Inactive Configuration Research Articles

Water and chloride as allosteric inhibitors in WNK kinase osmosensing.

Osmotic stress and chloride regulate the autophosphorylation and activity of the WNK1 and WNK3 kinase domains. The kinase domain of unphosphorylated WNK1 (uWNK1) is an asymmetric dimer possessing water molecules conserved in multiple uWNK1 crystal structures. Conserved waters are present in two networks, referred to here as conserved water networks 1 and 2 (CWN1and CWN2). Here we show that PEG400 applied to crystals of dimeric uWNK1 induces de-dimerization. Both the WNK1 the water networks and the chloride binding site and are disrupted by PEG400. CWN1 is surrounded by a cluster of pan-WNK-conserved charged residues. Here we mutagenized these charges in WNK3, a highly active WNK isoform kinase domain, and WNK1, the isoform best studied crystallographically. Mutation of E314 in the Activation Loop of WNK3 (WNK3/E314Q and WNK3/E314A, and the homologous WNK1/E388A) enhanced the rate of autophosphorylation, and reduced chloride sensitivity. Other WNK3 Cluster mutants reduced the rate of autophosphorylation activity coupled with greater chloride sensitivity than wild-type. The water and chloride regulation thus appear linked. The lower activity of some mutants may reflect effects on catalysis. Crystallography showed that activating mutants introduced conformational changes in similar parts of the structure to those induced by PEG400. WNK activating mutations and crystallography support a role for CWN1 in WNK inhibition consistent with water functioning as an allosteric ligand.

Spatially Localized Entropy-Driven Evolution of Nucleic Acid-Based Constitutional Dynamic Networks for Intracellular Imaging and Spatiotemporal Programmable Gene Therapy.

The primer-guided entropy-driven high-throughput evolution of the DNA-based constitutional dynamic network, CDN, is introduced. The entropy gain associated with the process provides a catalytic principle for the amplified emergence of the CDN. The concept is applied to develop a programmable, spatially localized DNA circuit for effective in vitro and in vivo theranostic, gene-regulated treatment of cancer cells. The localized circuit consists of a DNA tetrahedron core modified at its corners with four tethers that include encoded base sequences exhibiting the capacity to emerge and assemble into a [2 × 2] CDN. Two of the tethers are caged by a pair of siRNA subunits, blocking the circuit into a mute, dynamically inactive configuration. In the presence of miRNA-21 as primer, the siRNA subunits are displaced, resulting in amplified release of the siRNAs silencing the HIF-1α mRNA and fast dynamic reconfiguration of the tethers into a CDN. The resulting CDN is, however, engineered to be dynamically reconfigured by miRNA-155 into an equilibrated mixture enriched with a DNAzyme component, catalyzing the cleavage of EGR-1 mRNA. The DNA tetrahedron nanostructure stimulates enhanced permeation into cancer cells. The miRNA-triggered entropy-driven reconfiguration of the spatially localized circuit leads to the programmable, cooperative bis-gene-silencing of HIF-1α and EGR-1 mRNAs, resulting in the effective and selective apoptosis of breast cancer cells and effective inhibition of tumors in tumor bearing mice.

Stochasticity in biomolecular systems with sequestration mechanisms

We study how sequestration mechanisms, such as protein binding to decoy sites and the reversible formation of phase-separated condensates, alter the statistics of protein levels. To implement such a type of regulation, we consider simple birth-death processes in which protein molecules can reversibly switch between active (free-molecule) and inactive (sequestered) configurations with arbitrary concentration-dependent rates. When these transition rates depend only on the levels of the inactive protein, we show analytically that the steady-state distribution of the active protein level has Poisson statistics regardless of the details of the sequestration process. When transition rates depend on the active protein, the molecule copy number distribution is non-Poisson. We illustrate this deviation with the example of an enzyme-driven post-translational modification of an active protein into an inactive state, and we confirm the results using both analytical approximations and exact stochastic simulations. In summary, our results characterize the role of sequestration mechanisms in modulating the stochasticity of biochemical processes and identify noise-invariant processes.

