TRIM56 coiled-coil domain structure provides insights into its E3 ligase functions

Protein ubiquitination is a post-translation modification mediated by E3 ubiquitin ligases. The RING domain E3 ligases are the largest family of E3 ubiquitin ligases, they act as a scaffold, bringing the E2-ubiquitin complex and its substrate together to facilitate direct ubiquitin transfer. However, the quaternary structures of RING E3 ligases that perform ubiquitin transfer remain poorly understood. In this study, we solved the crystal structure of TRIM56, a member of the RING E3 ligase. The structure of the coiled-coil domain indicated that the two anti-parallel dimers bound together to form a tetramer at a small crossing angle. This tetramer structure allows two RING domains to exist on each side to form an active homodimer in supporting ubiquitin transfer from E2 to its nearby substrate recruited by the C-terminal domains on the same side. These findings suggest that the coiled-coil domain-mediated tetramer is a feasible scaffold for facilitating the recruitment and transfer of ubiquitin to accomplish E3 ligase activity.

Structural studies of the coiled-coil domain of TRIM75 reveal a tetramer architecture facilitating its E3 ligase complex

Protein ubiquitination plays a vital role in controlling the degradation of intracellular proteins and in regulating cell signaling pathways. Functionally, E3 ubiquitin ligases control the transfer of ubiquitin to the target substrates. As a major family of ubiquitin E3 ligases, the structural assembly of RING E3 ligases required to exert their ubiquitin E3 ligase activity remains poorly defined. Here, we solved the crystal structure of the coiled-coil domain of TRIM75, a member of the RING E3 ligase family, which showed that two disulfide bonds stabilize two antiparallel dimers at a small crossing angle. This tetrameric conformation confers two close RING domains on the same side to form a dimer. Furthermore, this architecture allows the RING dimer to present ubiquitin to a substrate on the same side. Overall, this structure reveals a disulfide bond-mediated unique tetramer architecture and provides a tetrameric structural model through which E3 ligases exert their function.

Structure, optical and electro-physical properties of tetramerized anion-radical salt (N-Xy-Qn)(TCNQ)2

The (N-Xy-Qn)(TCNQ)₂ anion-radical salt characterized by tetramerized stacks of the TCNQ acceptor molecules has been synthesized and characterized using vibrational spectroscopy and electrical resistivity measurements. The bond lengths analysis based on the crystal structure data, indicates that the TCNQ molecules are non-uniformly charged with -0.83 e localized on the inner B molecules and -0.33 e on the outer A molecules within ABBA tetramers. Both infrared and Raman spectra of (N-Xy-Qn)(TCNQ)₂ are dominated by vibrational modes of TCNQ and display splitting related to the tetramerized structure. Many of these features are affected by the strong electron-molecular vibration (EMV) coupling. Other charge-sensitive modes allowed estimation of charge localized on TCNQ, with the results that confirm the charges estimated on basis of the crystal data. Electrical measurements revealed the low-conducting behavior with room temperature conductivity value of 2.6 mS cm^-1 and temperature dependence of resistivity that can be explained within the band conduction model. The calculated activation energies range from 0.169 eV to 0.187 eV, depending on the crystallographic direction and thermal history of the sample.

A Combinatorial in-silico, in-vitro and in-vivo Approach to Quantitatively Study Peptide Induced MHC Stability

Here, we describe a combinatorial approach in reverse vaccinology to identify immunogenic class I major histocompatibility complex (MHC) displayed epitopes derived from a morbillivirus named pestes des petits ruminants (PPRV). The protocol describes an in silico prediction of immunogenic epitopes using an IEDB tool. The predicted peptides were further analysed by molecular docking with mouse class I MHC (H-2K^b), to assess their binding affinity, and their immunogenicity was validated, using acellular and cellular assays. Finally, an enumeration of the expanded PPRV-specific CD8⁺ T cells in infected or immunized mice against the immunogenic peptides was performed ex vivo. Synthetic peptide derivatives from different structural and non-structural proteins of PPRV were used to measure the extent of stabilized H2-K^b, using an ELISA based acellular assay and TAP deficient RMA/s cells. Fluorescently labelled H2-K^b-tetramers were generated by displacing a UV photocleavable conditional ligand with the PPRV-peptides. The resulting reagents were used to identify and enumerate virus-specific CD8⁺ T cells in immunized or PPRV-infected mice. The combinatorial approach described here could be used to identify immunogenic epitopes of any pathogen, autoantigens, as well as cancer antigens. Graphic abstract: Figure 1.General schematic to identify immunogenic peptides and their stabilization on MHC I molecule.

