• TVP23A is a DUF846 containing protein, which is homologous throughout TVP-type proteins. (wikipedia.org)
  • The proteins involved in homologous recombination have to work around other processes that go on inside the nucleus, such as the transcription of DNA in genes into RNA molecules. (elifesciences.org)
  • Both homologous recombination, in which the ends of the broken DNA seek out intact templates with the same sequence, and nonhomologous end-joining pathways are found in Saccharomyces as they are in humans. (brandeis.edu)
  • In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. (nature.com)
  • Two‐dimensional electrophoresis of human placental mitochondria and protein identification by mass spectrometry: toward a human mitochondrial proteome. (nature.com)
  • Ubiquitin functions as a reversible post-translational modifier of proteins to regulate many different cellular processes such as DNA repair, chromatin dynamics, cell cycle regulation, membrane and protein trafficking, endocytosis, autophagy, but most notably proteasome-dependent protein degradation [2-4]. (123dok.net)
  • We have shown that the invasion of DNA strands into a donor template region requires the action of the chromatin remodeling protein Rad54 that enables the recombination machinery to gain access to "closed" regions of DNA. (brandeis.edu)
  • The DNA in the cell is packaged with histone proteins into chromatin. (usc.edu)
  • HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. (embl.de)
  • Furthermore, AT-hook motifs are frequently associated with known functional domains seen in chromatin proteins and in DNA-binding proteins (e.g. histone folds, homeodomains and zinc fingers). (embl.de)
  • This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22). (biomedcentral.com)
  • Essential for recruitment of Atg proteins to the pre-autophagosomal structure, the putative site for autophagosome formation, under starvation condition, resulting in the sequestration of cytoplasmic proteins and organelles for bulk degradation. (yeastgenome.org)
  • The C-terminal tail of ribosomal protein Rps15 is engaged in cytoplasmic pre-40S maturation. (db-engine.de)
  • Recent developments in purification strategies, together with mass spectrometry (MS)-based proteomics, have identified numerous in vivo protein complexes and suggest the existence of many others. (ox.ac.uk)
  • We combine two existing methodologies to tackle these challenges: tandem affinity purification to isolate sufficient quantities of highly pure native complexes, and MS of the intact assemblies and subcomplexes to determine their structural organization. (ox.ac.uk)
  • The peroxisomal protein import machinery, which shares similarities with chloroplasts, is unique in transporting folded and large (up to 10 nm in diameter) protein complexes into peroxisomes. (tcdb.org)
  • Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes. (biomedcentral.com)
  • The EMBL-EBI Complex Portal (www.ebi.ac.uk/intact/complex) is a central service that provides manually curated information on stable, on macromolecular complexes from model organisms. (stanford.edu)
  • Transformation of Chaetomium thermophilum and affinity-purification of native thermostable protein complexes. (db-engine.de)
  • Small angle neutron scattering (SANS) provides unique insight into biomacromolecular complexes by combining solvent contrast variation (H2O:D2O exchange) with either natural contrast between different classes of biomolecules (proteins, RNA/DNA, lipids/detergents) and/or by applying artificial contrast, i.e. deuteration of specific biomolecules. (lu.se)
  • In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)
  • This diagram displays the protein subunits (blue) of the complex and how they interact with each other. (yeastgenome.org)
  • We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. (nature.com)
  • Fig. 2: Potential sources of new mitochondrial proteins. (nature.com)
  • Over two dozen proteins involved in protein import and membrane insertion, peroxins, encoded by PEX genes, have been characterized. (tcdb.org)
  • 2011) addresses two of these aspects, the translocation of soluble proteins into the peroxisomal matrix and the biogenesis of the peroxisomal membrane. (tcdb.org)
  • 2011 ) have reviewed the processes by which matrix and membrane proteins are incorporated into the peroxysome. (tcdb.org)
  • The membrane bound docking subcomplex includes several Pex proteins, Pex13p, 14p and 17p. (tcdb.org)
  • Pex4p is a membrane protein that may facilitate cycling of Pex5p back to the cytosol. (tcdb.org)
  • All the mutants showed temperature-dependent mislocalization of green fluorescence protein (GFP)-tagged nucleoporins (nups) and the pore-membrane protein Pom152. (tamu.edu)
  • The Hansenula polymorpha PER9 gene encodes a peroxisomal membrane protein essential for peroxisome assembly and integrity. (microbiologyresearch.org)