Complement factor I: Regulatory nexus, driver of immunopathology, and therapeutic

Complement factor I (FI) is the nexus for classical, lectin and alternative pathway complement regulation. FI is an 88 kDa plasma protein that circulates in an inactive configuration until it forms a trimolecular complex with its cofactor and substrate whereupon a structural reorganization allows the catalytic triad to cleave its substrates, C3b and C4b. In keeping with its role as the master complement regulatory enzyme, deficiency has been linked to immunopathology. In the setting of complete FI deficiency, a consumptive C3 deficiency results in recurrent infections with encapsulated microorganisms. Aseptic cerebral inflammation and vasculitic presentations are also less commonly observed. Heterozygous mutations in the factor I gene (CFI) have been demonstrated to be enriched in atypical haemolytic uraemic syndrome, albeit with a very low penetrance. Haploinsufficiency of CFI has also been associated with decreased retinal thickness and is a strong risk factor for the development of age-related macular degeneration. Supplementation of FI using plasma purified or recombinant protein has long been postulated, however, technical difficulties prevented progression into clinical trials. It is only using gene therapy that CFI supplementation has reached the clinic with GT005 in phase I/II clinical trials for geographic atrophy.

Switchable Fluorescent Light‐Up Aptamers Based on Riboswitch Architectures

AbstractFluorescent light‐up RNA aptamers (FLAPs) such as Spinach or Mango can bind small fluorogens and activate their fluorescence. Here, we adopt a switching mechanism otherwise found in riboswitches and use it to engineer switchable FLAPs that can be activated or repressed by trigger oligonucleotides or small metabolites. The fluorophore binding pocket of the FLAPs comprises guanine (G) quadruplexes, whose critical nucleotides can be sequestered by corresponding anti‐FLAP sequences, leading to an inactive conformation and thus preventing association with the fluorophore. We modified the FLAPs with designed toehold hairpins that carry either an anti‐FLAP or an anti‐anti‐FLAP sequence within the loop region. The addition of an input RNA molecule triggers a toehold‐mediated strand invasion process that refolds the FLAP into an active or inactive configuration. Several of our designs display close‐to‐zero leak signals and correspondingly high ON/OFF fluorescence ratios. We also modified purine aptamers to sequester a partial anti‐FLAP or an anti‐anti‐FLAP sequence to control the formation of the fluorogen‐binding conformation, resulting in FLAPs whose fluorescence is activated or deactivated in the presence of guanine or adenine. We demonstrate that switching modules can be easily combined to generate FLAPs whose fluorescence depends on several inputs with different types of input logic.

Switchable Fluorescent Light-Up Aptamers Based on Riboswitch Architectures.

Fluorescent light-up RNA aptamers (FLAPs) such as Spinach or Mango can bind small fluorogens and activate their fluorescence. Here, we adopt a switching mechanism otherwise found in riboswitches and use it to engineer switchable FLAPs that can be activated or repressed by trigger oligonucleotides or small metabolites. The fluorophore binding pocket of the FLAPs comprises guanine (G) quadruplexes, whose critical nucleotides can be sequestered by corresponding anti-FLAP sequences, leading to an inactive conformation and thus preventing association with the fluorophore. We modified the FLAPs with designed toehold hairpins that carry either an anti-FLAP or an anti-anti-FLAP sequence within the loop region. The addition of an input RNA molecule triggers a toehold-mediated strand invasion process that refolds the FLAP into an active or inactive configuration. Several of our designs display close-to-zero leak signals and correspondingly high ON/OFF fluorescence ratios. We also modified purine aptamers to sequester a partial anti-FLAP or an anti-anti-FLAP sequence to control the formation of the fluorogen-binding conformation, resulting in FLAPs whose fluorescence is activated or deactivated in the presence of guanine or adenine. We demonstrate that switching modules can be easily combined to generate FLAPs whose fluorescence depends on several inputs with different types of input logic.

Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication.

The virtual circular genome (VCG) model was proposed as a means of going beyond template copying to indefinite cycles of nonenzymatic RNA replication during the origin of life. In the VCG model, the protocellular genome is a collection of short oligonucleotides that map to both strands of a virtual circular sequence. Replication is driven by templated nonenzymatic primer extensions on a subset of kinetically trapped partially base-paired configurations, followed by the shuffling of these configurations to enable continued oligonucleotide elongation. Here, we describe initial experimental studies of the feasibility of the VCG model for replication. We designed a small 12-nucleotide model VCG and synthesized all 247 oligonucleotides of lengths 2 to 12 corresponding to this genome. We experimentally monitored the fate of individual labeled primers in the pool of VCG oligonucleotides following the addition of activated nucleotides and investigated the effect of factors such as oligonucleotide length, concentration, composition, and temperature on the extent of primer extension. We observe a surprisingly prolonged equilibration process in the VCG system that enables a considerable extent of reaction. We find that environmental fluctuations would be essential for continuous templated extension of the entire VCG system since the shortest oligonucleotides can only bind to templates at low temperatures, while the longest oligonucleotides require high-temperature spikes to escape from inactive configurations. Finally, we demonstrate that primer extension is significantly enhanced when the mix of VCG oligonucleotides is preactivated. We discuss the necessity of ongoing in situ activation chemistry for continuous and accurate VCG replication.