Stability of p53 oligomers: Tetramerization of p53 impinges on its stability

The p53 protein has been known to exist structurally in three different forms inside the cells. Earlier studies have reported the predominance of the lower oligomeric forms of p53 over its tetrameric form inside the cells, although only the tetrameric p53 contributes to its transcriptional activity. However, it remains unclear the functional relevance of the existence of other p53 oligomers inside the cells. In this study, we characterize the stability and conformational state of tetrameric, dimeric and monomeric p53 that spans both DNA Binding Domain (DBD) and Tetramerization Domain (TD) of human p53 (94-360 amino acid residues). Intriguingly, our studies reveal an unexpected drastic reduction in tetrameric p53 thermal stability in comparison to its dimeric and monomeric form with a higher propensity to aggregate at physiological temperature. Our EMSA study suggests that tetrameric p53, not their lower oligomeric counterpart, exhibit rapid loss of binding to their consensus DNA elements at the physiological temperature. This detrimental effect of destabilization is imparted due to the tetramerization of p53 that drives the DBDs to misfold at a faster pace when compared to its lower oligomeric form. This crosstalk between DBDs is achieved when it exists as a tetramer but not as dimer or monomer. Our findings throw light on the plausible reason for the predominant existence of p53 in dimer and monomer forms inside the cells with a lesser population of tetramer form. Therefore, the transient disruption of tetramerization between TDs could be a potential cue for the stabilization of p53 inside the cells.

Measuring Drp1 Activity in Mitochondrial Fission In Vivo

Mitochondrial fission is mainly regulated by a number of dynamin superfamily proteins or DSPs, of which dynamin-like protein 1 (Drp1) is responsible for the scission process during mitochondrial fission. Here we describe several methods, including monitoring mitochondrial distribution, phosphorylation, and tetramer level of Drp1, to examine the activity of Drp1 in mitochondrial fission in vivo.

The tetramerization domain of the tree shrew p53 protein displays unique thermostability despite sharing high sequence identity with the human p53 protein

The p53 protein plays a number of roles in protecting organisms from different genotoxic stresses and this includes DNA damage induced by acetaldehyde, a metabolite of alcohol. Since the common tree shrew ingests high levels of alcohol as part of its normal diet, this suggests that its p53 protein may possess unique properties. Using a combination of biophysical and modeling studies, we demonstrate that the tetramerization domain of the tree shrew p53 protein is considerably more stable than the corresponding domain from humans despite sharing almost 90% sequence identity. Based on modeling and mutagenesis studies, we determine that a glutamine to methionine substitution at position 354 plays a key role in this difference. Given the link between stability of the p53 tetramerization domain and its transcriptional activity, the results suggest that this enhanced stability could lead to important consequences at p53-regulated genes in the tree shrew.

Control mechanisms in germ cells mediated by p53 family proteins

Germ cells are totipotent and, in principle, immortal as they are the source for new germ cells in each generation. This very special role requires tight quality control systems. The p53 protein family constitutes one of the most important quality surveillance systems in cells. Whereas p53 has become famous for its role as the guardian of the genome in its function as the most important somatic tumor suppressor, p63 has been nicknamed 'guardian of the female germ line'. p63 is strongly expressed in resting oocytes and responsible for eliminating those that carry DNA double-strand breaks. The third family member, p73, acts later during oocyte and embryo development by ensuring correct assembly of the spindle assembly checkpoint. In addition to its role in the female germ line, p73 regulates cell-cell contacts between developing sperm cells and supporting somatic cells in the male germ line. Here, we review the involvement of the p53 protein family in the development of germ cells with a focus on quality control in the female germ line and discuss medical implications for cancer patients.

