databases, software, and tools have been developed to enhance our understanding of the various PTMs that affect human plasma proteins and help to simplify the analysis of complex PTM data [4]. These PTM databases and tools contain significant information and are a valuable resource for the research community. Key databases include dbPTM, UniProt, and PubChem. Utilising these databases, protein-related information like substrate peptides, amino acid sequence numbers, and experimentally validated PTM sites can be identified and curated.</p> <p>This dataset presents curated information regarding PTM-related changes in the physicochemical properties of the 16 most abundant plasma proteins [5], i.e., Serum Albumin, Serotransferrin, Antithrombin-III, Apolipoprotein A-I, Apolipoprotein A-IV, Apolipoprotein B-100, Apolipoprotein C-II, Apolipoprotein C-III, Apolipoprotein E, Clusterin, Complement C3, Haptoglobin, Histidine-rich glycoprotein, Mannose-binding protein C, Hemoglobin, and Fibrinogen alpha chain. The physicochemical properties studied, and the impact of different PTMs on the properties, include the protein molecular weight, isoelectric point, surface hydrophobicity, and solubility. The PTMs explored include phosphorylation, acetylation, glycosylation, methylation, ubiquitination, SUMOylation, lipidation, glutathionylation, nitrosylation, sulfoxidation, succinylation, neddylation, malonylation, hydroxylation, oxidation, and palmitoylation.</p> <p>References</p> <ol> <li>Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Analyzing Protein Structure and Function.</li> <li>Chen, H.; Venkat, S.; McGuire, P.; Gan, Q.; Fan, C. Recent Development of Genetic Code Expansion for Posttranslational Modification Studies. Molecules 2018, 23, 1662.</li> <li>Marc Oeller, Ryan Kang, Hannah Bolt, Ana Gomes dos Santos, Annika Langborg Weinmann, Antonios Nikitidis, Pavol Zlatoidsky, Wu Su, Werngard Czechtizky, Leonardo De Maria,Pietro Sormanni, Michele Vendruscolo: Sequence-based prediction of the solubility of peptides containing non-natural amino acids [bioRiv].</li> <li>Ramazi S, Zahiri J. Posttranslational modifications in proteins: resources, tools and prediction methods. Database (Oxford). 2021 Apr 7;2021:baab012.</li> </ol>
qPCR analysis: Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications
<p>Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications' qPCR data following the MIQE guidelines.</p>
The burden of post-translational modification (PTM) – disrupting mutations in the tumor matrisome
<p>A Pan-cancer analysis of the post-translational modification (PTM) – disrupting mutations in the tumor matrisome</p>
Data from: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications
<p></p><p>Microtubules are cytoskeletal structures involved in stability, transport and organization in the cell. The building blocks, the α- and β-tubulin heterodimers, form protofilaments that associate laterally into the hollow microtubule. Microtubule also exists as highly stable doublet microtubules in the cilia where stability is needed for ciliary beating and function. The doublet microtubule maintains its stability through interactions at its inner and outer junctions where its A- and B-tubules meet. Here, using cryo-electron microscopy, bioinformatics and mass spectrometry of the doublets of Chlamydomonas reinhardtii and Tetrahymena thermophila, we identified two new inner junction proteins, FAP276 and FAP106, and an inner junction-associated protein, FAP126, thus presenting the complete answer to the inner junction identity and localization. Our structural study of the doublets shows that the inner junction serves as an interaction hub that involves tubulin post-translational modifications. These interactions contribute to the stability of the doublet and hence, normal ciliary motility.</p><p></p>
Crosstalk assessment for multi-colour immunofluorescence of Histone 3 and Polymerase II post-translational modifications in pluripotent zebrafish embryos
<p>Microscopy images recorded to assess the extent of crosstalk from the detection channels of H3K27ac and recruited RNA polymerase II (Serine 5 phosphorylation of the C-terminal domain heptad repeat of subunit 1) to the detection channel of elongating RNA polymerase II (Serine 5 phosphorylation of the C-terminal domain heptad repeat of subunit 1). Sample preparation and image recording was carried out jointly by Süheyla Eroğlu-Kayikci, Elisa Kämmer, and Lennart Hilbert.</p>
Data from: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications
Open the record for dataset details and reuse information.
Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages
Open the record for dataset details and reuse information.