The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements

G protein-coupled receptors (GPCRs) are known to dimerize, but the molecular and structural basis of GPCR dimers is not well understood. In this study, we developed a computational framework to generate models of symmetric and asymmetric GPCR dimers using different monomer activation states and identified their most likely interfaces with molecular details. We chose the dopamine receptor D2 (D2R) homodimer as a case study because of its biological relevance and the availability of structural information. Our results showed that transmembrane domains 4 and 5 (TM4 and TM5) are mostly found at the dimer interface of the D2R dimer and that these interfaces have a subset of key residues that are mostly nonpolar from TM4 and TM5, which was in line with experimental studies. In addition, TM2 and TM3 appear to be relevant for D2R dimers. In some cases, the inactive configuration is unaffected by the partnered protomer, whereas in others, the active protomer adopts the properties of an inactive receptor. Additionally, the β-arrestin configuration displayed the properties of an active receptor in the absence of an agonist, suggesting that a switch to another meta-state during dimerization occurred. Our findings are consistent with the experimental data, and this method can be adapted to study heterodimers and potentially extended to include additional proteins such as G proteins or β-arrestins. In summary, this approach provides insight into the impact of the conformational status of partnered protomers on the overall quaternary GPCR macromolecular structure and dynamics.

SY31-1 Molecular targeted therapy with FLT3 inhibitor in AML

Two main types of FLT3 mutations are commonly identified in AML, internal tandem duplications (ITD) and kinase domain (KD) mutations. FLT3 mutations result in constitutive kinase activation and are associated with poor outcome. FLT3 inhibitors (FLT3i) include type 1 inhibitors (e.g., gilteritinib, lestaurtinib, midostaurin, crenolanib) that bind to the ATP binding site in both its active and inactive configuration, inhibiting both ITD and KD mutations. Type 2 inhibitors (e.g., quizartinib, sorafenib, ponatinib) bind to a hydrophobic domain adjacent to the ATP binding are only accessible in its inactive configuration.

A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC\xb7DNA\xb7Cdc6

The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to DNA initiates the ATP-dependent recruitment of Cdc6, Cdt1 and Mcm2-7 loading, but the structural details for timely ATPase site regulation and for how loading can be impeded by inhibitory signals, such as cyclin-dependent kinase phosphorylation, are unknown. Using cryo-electron microscopy, we have determined several structures of S. cerevisiae ORC·DNA·Cdc6 intermediates at 2.5–2.7 Å resolution. These structures reveal distinct ring conformations of the initiator·co-loader assembly and inactive ATPase site configurations for ORC and Cdc6. The Orc6 N-terminal domain laterally engages the ORC·Cdc6 ring in a manner that is incompatible with productive Mcm2-7 docking, while deletion of this Orc6 region alleviates the CDK-mediated inhibition of Mcm7 recruitment. Our findings support a model in which Orc6 promotes the assembly of an autoinhibited ORC·DNA·Cdc6 intermediate to block origin licensing in response to CDK phosphorylation and to avert DNA re-replication.

Development and validation of a label-free colorimetric aptasensor based on the HCR and hemin/G-quadruplex DNAzyme for the determination of patulin in fruits and fruit-based products from Xinjiang (China).