  • The important components of this system are various cell membrane-associated proteins such as complement receptor 1 (CR1), complement receptor 2 (CR2), and decay accelerating factor (DAF). (medscape.com)
  • UniProt: the universal protein knowledgebase Nucleic Acids Res. (udel.edu)
  • Taken with the present results, this suggests that the potential use of inhibitors of prolyl 4-hydroxylase to control excessive collagen deposition in pathological fibrosis may be limited by the need to maintain continuous inhibition of collagen hydroxylation so as to facilitate intracellular degradation of the accumulated protein. (embl.de)
  • Biochemical and morphological studies demonstrate that the selective uptake of peroxisomes into the vacuole for degradation requires Cvt9 or Gsa9, but nonselective macroautophagy induced by nitrogen starvation does not require either protein. (rupress.org)
  • 10% of that in control cells, due to a very rapid degradation of protein newly synthesized in the mitochondria. (rhea-db.org)
  • b) In cells from patient 2, the rate of degradation of newly synthesized trifunctional protein was faster than that in control cells, giving rise to a trifunctional protein amounting to 60% of the control levels. (rhea-db.org)
  • Most other protein bands represent minor partial degradation of the same protein. (baltymas.lt)
  • In a collaborative project with the biotech company Intact Genomics, her team used heterologous expression of FACs in A. nidulans , paired with metabolomics to identify promising new fungal natural products (1). (drugdiscoverynews.com)
  • Following GEN pretreatment of HUVECs, H2O2 was added, and apoptosis was detected by flow cytometry, and the expression of relevant genes and proteins was detected by PCR and westerner blot. (bvsalud.org)
  • Ubiquitin is a highly conserved small eukaryotic protein. (123dok.net)
  • Ubiquitin is a small eukaryotic protein of 76 amino acids whose name (i.e., it occurs ubiquitously) results from its remarkable evolutionary conservation [1]. (123dok.net)
  • Structural inventory of cotranslational protein folding by the eukaryotic RAC complex, Structural inventory of cotranslational protein folding by the eukaryotic RAC complex, Nat. (db-engine.de)
  • We have classified these motifs into three types according to their sequence similarity and have found that they are prevalent in many eukaryotic nuclear proteins in single or multiple copies. (embl.de)
  • The AT-hook is a small DNA-binding protein motif which was first described in the high mobility group non-histone chromosomal protein HMG-I(Y). Since its discovery, this motif has been observed in other DNA-binding proteins from a wide range of organisms. (embl.de)
  • Trans-Golgi network vesicle protein 23 A (TVP23A) is a protein coded for the TVP23A gene, formerly known as FAM18A. (wikipedia.org)
  • Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. (nature.com)
  • Weighted gene correlation network analysis (WGCNA) can identify groups of biologically related proteins using only protein intensity values by constructing protein correlation networks. (stanford.edu)
  • Many of these proteins are regulators of gene expression. (embl.de)
  • Genes that encode the proteins of complement components or their isotypes are distributed throughout different chromosomes, with 19 genes comprising 3 significant complement gene clusters in the human genome. (medscape.com)
  • These single-stranded DNA 'tails' are then free to interact with an intact copy of the same DNA sequence from elsewhere in the cell's nucleus, which is used as a guide when repairing the damage. (elifesciences.org)
  • Using pattern searches and position-dependent matrices, we have extracted the AT-hook motifs present in a non-redundant protein sequence database. (embl.de)
  • The HMG family of proteins comprises members with multiple HMG domains that bind DNA with low sequence specificity, and members with single HMG domains that recognize specific nucleotide sequences. (embl.de)
  • Transition of the preRC to an active initiation complex is regulated by cyclin-dependent kinases and other signaling molecules, which promote further protein assembly and activate the mini chromosome maintenance helicase. (usc.edu)
  • The hypothesized function of TVP23A is a transmembrane protein involved in retrograde transport of vesicles from early endosomes into the late Golgi apparatus. (wikipedia.org)
  • A large pore is formed by transmembrane proteins. (tcdb.org)
  • The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. (academicinfluence.com)
  • Ubiquitin fusion to other r-proteins, such as P1 or P2, and even to non-ribosomal proteins such as actin, has been reported in diverse genera of rare single-celled algae as, for example, Bigelowiella [6]. (123dok.net)