Histone H1 variants in Arabidopsis are subject to numerous post-translational modifications, both conserved and previously unknown in histones, suggesting complex functions of H1 in plants - raw data
<p>Data from HPLC coupled with mass spectrometer acquired during experiments.<br /> </p>
Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase
<p>MD simulations for MprE7 alone and MprE7 in complex with SprI</p>
Dataset related to: Post-translational modifications by SIRT3 de-2-hydroxyisobutyrylase activity regulate glycolysis and enable nephrogenesis
<p>The file contains all the dataset included in the manuscript, divided by figure in each tab</p> <p> </p> <p><strong>Abstract</strong></p> <p>Abnormal kidney development leads to lower nephron number, predisposing to renal diseases in adulthood. In embryonic kidneys, nephron endowment is dictated by the availability of nephron progenitors, whose self-renewal and differentiation require a relatively repressed chromatin state. More recently, NAD<sup>+</sup>-dependent deacetylase sirtuins (SIRTs) have emerged as possible regulators that link epigenetic processes to the metabolism. Here, we discovered a novel role for the NAD<sup>+</sup>-dependent deacylase SIRT3 in kidney development. In the embryonic kidney, SIRT3 was highly expressed only as a short isoform, with nuclear and extra-nuclear localisation. The nuclear SIRT3 did not act as deacetylase but exerted de-2-hydroxyisobutyrylase activity on lysine residues of histone proteins. Extra-nuclear SIRT3 regulated lysine 2-hydroxyisobutyrylation (Khib) levels of phosphofructokinase (PFK) and Sirt3 deficiency increased PFK Khib levels, inducing a glycolysis boost. This altered Khib landscape in <em>Sirt3<sup>-/-</sup></em> metanephroi was associated with decreased nephron progenitors, impaired nephrogenesis and a reduced number of nephrons. These data describe an unprecedented role of SIRT3 in controlling early renal development through the regulation of epigenetics and metabolic processes.</p>
Cysteine S-acetylation is a post-translational modification involved in metabolic regulation
<p><span>Cysteine is a reactive amino acid central to the catalytic activities of many enzymes. It is also a common target of post-translational modifications (PTMs), such as palmitoylation. This long-chain acyl PTM can modify cysteine residues and induce changes in protein subcellular localization. We hypothesized that cysteine could also be modified by short-chain acyl groups, such as cysteine <em>S</em>-acetylation. To test this, we developed sample preparation and non-targeted mass spectrometry protocols to analyze the mouse liver proteome for cysteine acetylation. Our findings revealed hundreds of sites of cysteine acetylation across multiple tissue types, revealing a previously uncharacterized cysteine acetylome. Cysteine acetylation shows a marked cytoplasmic subcellular localization signature, with tissue-specific acetylome patterns and specific changes upon metabolic stress. This study uncovers a novel aspect of cysteine biochemistry, highlighting short-chain modifications alongside known long-chain acyl PTMs. These findings enrich our understanding of the landscape of acyl modifications and suggest new research directions in enzyme activity regulation and cellular signaling in metabolism.</span></p>
Identification and Characterization of the Novel Post-Translational Modification Cysteine S-Acetylation
<p><span>Protein modifications modulate nearly every aspect of cell biology in organisms ranging from Archaea to Eukaryotes. The earliest evidence of covalent protein modifications was found in the early 20<sup>th</sup> century by studying the amino acid composition of proteins by chemical hydrolysis. These discoveries challenged what defined a canonical amino acid. The advent and rapid adoption of mass spectrometry-based proteomics in the latter part of the 20<sup>th</sup> century enabled a veritable explosion in the number of known protein modifications, with over 500 discrete modifications counted today. Now, new computational tools in data science, machine learning, and artificial intelligence are poised to allow researchers to make significant progress discovering new protein modifications and determining their function. </span></p> <p><span>Lysine acetylation is one of the most well-known post translational modifications. Acetylation is not limited to lysine with acetylation of serine and threonine having also been reported in the literature. Lysine acetylation is known to occur both enzymatically and non-enzymatically.<span> </span>Cysteine is a reactive amino acid central to the catalytic activities of many enzymes. Given the highly reactive nature of the cysteine side-chain, non-enzymatic acetylation of cysteine would be expected to be more favorable than non-enzymatic acetylation of lysine.<span> </span>Cysteine is also a common target of post-translational modifications (PTMs), such as palmitoylation. This long-chain acyl PTM can modify cysteine residues and induce changes in protein sub-cellular localization.