Tetramerization of SATB1 is essential for regulating of gene expression

Special AT-rich sequence-binding protein 1 (SATB1) functions as a 'genome organizer' in tumorigenesis. Our previous report showed that SATB1 forms a tetramer through its N-terminal ubiquitin like domain rather than the proposed PDZ domain. In the present study, we aim to illustrate whether this oligomerization is critical to its function as a global repressor of gene expression in vivo. Luciferase and GST pull-down assays demonstrated that disrupting SATB1's tetramerization not only affects the activities of promoters but also influences the recruitment of interaction partners. Furthermore, we developed stable cell lines that overexpressed either the SATB1 tetramer or STAB1 dimer (KWN-AAA) and monitored global gene expression. Gene expression profiling revealed that over 1000 genes were significantly upregulated or downregulated upon the overexpression of SATB1 or the SATB1 (KWN-AAA) mutant. These data implied that SATB1 might regulate gene expression through its different oligomerization state. In conclusion, we inferred that the oligomerization of SATB1 is pivotal to its function of different biological processes.

The two interfaces of the STAT1 N-terminus exhibit opposite functions in IFNγ-regulated gene expression

Defective cooperative DNA binding of STAT1 (signal transducer and activator of transcription 1) transcription factor has impact on interferon-γ(IFNγ)-regulated transcriptional responses. In this study, we generated N-terminal gain-of-function mutants of this protein which exhibited hyperactive cooperativity and assessed their functional consequences on gene expression. Our data show that four negatively charged, surface-exposed amino acid residues in the N-terminal domain dimer are engaged in the disassembly of tyrosine-phosphorylated tetrameric complexes on DNA and prevent the occurrence of higher-order STAT1 oligomers on low-affinity DNA binding sites. Owing to their improved tetramer stability, the N-terminal mutants showed relaxed sequence requirements for the binding to DNA as compared to the wild-type protein. Similarly to a STAT1 mutant with impaired tetramerization, the N-terminal gain-of-function mutants showed elevated tyrosine-phosphorylation levels and prolonged nuclear accumulation upon stimulation of cells with IFNγ. However, in contrast to the global impairment of IFNγ signalling in tetramerization-deficient mutants, the transcriptional consequences of the N-terminal gain-of-function mutants are rather distinct and affect gene expression locally in a promoter-specific manner. Thus, we conclude that the STAT1 N-domain acts as a double-edged sword: while one interface is crucial for the formation of tetrameric complexes on IFNγ-regulated promoters, the opposite interface harbours an inhibitory mechanism that limits the accumulation of higher-order oligomers simply by disrupting cooperative DNA binding.

Novel mechanisms for superoxide-scavenging activity of human manganese superoxide dismutase determined by the K68 key acetylation site

Superoxide is the primary reactive oxygen species generated in the mitochondria. Manganese superoxide dismutase (SOD2) is the major enzymatic superoxide scavenger present in the mitochondrial matrix and one of the most crucial reactive oxygen species-scavenging enzymes in the cell. SOD2 is activated by sirtuin 3 (SIRT3) through NAD(+)-dependent deacetylation. However, the exact acetylation sites of SOD2 are ambiguous and the mechanisms underlying the deacetylation-mediated SOD2 activation largely remain unknown. We are the first to characterize SOD2 mutants of the acetylation sites by investigating the relative enzymatic activity, structures, and electrostatic potential of SOD2 in this study. These SOD2 mutations affected the superoxide-scavenging activity in vitro and in HEK293T cells. The lysine 68 (K68) site is the most important acetylation site contributing to SOD2 activation and plays a role in cell survival after paraquat treatment. The molecular basis underlying the regulation of SOD2 activity by K68 was investigated in detail. Molecular dynamics simulations revealed that K68 mutations induced a conformational shift of residues located in the active center of SOD2 and altered the charge distribution on the SOD2 surface. Thus, the entry of the superoxide anion into the coordinated core of SOD2 was inhibited. Our results provide a novel mechanistic insight, whereby SOD2 acetylation affects the structure and charge distribution of SOD2, its tetramerization, and p53-SOD2 interactions of SOD2 in the mitochondria, which may play a role in nuclear-mitochondrial communication during aging.