  • Double-labelled immunofluorescence showed that both p33 and p92 replicase proteins localized to peroxisomes, independently of one another and of the presence of the replication template. (microbiologyresearch.org)
  • It is suggested that these proteins are sorted initially from the cytosol to the endoplasmic reticulum and then to peroxisomes. (microbiologyresearch.org)
  • Bod1-depleted cells form syntelic attachments that can oscillate and generate enough force to separate sister kinetochores, suggesting that microtubule-kinetochore interactions were intact. (rupress.org)
  • Bod1 depletion does not affect the activity or localization of Aurora B but does cause mislocalization of the microtubule depolymerase mitotic centromere- associated kinesin and prevents its efficient phosphorylation by Aurora B. Therefore, Bod1 is a novel kinetochore protein that is required for the detection or resolution of syntelic attachments in mitotic spindles. (rupress.org)
  • Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature. (udel.edu)
  • In adherent cells, treatment with cytochalasin D, but not colchicine, inhibits nuclear translocation and downstream activity of ERK, suggesting that integrin-actin interactions, but not intact microtubules, are important for ERK translocation. (rupress.org)
  • High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. (embl.de)
  • HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. (embl.de)
  • SARS coronavirus recombinant protein (SARS-rN) was produced by Baltymas for comparison with homologue SARS-CoV-2 nucleoprotein. (baltymas.lt)
  • It has been shown that, due to high similarity of these proteins, SARS-CoV nucleoprotein may also be used for the detection of specific antibodies against SARS-CoV-2. (baltymas.lt)
  • We further present several functional assays that confirm the variation in diastatic activity across STA1+ strains and show a clear correlation with earlier onset and increasing strength in strains that contain an intact STA1 promoter. (omegayeast.com)
  • These strains are characterized by the ability to secrete a glucoamylase protein that degrades dextrins. (omegayeast.com)
  • Both are composed of type-specific HPV L1 protein, the major capsid protein of HPV. (cdc.gov)
  • We are interested in understanding at the molecular level how recombination occurs and what roles are played by the many proteins involved in DNA recombination, repair and replication. (brandeis.edu)
  • We are interested in determining what are the specific biochemical roles played by the many proteins implicated in DNA recombination, repair and replication. (brandeis.edu)
  • We have identified the proteins necessary to carry out the initial steps in strand invasion and the beginning of new DNA synthesis, which is significantly different from the normal process of replication. (brandeis.edu)
  • Replication origins in the DNA nucleate the ordered assembly of protein factors to form a prereplication complex (preRC) that is poised for DNA synthesis. (usc.edu)
  • We conclude that ubiquitin might serve as a cis-acting molecular chaperone that assists in the folding and synthesis of the fused eL40 and eS31 ribosomal proteins. (123dok.net)
  • The defects did not affect the stability of existing NPCs, and nup mislocalization was dependent on de novo protein synthesis and continued cell growth. (tamu.edu)
  • Proteins targeted to the peroxisome (in plants called glyoxisomes) are synthesized in the cytoplasm of the cell and are targeted to the peroxisome post-translationally, possibly via multiple pathways. (tcdb.org)
  • We further identified changes in module eigenproteins indicative of dysregulation in protein translation and trafficking pathways. (stanford.edu)
  • dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. (udel.edu)
  • Four mutant complementation groups were characterized that correspond to respective mutations in genes encoding Ran (gsp1), and essential Ran regulatory factors Ran GTPase-activating protein (rna1), Ran guanine nucleotide exchange factor (prp20), and the RanGDP import factor (ntf2). (tamu.edu)
  • Deficiency of any of these regulatory proteins results in a state of overactivation of the complement system, with damaging inflammatory effects. (medscape.com)
  • The clean-up step is designed to desalt the fractions and rid them of urea and ampholytes prior to analysis by LC-MS-MS. Fifty milligrams of protein were separated into 20 fractions by liquid-phase isoelectric focusing, spanning a pH range of 3-10. (usuhs.edu)
  • To demonstrate the power of TMTProC, we analyzed a human and yeast interference sample and were able to quantify 13,290 proteins in 24 fractions. (biorxiv.org)
  • Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. (stanford.edu)
  • In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. (nature.com)