<span> </span>Transfer of an acetyl moiety from the side-chain of cysteine to the side-chain of lysine has been shown <em>in vitro</em>.<span> </span>Cysteine side-chain acetylation has never been shown <em>in vivo</em>.<span> </span>We hypothesized that cysteine could also be modified by short-chain acyl groups, such as cysteine <em>S</em>-acetylation. To test this, we developed sample preparation and non-targeted mass spectrometry protocols to analyze the mouse liver proteome for cysteine acetylation. Our findings revealed hundreds of sites of cysteine acetylation across multiple tissue types, revealing a previously uncharacterized cysteine acetylome. The cysteine acetylome shows distinct patterns in different sub-cellular compartments and is most abundant in the cytoplasm. Cysteine acetylation is present in all tissue types tested and has tissue-specific acetylome patterns.<span> </span>Metabolic stress led to targeted changes in the cysteine acetylome of BAT.<span> </span>Acetylation of the active site cysteines of GAPDH led to a sharp reduction in activity. This study uncovers a novel aspect of cysteine biochemistry, highlighting short-chain modifications alongside known long-chain acyl PTMs. These findings enrich our understanding of the landscape of acyl modifications and suggest new research directions in enzyme activity regulation and cellular signaling in metabolism.</span></p>
Data deposit for "Resolving sulfation post-translational modifications on a peptide hormone using nanopores"
<p><strong>Data and code deposit for the <a href="https://www.biorxiv.org/content/10.1101/2024.05.08.593138v1" target="_blank" rel="noopener">pre-print</a> and the <a href="https://doi.org/10.1021/acsnano.4c09872">published</a> manuscript at ACS nano.</strong></p> <p><strong>See README.md for more information.</strong></p>
Asymmetric post-translational modifications regulate the nuclear translocation of STAT3 3 homodimers in response to leukemia inhibitory factor
<p>Proteomic characterisation of cell lines expressing different variants of STAT3 dimers (WT-WT, WT-Y507F, Y507F-Y507F, with and without LIF stimulation).</p>
Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore
Open the record for dataset details and reuse information.
Post-Translational Modification Prediction via Prompt-Based Fine-Tuning of a GPT-2 Model
<p>Training and Benchmark datasets for 19 PTMGPT2 models</p>
Malondialdehyde adducts and 3-nitrotyrosine oxidative post-translational modifications on RyR1 result in FKBP12 dissociation and higher channel open probability
Open the record for dataset details and reuse information.
Raw mass spectrometry data for "Lysyl hydroxylase 2 mediated collagen post-translational modifications and functional outcomes"
<p><strong>Abstract:</strong> Lysyl hydroxylase 2 (LH2) is a member of LH family of enzymes (LH1-3) that catalyze the hydroxylation<br> of lysine (Lys) residues on collagen, and this particular isozyme has been implicated in Bruck syndrome,<br> fibrosis and cancer metastasis. Previously, we proposed LH2 as a telopeptidyl LH for type I collagen and<br> this specific function is now generally accepted. However, several fundamental questions remain<br> unanswered: 1, Is LH2 responsible for both N- (α1 and 2 chains) and C-telopeptidyl (α1 chain) Lys<br> hydroxylation? 2, Is LH2 involved in the helical Lys hydroxylation? 3, what are the functional<br> consequences when LH2 is completely lacking? To answer these questions, we generated LH2-null MC3T3<br> cells (LH2 KO) using CRISPR/Cas9, and extensively characterized the molecular and fibrillar phenotypes<br> of type I collagen. Cross-link analysis demonstrated that the hydroxylysine-aldehyde (Hyl<sup>ald</sup>)-derived crosslinks<br> were completely absent from LH2 KO collagen with concomitant increases in the Lys<sup>ald</sup>-derived crosslinks.<br> Mass spectrometric analysis revealed that, in LH2 KO type I collagen, telopeptidyl Lys hydroxylation<br> was completely abolished at all sites while helical Lys hydroxylation was slightly diminished in a sitespecific<br> manner. Moreover, di-glycosylated Hyl was diminished at the expense of mono-glycosylated Hyl.<br> Furthermore, prolyl 3-hydroxylation was slightly increased in LH2 KO type I collagen. In LH2 KO samples,<br> collagen solubility was markedly increased, fibril diameters are significantly diminished, and<br> mineralization severely impaired. Together, these data underscore the critical role of LH2-catalyzed<br> collagen modifications and consequent cross-linking in matrix stability, organization and mineralization.</p>
Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition
GEO Series GSE119697. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
An Improved SNAP-ADAR Tool Enables Efficient RNA Base Editing to Interfere with Post-translational Protein Modification
GEO Series GSE264114. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.