High resolution structures of Plasmodium falciparum GST complexes provide novel insights into the dimer-tetramer transition and a novel ligand-binding site

Protection from oxidative stress and efficient redox regulation are essential for malarial parasites which have to grow and multiply rapidly in pro-oxidant rich environments. Therefore, redox active proteins currently belong to the most attractive antimalarial drug targets. The glutathione S-transferase from Plasmodium falciparum (PfGST) is a redox active protein displaying a peculiar dimer-tetramer transition that causes full enzyme-inactivation. This distinct structural feature is absent in mammalian GST isoenzyme counterparts. A flexible loop between residues 113-119 has been reported to be necessary for this tetramerization process. However, here we present structural data of a modified PfGST lacking loop 113-119 at 1.9 Å resolution. Our results clearly show that this loop is not essential for the formation of stable tetramers. Moreover we present for the first time the structures of both, the inactive and tetrameric state at 1.7 Å and the active dimeric state in complex with reduced glutathione at 2.4 Å resolution. Surprisingly, the structure of the inactive tetrameric state reveals a novel non-substrate binding-site occupied by a 2-(N-morpholino) ethane sulfonic acid (MES) molecule in each monomer. Although it is known that the PfGST has the ability to bind lipophilic anionic ligands, the location of the PfGST ligand-binding site remained unclear up to now.

β-Apo-13-carotenone regulates retinoid X receptor transcriptional activity through tetramerization of the receptor

Retinoid X receptor (RXRα) is activated by 9-cis-retinoic acid (9cRA) and regulates transcription as a homodimer or as a heterodimer with other nuclear receptors. We have previously demonstrated that β-apo-13-carotenone, an eccentric cleavage product of β-carotene, antagonizes the activation of RXRα by 9cRA in mammalian cells overexpressing this receptor. However, the molecular mechanism of β-apo-13-carotenone's modulation on the transcriptional activity of RXRα is not understood and is the subject of this report. We performed transactivation assays using full-length RXRα and reporter gene constructs (RXRE-Luc) transfected into COS-7 cells, and luciferase activity was examined. β-Apo-13-carotenone was compared with the RXRα antagonist UVI3003. The results showed that both β-apo-13-carotenone and UVI3003 shifted the dose-dependent RXRα activation by 9cRA. In contrast, the results of assays using a hybrid Gal4-DBD:RXRαLBD receptor reporter cell assay that detects 9cRA-induced coactivator binding to the ligand binding domain demonstrated that UVI3003 significantly inhibited 9cRA-induced coactivator binding to RXRαLBD, but β-apo-13-carotenone did not. However, both β-apo-13-carotenone and UVI3003 inhibited 9-cRA induction of caspase 9 gene expression in the mammary carcinoma cell line MCF-7. To resolve this apparent contradiction, we investigated the effect of β-apo-13-carotenone on the oligomeric state of purified recombinant RXRαLBD. β-Apo-13-carotenone induces tetramerization of the RXRαLBD, although UVI3003 had no effect on the oligomeric state. These observations suggest that β-apo-13-carotenone regulates RXRα transcriptional activity by inducing the formation of the "transcriptionally silent" RXRα tetramer.

The E3 ubiquitin protein ligase HERC2 modulates the activity of tumor protein p53 by regulating its oligomerization

The tumor suppressor p53 is a transcription factor that coordinates the cellular response to several kinds of stress. p53 inactivation is an important step in tumor progression. Oligomerization of p53 is critical for its posttranslational modification and its ability to regulate the transcription of target genes necessary to inhibit tumor growth. Here we report that the HECT E3 ubiquitin ligase HERC2 interacts with p53. This interaction involves the CPH domain of HERC2 (a conserved domain within Cul7, PARC, and HERC2 proteins) and the last 43 amino acid residues of p53. Through this interaction, HERC2 regulates p53 activity. RNA interference experiments showed how HERC2 depletion reduces the transcriptional activity of p53 without affecting its stability. This regulation of p53 activity by HERC2 is independent of proteasome or MDM2 activity. Under these conditions, up-regulation of cell growth and increased focus formation were observed, showing the functional relevance of the HERC2-p53 interaction. This interaction was maintained after DNA damage caused by the chemotherapeutic drug bleomycin. In these stressed cells, p53 phosphorylation was not impaired by HERC2 knockdown. Interestingly, p53 mutations that affect its tetramerization domain disrupted the HERC2-p53 interaction, suggesting a role for HERC2 in p53 oligomerization. This regulatory role was shown using cross-linking assays. Thus, the inhibition of p53 activity after HERC2 depletion can be attributed to a reduction in p53 oligomerization. Ectopic expression of HERC2 (residues 2292-2923) confirmed these observations. Together, these results identify HERC2 as a novel regulator of p53 signaling.