  • We analyzed the organization and function of mitochondrial DNA in a stable human cell line (ECV304, which is also known as T-24) containing mitochondria tagged with the yellow fluorescent protein. (biomedcentral.com)
  • We now examine the organization of mitochondrial genomes in a human cell line that contains mitochondria tagged with the yellow fluorescent protein (YFP). (biomedcentral.com)
  • Klapholz-Brown Z, Walmsley GG, Nusse YM, Nusse R, Brown PO "Transcriptional program induced by wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments. (openwetware.org)
  • This control is propagated through the alpha-subunit of prolyl 4-hydroxylase where protein levels were previously shown to rise fivefold with increasing cell density. (embl.de)
  • Using a fluorescent sulfhydryl probe as well as a sulfhydryl inhibitor, one observes a strong cell density response, supporting the hypothesis that cellular redox potential could alter protein stability. (embl.de)
  • Emma Lundberg's group has a wealth of experience in using microscopy to yield biological images that paint a picture of this cell-to-cell heterogeneity of protein expression information, and joining her lab has deepened my expertise in integrating datasets to perform innovative analyses of single-cell protein expression. (stanford.edu)
  • The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. (stanford.edu)
  • We examined the enzyme protein and biosynthesis of human trifunctional protein harboring enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and 3-ketoacyl-CoA thiolase activity in cultured skin fibroblasts from two patients with long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency. (rhea-db.org)
  • 2015) Structural organization of an intact phycobilisome and its association with photosystem II. (tsinghua.edu.cn)
  • When available from the Protein Data Bank (PDB), the physical structure of the macromolecular complex is displayed. (yeastgenome.org)
  • The first of these is Bod1, a protein conserved throughout metazoans that associates with a large macromolecular complex and localizes with kinetochores and spindle poles during mitosis. (rupress.org)
  • This increased sensitivity results in ~65% more proteins quantified compared to TMTPro-MS3 and even slightly outperforms TMTPro-MS2. (biorxiv.org)
  • We have analyzed the phenotypic effects of a genomic ubi1∆ub-HA ubi2∆ mutant, which expresses a ubiquitin-free HA-tagged eL40A protein as the sole source of cellular eL40. (123dok.net)
  • This mutant shows a severe slow-growth phenotype, which could be fully suppressed by increased dosage of the ubi1∆ub-HA allele, or partially by the replacement of ubiquitin by the ubiquitin-like Smt3 protein. (123dok.net)
  • for example, the proteins factor H and factor I inhibit the formation of the enzyme C3 convertase of the alternative pathway. (medscape.com)
  • One puzzle involves the ability of an IFIT protein previously known as IFIT1 to distinguish between cellular (mammalian) mRNAs and viral mRNAs. (elifesciences.org)
  • Human IFIT1 protein, by contrast, is not tricked by the disguise and targets both cap0 and cap1 viral mRNAs. (elifesciences.org)
  • This suggests that human IFIT1 protein recognizes viral mRNA by a different and as-yet-unknown means. (elifesciences.org)
  • These findings can be applied in the design of new antibody/antigen interaction-based analytical systems dedicated for the determination of anti-SCoV2-N antibodies and for the development of new anti-SARS-CoV-2 medications based on proteins that are blocking viral SCoV2-N proteins. (baltymas.lt)
  • Normally, the conjugation of ubiquitin to other proteins involves the formation of an isopeptide bond between the α-carboxyl group of the C-terminal glycine of a ubiquitin molecule with an ε-amino group of a specific lysine residue within the target protein [2,3]. (123dok.net)
  • Protein-coding regions of the resulting RNAs are translated by ribosomes within the mitochondrion. (biomedcentral.com)
  • Expression of the L1 protein using recombinant DNA technology produces noninfectious virus-like particles (VLPs). (cdc.gov)
  • Global analysis of protein expression in yeast. (ymdb.ca)
  • Co-expression of Ov-phy-1 with the O. volvulus homologue of protein disulfide isomerase in a baculovirus system resulted in the production of enzymatically active O. volvulus prolyl 4-hydroxylase. (embl.de)
  • Hence, we investigated the immunohistochemical expression of Gpx-2 protein in colon adenocarcinoma samples derived from patients with colon adenocarcinoma who did not receive any form of treatment prior to the surgical procedure. (bvsalud.org)
  • In total, 101 (80.80%) samples had strong Gpx-2 protein expression and 24 (19.20%) samples were characterized with low expression. (bvsalud.org)
  • We found a decrease in cytoskeleton-related protein expression, a known hallmark of prostate tumors. (stanford.edu)