In this study, a simple, novel and practical label-free colorimetric aptasensor was successfully prepared for the ultrasensitive detection of patulin, based on the hybridization chain reaction (HCR) and hemin/G-quadruplex DNAzyme-signal amplification strategy. In this aptasensor, a detection probe was designed consisting of the aptamer sequence for the patulin and an initiator sequence to trigger the HCR. Two hairpin structures (H1 and H2) that included the G-quadruplex sequences in inactive configuration were used as functional elements. The presence of patulin triggered the opening of the hairpin structure and the beginning of the HCR. After the addition of hemin, G-rich DNA self-assembled into the peroxidase-mimicking hemin/G-quadruplex DNAzymes, which catalyzed a colorimetric reaction. Under optimized conditions, patulin was measured within a linear range of 0.1-200 ng mL-1, and the detection limit was 0.060 ng mL-1. The recovery rates ranged from 91.4 to 105% for fruits and fruit-based products. Subsequently, a total of 311 samples comprising fruits, fruit-based products and dried fruits were collected from supermarkets, production bases and farmers' markets in Xinjiang, and analyzed for patulin using the proposed aptasensor. Patulin was detected in 16 samples (5.14%) at concentrations ranging from 1.23 to 16.4 μg kg-1. None of the samples exceeded the maximal level set by the EU commission (50 μg kg-1). The positivity in fresh fruits (7.69%) was significantly higher than that of fruit-based products (4.00%) and dried fruits (1.25%). In summary, the proposed aptasensor can quickly detect patulin in food samples, thus providing a warning for mycotoxin contamination.

Asymmetric activation of the calcium-sensing receptor homodimer.

The calcium-sensing receptor (CaSR), a cell-surface sensor for Ca2+, is the master regulator of calcium homeostasis in humans and is the target of calcimimetic drugs for the treatment of parathyroid disorders1. CaSR is a family C G-protein-coupled receptor2 that functions as an obligate homodimer, with each protomer composed of a Ca2+-binding extracellular domain and a seven-transmembrane-helix domain (7TM) that activates heterotrimeric G proteins. Here we present cryo-electron microscopy structures of near-full-length human CaSR in inactive or active states bound to Ca2+ and various calcilytic or calcimimetic drug molecules. We show that, upon activation, the CaSR homodimer adopts an asymmetric 7TM configuration that primes one protomer for G-protein coupling. This asymmetry is stabilized by 7TM-targeting calcimimetic drugs adopting distinctly different poses in the two protomers, whereas the binding of a calcilytic drug locks CaSR 7TMs in an inactive symmetric configuration. These results provide a detailed structural framework for CaSR activation and the rational design of therapeutics targeting this receptor.

Selective Photoswitchable Allosteric Agonist of a G Protein-Coupled Receptor.

G protein-coupled receptors (GPCRs) are the most common targets of drug discovery. However, the similarity between related GPCRs combined with the complex spatiotemporal dynamics of receptor activation in vivo has hindered drug development. Photopharmacology offers the possibility of using light to control the location and timing of drug action by incorporating a photoisomerizable azobenzene into a GPCR ligand, enabling rapid and reversible switching between an inactive and active configuration. Recent advances in this area include (i) photoagonists and photoantagonists that directly control receptor activity but are nonselective because they bind conserved sites, and (ii) photoallosteric modulators that bind selectively to nonconserved sites but indirectly control receptor activity by modulating the response to endogenous ligand. In this study, we designed a photoswitchable allosteric agonist that targets a nonconserved allosteric site for selectivity and activates the receptor on its own to provide direct control. This work culminated in the development of aBINA, a photoswitchable allosteric agonist that selectively activates the Gi/o-coupled metabotropic glutamate receptor 2 (mGluR2). aBINA is the first example of a new class of precision drugs for GPCRs and other clinically important signaling proteins.

A Phosphorylated Intermediate in the Activation of WNK Kinases.

WNK kinases autoactivate by autophosphorylation. Crystallography of the kinase domain of WNK1 phosphorylated on the primary activating site (pWNK1) in the presence of AMP-PNP reveals a well-ordered but inactive configuration. This new pWNK1 structure features specific and unique interactions of the phosphoserine, less hydration, and smaller cavities compared with those of unphosphorylated WNK1 (uWNK1). Because WNKs are activated by osmotic stress in cells, we addressed whether the structure was influenced directly by osmotic pressure. pWNK1 crystals formed in PEG3350 were soaked in the osmolyte sucrose. Suc-WNK1 crystals maintained X-ray diffraction, but the lattice constants and pWNK1 structure changed. Differences were found in the activation loop and helix C, common switch loci in kinase activation. On the basis of these structural changes, we tested for effects on in vitro activity of two WNKs, pWNK1 and pWNK3. The osmolyte PEG400 enhanced ATPase activity. Our data suggest multistage activation of WNKs.

