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408 results for “ubiquitin”
Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units
<p>These are the original data used to make figures for the manuscript titled "Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units" by Sarasi Galagedera et al.</p> <p> </p>
SEC-MALS: USP5 and Ubiquitin
<p>Determination of the stoichiometry of binding of monoubiquitin (Ubq) to the <a href="https://zenodo.org/record/1495189#.XnS84ohKjIV">full-length wildtype</a> USP5 and <a>R221A mutant</a> protein by size exclusion chromatography-multiple angle light scattering (SEC-MALS) to elucidate the binding properties of native Ubq for future cell-based and activity studies.</p>
USP5 zinc-finger ubiquitin binding domain with L-cysteine(residue195)-glutathione disulfide structure solution
<p>USP5 zinc-finger ubiquitin binding domain with L-cysteine(residue195)-glutathione disulfide structure solution to 1.6 Å resolution</p>
Figure 1 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 1. The nucleotide and deduced amino acid sequences of the P. xylostella RpS27a gene coding region. The deduced amino acid sequence is presented below the nucleotide sequence in a single letter. The nuclear localization signal sequence is shaded. The initial and termination codon are underlined. The stop codon is denoted with an asterisk.
Figure 5. Phylogenetic relationship between P. xylostella RpS27a in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 5. Phylogenetic relationship between P. xylostella RpS27a and some other species. Corresponding GenBank accession numbers are: M. sexta: ACY95367.1; P. dardanus: CAH04128.1; Bombyx mori: NP_001091826.1; P. polytes: BAM18943.1; P. xuthus: BAM17728.1; S. frugiperda: AAL62473.1; D. plexippus: EHJ77179.1; A. yamamai: BAD05031.1; P. xylostella: JX437934; T. rubida: AER92457.1; D. melanogaster: NP_476778.1; A. aegypti: AAS79344.1; C. quinquefasciatus: XP_001844485.1.
Figure 6 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 6. mRNA level of RpS27a in DS-strain and DR-strain of P. xylostella. All values are expressed as means ± SD. DS-strain: deltamethrin-susceptible strain; DR-strain: deltamethrinresistant strain. *P <0.01.
Multi-body cryo-em maps and models of a pentameric KCTD5/Cullin3/Gβγ E3 ubiquitin ligase complex
<p>Heterotrimeric G proteins can be regulated by post-translational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain (CTD), engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3<sup>KCTD5</sup>) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3<sup>NTD</sup>/Gβ<sub>1</sub>γ<sub>2</sub> assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5<sup>BTB</sup>/CUL3<sup>NTD</sup> and KCTD5<sup>CTD</sup>/Gβγ moieties of the structure. CRL3<sup>KCTD5</sup> engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 super-assembly, and extension of the structure to include full-length CUL3<sup> </sup>with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3<sup>NTD</sup> Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex.</p>
Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments
<p>Poly-ubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable their molecular recognition by a large number of partners in multiple biological pathways. By using alternative linkage, it is possible to obtain poly-ubiquitin molecules with different dynamical properties. This flexibility is further increased by the possibility to tune the length of poly-ubiquitin chains. Characterizing the dynamics of poly-ubiquitins as a function of their length is thus relevant to understand their biology. Structural characterization of poly-ubiquitin conformational dynamics is challenging both experimentally and computationally due to increasing system size and conformational variability. Here, by developing highly efficient and accurate small-angle X-ray scattering driven Martini coarse-grain simulations, we characterize the dynamics of linear M1-linked di-, tri- and tetra-ubiquitin chains. Our data show that the behavior of the di-ubiquitin subunits is independent of the presence of additional ubiquitin modules. We propose that the conformational space sampled by linear poly-ubiquitins, in general, may follow a simple self-avoiding polymer model. These results, combined with experimental data from small angle X-ray scattering, biophysical techniques and additional simulations show that binding of NEMO, a central regulator in the NF-κB pathway, to linear poly-ubiquitin obeys a 2:1 (NEMO:poly-ubiquitin) stoichiometry in solution, even in the context of four ubiquitin units. Eventually, we show how the conformational properties of long poly-ubiquitins may modulate the binding with their partners in a length-dependent manner.</p>
The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Aging Phenotype with Diastolic Heart Failure
<p><strong><em>Aims</em></strong>. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the aging HFpEF phenotype.</p> <p><strong><em>Methods and Results.</em></strong> Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. However, at 8 weeks of age, LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation) - all p<0.05. Collagen percent area increased by over two-fold and fibrillar collagen expression (rtPCR) by over 1.5 fold (p<0.05) with WWP1 O/E. WWP1 with an anti-WWP1 antibody could be identified in isolated cardiac fibroblasts with WWP1 increased by over two-fold in O/E fibroblasts (p<0.05).</p> <p><strong><em>Conclusion.</em></strong> Inducing WWP1 expression caused LVH, preserved systolic function, but impaired diastolic dysfunction, consistent with the HFpEF phenotype. Targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with aging.</p>
