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246 results for “Protein translation”
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>
Data supporting "Slowest-first translation scheme: Structural asymmetry along protein sequences and co-translational folding"
<p>Contains data for a set of 16,200 non-redundant protein structures taken from the Protein Data Bank. Associated code can be found at https://github.com/jomimc/FoldAsymCode.</p>
Double-stranded RNA structural elements holding the key to translational regulation in cancer: the case of editing in RNA Binding Motif Protein 8A
<p>Raw data supporting the manuscript</p> <p>Abukar, A.;Wipplinger, M.;<br> Hariharan, A.; Sun, S.; Ronner, M.;<br> Sculco, M.; Okonska, A.;<br> Kresoja-Rakic, J.; Rehrauer, H.; Qi, W.;<br> et al. Double-Stranded RNA<br> Structural Elements Holding the Key<br> to Translational Regulation in Cancer:<br> The Case of Editing in RNA-Binding<br> Motif Protein 8A. Cells 2021, 10, 3543.<br> https://doi.org/10.3390/<br> cells10123543</p>
Saccharomyces cerevisiae protein phosphorylation and translation accuracy
<p>Protein-protein and protein-rRNA interactions involving ribosomal proteins uS4 and uS5 are thought to maintain the accuracy of protein synthesis by increasing selection of cognate aminoacyl-tRNAs. Selectivity involves a major conformational change—domain closure—that stabilizes aminoacyl-tRNA in the ribosomal acceptor (A) site. This has been thought a constitutive function of the ribosome ensuring consistent accuracy. Recently, the <em>Saccharomyces cerevisiae</em> Ctk1 cyclin-dependent kinase was demonstrated to ensure translational accuracy and Ser238 of uS5 proposed as its target. Surprisingly, Ser238 is outside the uS4-uS5 interface and no obvious mechanism has been proposed to explain its role. We show that the true target of Ctk1 regulation is another uS5 residue, Ser176, which lies in the interface opposite to Arg57 of uS4. Based on site-specific mutagenesis, we propose that phospho-Ser176 forms a salt bridge with Arg57, which should increase selectivity by strengthening the interface. Genetic data show that Ctk1 regulates accuracy indirectly by stimulating phosphorylation of Ser176 by the kinase Ypk2. A second kinase pathway involving TORC1 and Pkc1 can inhibit this effect. The level of accuracy appears to depend on competitive action of these two pathways to regulate the level of Ser176 phosphorylation.</p>
AF2 models for "Co-translational assembly promotes functional diversification of paralogous proteins" by Mallik, et al.
<p>AF2 models used for analyses presented in "Co-translational assembly promotes functional diversification of paralogous proteins" by Saurav Mallik, Angel F. Cisneros, Christian R. Landry, and Emmanuel D. Levy.</p> <p>These models were used to analyze the structural divergence of 3703 Obligatory Homomer, 697 Mixed, and 181 Obligatory Heteromer pairs.</p> <p>Folders are separated into different categories:<br>- Models of homomers (from Schweke et al., 2024. Cell):<br> . AF2_HM_full_models: Full structures of homodimeric models.<br> . AF2_HM_nodiso3: Core structures of homomeric models, trimmed using scripts from Schweke et al. (2023).</p> <p>- Models of heteromers (generated in this work):<br> . AF2_HET_full_models: Full structures of heterodimeric models.<br> . AF2_HET_nodiso3: Core structures of heteromeric models, trimmed using a modified version of the code from Schweke et al. (2023) to work with heterodimers.</p>
Mining Proteomic Databases of a Model Plant Medicago truncatula for Mosaic Proteins and Other Unconventional Translation Products
<p><strong>How many different proteins can be produced from a single spliced transcript? Genome annotation projects do not consider the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins (altProts), have been shown to carry out important functions in various organisms. Overlapping altORFs may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is technically very challenging. If confirmed, this concept will revolutionize modern genetics. In this project, we would like to follow a unique strategy for the detection of mosaic proteins in proteomic databases publicly available for a very important model plant <em>Medicago truncatula</em>. The proposed analysis will be based on our own preliminary data already generated in the course of an ongoing TÜBİTAK1002 project. Regardless of whether the evidence for mosaic translation is found in this study, this effort will help identify such proteins later when more proteomic data become available. Finally, our approach can reveal unconventional frameshifting products that derive from the omission of several nucleotides by ribosomes (for example, +2 to +16 frameshifts). Regardless of whether such frameshifted products are parts of mosaic proteins, the potential for their detection makes this project very novel, because frameshifts longer than one nucleotide in the forward direction have not been described so far.</strong></p>
Saccharomyces cerevisiae protein phosphorylation and translation accuracy
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Post-Translational Site-selective Protein Backbone α-Deuteration
<p>This folder TS_xyz contains all the TS structures from conformational sampling in .xyz format accompanying the paper</p> <p>"Post-Translational Site-selective Protein α-Deuteration: Protein Backbone Modification and Use as a Tool for Protein Mechanism" by Galan et al.</p> <p><br> Two subfolders, indicated by the identity of the base used int the studies, with the following substructures, can be found:</p> <p> <br> |------ THTCD_deprotonation: all TSs from deprotonation of tetrahydrothiophene ring<br> | <br> 1_hydroxide_base --------|------ intramolecular deprotonation: all TSs from intramolecular deprotonation by sulfonium ylid<br> |<br> |------ E2_deprotonation: all TSs from deprotonation of alpha-carbon of cysteine<br> |<br> |------ sulfonium_ylid_deprotonation: all TSs from sulfonium ylid decomposition via cycloreversion</p> <p> |------ THTCD_deprotonation: lowest (and the only found) TS for deprotonation of tetrahydrothiophene ring <br> | <br> 2_dihydrogen_phosphate_base --------|<br> |<br> |------ E2_deprotonation: all TSs from deprotonation of alpha-carbon of cysteine<br> </p>
Rapid Flow-Based Synthesis of Post-Translationally Modified Peptides and Proteins: A Case Study on MYC's Transactivation Domain
<p>Raw data for the project "Rapid Flow-Based Synthesis of Post-Translationally Modified Peptides and Proteins: A Case Study on MYC's Transactivation Domain".</p> <p>Manuscript and supporting information available on Chemical Science: <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D4SC00481G">https://doi.org/10.1039/D4SC00481G</a></p>
Stereoretentive Post-Translational Protein Editing
<p>This dataset contains raw LCMSMS files used to confirm chemical post-translational modifications described in the article.</p>
Ribosome profiling reveals a functional role for autophagy in protein translational control
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Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore
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Data from: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus
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Data from: Amyloid precursor protein translation is regulated by a 3'UTR guanine quadruplex
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Cell type specific profiling of alternative translation identifies novel protein isoforms in the mouse brain
GEO Series GSE115483. Mus musculus. 4 samples. Type: Expression 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.
Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris
GEO Series GSE116415. Komagataella pastoris. 60 samples. Type: Expression profiling by high throughput sequencing.
mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
GEO Series GSE128265. Homo sapiens. 6 samples. Type: Other.
Systems-level computational translation of mouse and human transcriptomics reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection
GEO Series GSE281697. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Aldolase A Accelerates Cancer Progression by Modulating mRNA Translation and Protein Biosynthesis via Noncanonical Mechanisms
GEO Series GSE224922. Homo sapiens. 4 samples. Type: Other.
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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
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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.
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