Eltrombopag Creates a Transient Chemical Phenocopy of TET2 Loss of Function That Contributes to Hematopoietic Precursor Expansion

Eltrombopag (Epag) is FDA approved for immune thrombocytopenic purpura (ITP) and aplastic anemia (AA), in which it induces tri-lineage responses in primary and refractory settings. These biologic effects suggest that Epag helps to regenerate not only committed megakaryocytic progenitors, but also hematopoietic stem and progenitor cells (HSPCs). Epag is a small molecule thrombopoietin receptor (TpoR) agonist that activates the JAK-STAT pathway to increase platelet counts similar to the polypeptide based TpoR agonist Nplate. In addition, some of Epag's activity may, unlike that of Nplate, be independent of TpoR. Epag increases HSC self-renewal in mice despite the lack of binding to murine TpoR and showed efficacy in a TpoR-deficient strain. Here we show that Epag binds and inhibits TET2 in an iron-chelation independent manner, to in this way increase precursor expansion. Since iron is a key prosthetic component of the TET2 enzyme, we determined if Epag sequestration of iron in HSPCs inhibits TET2 function. In silico modeling indicated that Epag can form a tripartate complex with Fe2+, αKG and TET2 (Fig.A). Epag interacted with TET2 via N1387 and H1984 forming a two-way H-bond and also coordinating Fe2+ sandwiched between N-Oxalylglycine a surrogate for aKG and H1381 residues of TET2 (Fig.A). To experimentally confirm the computational structural model and study the effect of Epag on TET2, we used an ELISA-based TET2 activity assay in a cell-free system. We found that Epag inhibits TET2 in a dose-dependent manner with an IC50 of 1.6±0.1 µM in the presence of 25 µM each of aKG and Fe2+ (Fig.B). Interestingly, this observed IC50 of Epag for TET2 inhibition is 10-fold lower than the plasma Cmax of Epag that is produced in humans at standard clinical doses. Therefore, we performed a dose dependent TET2 rescue experiment by increasing aKG and Fe2+. There was no proportional effect on the TET2 inhibitory IC50 of Epag upon increasing either Fe2+ or αKG suggesting the inhibition of TET2 is independent of both these co-factors (Fig.B). This was consistent with in silico structural model data indicating that Epag specifically binds and traps TET2 in an inactive state, explaining why increasing concentration of Fe2+ or Fe3+ failed to rescue TET2 activity (Fig.C). Also consistent with this model of how Epag inhibits TET2, we did not experimentally observe any significant effect of ascorbic acid (100 µM), known to activate TET2 through maintenance of Fe3+↔Fe2+ homeostasis during TET2 catalysis. Underscoring likely relevance of TpoR independent actions of Epag, Epag treatment of K562 cells displaying undetectable levels of TpoR mRNA as well as protein, significantly reduced levels of 5hmC, while Tpo had no effects on 5hmC (Fig.D). We are currently measuring, after written informed consent on an IRB approved protocol, 5hmc levels serially in patients who are receiving Epag. In summary, we demonstrate TpoR-independent actions of Epag, its direct inhibition of TET2 activity, most likely by locking TET2 in an inactive configuration. Given the fundamental role of TET2 in promoting differentiation, this mechanism-of-action of Epag could be one pathway by which it expands HSPCs, independent of TpoR. In short, Epag creates a transient chemical phenocopy of TET2 loss of function, simultaneously having the capacity to activate JAK-STAT signaling via TpoR. These actions together can explain the clinical potency of Epag. Figure Disclosures Nazha: Abbvie: Consultancy; Tolero, Karyopharma: Honoraria; Daiichi Sankyo: Consultancy; Incyte: Speakers Bureau; MEI: Other: Data monitoring Committee; Novartis: Speakers Bureau; Jazz Pharmacutical: Research Funding. Saunthararajah:Novo Nordisk: Consultancy; EpiDestiny: Consultancy, Equity Ownership, Patents & Royalties. Sekeres:Celgene: Membership on an entity's Board of Directors or advisory committees; Millenium: Membership on an entity's Board of Directors or advisory committees; Syros: Membership on an entity's Board of Directors or advisory committees. Maciejewski:Novartis: Consultancy; Alexion: Consultancy.

Mechanisms of opening and closing of the bacterial replicative helicase.

Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.

Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori.

Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5’-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT.