Discovery and characterization of non-canonical ubiquitin conjugating enzymes
<p>Ubiquitin conjugating enzymes (E2s) play a central role in the enzymatic cascade that leads to the attachment of ubiquitin to a substrate. This process, termed ubiquitylation is required to maintain cellular homeostasis and impacts almost all cellular process. By interacting with multiple E3 ligases, E2s dictate the ubiquitylation landscape within the cell. Since its discovery, ubiquitylation has been regarded as a post-translational modification (PTM) that specifically targets lysine side chains (canonical ubiquitylation). We used Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) Mass Spectrometry (MS), to discover and characterize a family of E2s that are instead able to conjugate ubiquitin to serine and/or threonine. We employed structural modelling and prediction tools to identify the key activity determinants that these E2s use to interact with ubiquitin as well as their substrates. Our results identify the missing E2s required for non-canonical ubiquitylation, highlight the versatility of ubiquitin modifications and challenge the view of ubiquitylation as an exclusively lysine specific PTM.</p>
Apo USP5 zinc-finger ubiquitin binding domain structure solution 2018/03/30
<p>USP5 zinc-finger ubiquitin binding domain structure solution to 1.55 Å resolution</p>
The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Ageing Phenotype with Diastolic Heart Failure
<p><strong><em>Aims</em></strong>. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the ageing HFpEF phenotype.</p> <p><strong><em>Methods and Results.</em></strong> Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. LVH and diastolic dysfunction occurred with WWP1 O/E wherein LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation). Collagen percent area increased by over two-fold with WWP1 O/E and increased expression of determinants of fibrosis and growth (qPCR) were also concomitantly increased.</p> <p><strong><em>Conclusion.</em></strong> Inducing WWP1 expression caused LVH with significant diastolic dysfunction, consistent with the HFpEF phenotype. Thus, targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with ageing</p>
Bigwig files for paper "STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading"
<p>Bigwig files for paper "STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading". </p>
Supplementary materials for "High-Throughput Discovery of Substrate Peptide Sequences for E3 Ubiquitin Ligases Using a cDNA Display Method."
<p>The next-generation sequencing (NGS) data of the 5th rounds' samples for LX9 library and p53deg library. The csv files contain DNA sequences read out, amino acid sequences and their read counts in descending order. </p>
Data for: HPV upregulates MARCHF8 ubiquitin ligase and inhibits apoptosis by degrading the death receptors in head and neck cancer
<p>The membrane-associated RING-CH-type finger ubiquitin ligase MARCHF8 is a human homolog of the viral ubiquitin ligases Kaposi's sarcoma herpesvirus K3 and K5 that promote host immune evasion. Previous studies have shown that MARCHF8 ubiquitinates several immune receptors, such as the major histocompatibility complex II and CD86. While human papillomavirus (HPV) does not encode any ubiquitin ligase, the viral oncoproteins E6 and E7 are known to regulate host ubiquitin ligases. Here, we report that MARCHF8 expression is upregulated in HPV-positive head and neck cancer (HNC) patients but not in HPV-negative HNC patients compared to normal individuals. The MARCHF8 promoter is highly activated by HPV oncoprotein E6-induced MYC/MAX transcriptional activation. The knockdown of MARCHF8 expression in human HPV-positive HNC cells restores cell surface expression of the tumor necrosis factor receptor superfamily (TNFRSF) death receptors, FAS, TRAIL-R1, and TRAIL-R2, and enhances apoptosis. MARCHF8 protein directly interacts with and ubiquitinates the TNFRSF death receptors. Further, MARCHF8 knockout in mouse oral cancer cells expressing HPV16 E6 and E7 augments cancer cell apoptosis and suppresses tumor growth in vivo. Our findings suggest that HPV inhibits host cell apoptosis by upregulating MARCHF8 and degrading TNFRSF death receptors in HPV-positive HNC cells.</p>
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
<p>The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub<sub>2</sub>) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub<sub>2</sub> combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub<sub>2</sub> are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub<sub>2</sub> modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.</p>
Molecular dynamics-generated ensemble dataset of ubiquitin; for "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles"
<p>The molecular dynamics-generated ensemble dataset (229Mb zip file) for ubiquitin, used in the manuscript "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles", submitted to the Journal of Chemical Information and Modeling (JCIM). The dataset consists of 6 .dcd files, and one .pdb file. </p>
Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
<p>Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)</p>
Data for: HPV upregulates MARCHF8 ubiquitin ligase and inhibits apoptosis by degrading the death receptors in head and neck cancer
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NMR raw data for: DTX3L ubiquitin ligase ubiquitinates single-stranded nucleic acids
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