The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel

Ubiquitin-specific protease 15 (USP15) regulates important cellular processes, including transforming growth factor β (TGF-β) signaling, mitophagy, mRNA processing, and innate immune responses; however, structural information on USP15's catalytic domain is currently unavailable. Here, we determined crystal structures of the USP15 catalytic core domain, revealing a canonical USP fold, including a finger, palm, and thumb region. Unlike for the structure of paralog USP4, the catalytic triad is in an inactive configuration with the catalytic cysteine ∼10 Å apart from the catalytic histidine. This conformation is atypical, and a similar misaligned catalytic triad has so far been observed only for USP7, although USP15 and USP7 are differently regulated. Moreover, we found that the active-site loops are flexible, resulting in a largely open ubiquitin tail–binding channel. Comparison of the USP15 and USP4 structures points to a possible activation mechanism. Sequence differences between these two USPs mainly map to the S1′ region likely to confer specificity, whereas the S1 ubiquitin–binding pocket is highly conserved. Isothermal titration calorimetry monoubiquitin- and linear diubiquitin-binding experiments showed significant differences in their thermodynamic profiles, with USP15 displaying a lower affinity for monoubiquitin than USP4. Moreover, we report that USP15 is weakly inhibited by the antineoplastic agent mitoxantrone in vitro. A USP15–mitoxantrone complex structure disclosed that the anthracenedione interacts with the S1′ binding site. Our results reveal first insights into USP15's catalytic domain structure, conformational changes, differences between paralogs, and small-molecule interactions and establish a framework for cellular probe and inhibitor development.

PPARγ in Complex with an Antagonist and Inverse Agonist: a Tumble and Trap Mechanism of the Activation Helix

SummaryPeroxisome proliferator activated receptor γ (PPARγ) is a nuclear receptor and target for antidiabetics that increase insulin sensitivity. Owing to the side effects of PPARγ full agonists, research has recently focused on non-activating ligands of PPARγ, which increase insulin sensitivity with decreased side effects. Here, we present the crystal structures of inverse agonist SR10171 and a chemically related antagonist SR11023 bound to the PPARγ ligand-binding domain, revealing an allosteric switch in the activation helix, helix 12 (H12), forming an antagonist conformation in the receptor. H12 interacts with the antagonists to become fixed in an alternative location. Native mass spectrometry indicates that this prevents contacts with coactivator peptides and allows binding of corepressor peptides. Antagonists of related nuclear receptors act to sterically prevent the active configuration of H12, whereas these antagonists of PPARγ alternatively trap H12 in an inactive configuration, which we have termed the tumble and trap mechanism.

Dissection of the Erv41‐Erv46 retrieval pathway suggests a redox‐regulated mechanism

The early secretory pathway consists of ER‐ and Golgi‐resident proteins involved in synthesis, folding, quality control, and post translational modifications of secretory proteins. Anterograde flux through this pathway can lead to the mislocalization of ER‐resident proteins as they passively leak to the Golgi. Fortunately there are several retrieval mechanisms to return mislocalized ER‐residents back to the ER. One such retrieval process identified by our lab relies on the Erv41‐Erv46 complex, which recognizes specific non‐HDEL ER‐residents in the Golgi and returns them to the ER in a COPI‐dependent manner. The focus of our work is to determine the mechanism by which the Erv41‐Erv46 retrograde receptor binds to escaped ER‐residents in the Golgi and releases this cargo in the ER.Site‐directed mutagenesis to introduce Erv41 and Erv46 mutations in Saccharomyces cerevisiae revealed key residues involved in retrieval of non‐HDEL ER‐residents. One such series of mutations involves a cysteine rich region of Erv46 where Cys to Ser mutants result in a complete loss of function. This cysteine rich region contains two CXXC motifs typically found in redox proteins. As observed in other redox proteins, the residues between the vicinal cysteines in this region of Erv46 are important suggesting that the redox potential of these cysteines is finely tuned for activity. Furthermore, mutations of a four residue hydrophobic patch within the cysteine rich region as well as a distal basic residue in Erv46 leads to a failure in retrieval of ER‐residents. These residues, but not the cysteines, are conserved in Erv41, however concomitant mutations in Erv41 do not affect retrieval suggesting Erv46 is predominantly involved in binding while Erv41 may play a distinct role.Based on our results, we propose the redox state of Erv46 is highly dynamic resulting in active and inactive disulfide configurations which can expose or mask a cargo binding hydrophobic patch. Defining the Erv41‐Erv46 binding mechanism may allow for a more complete understanding of ER homeostasis as well as providing a potential target to block pathogenic toxins that exploit Erv41‐Erv46 mediated retrieval for efficient delivery to the ER.Support or Funding InformationNIH GM52549This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.