Journal: Nature chemical biology

Article Title: Targeting a Helix-in-Groove Interaction Between E1 and E2 Blocks Ubiquitin Transfer

doi: 10.1038/s41589-020-0625-7

Figure Lengend Snippet: ( a ) Structure of the binding interface between the UFD of S. pombe Uba1 (interacting residues colored pink) and the alpha-1 helix (aa 1–18, colored by amino acid property) of the E2 Ubc15 (cyan), as revealed by the x-ray structure of the S. pombe Uba1/Ubc15 complex (PDB: 5KNL) . ( b ) Amino acid sequences of the SAH-Ubc15 E7R staple-scanning library, which was generated by inserting all-hydrocarbon i, i+4 or i, i+7 staples sequentially along the length of the Ubc15 E7R peptide. X, S5-pentenyl alanine; 8, R5-octenyl alanine; B, norleucine (replacement for methionine, whose sulfur residue decreases the efficiency of ruthenium-catalyzed olefin metathesis). ( c ) Helical wheel depiction of SAH-Ubc15 E7R peptides and their staple positions (helical residues span from aa 5–18). ( d ) Inhibition of UBE1-mediated thioester transfer of ubiquitin to the E2 enzyme UBE2D2 by the indicated SAH-UBC15 E7R stapled peptides. Thioester transfer activity was monitored by the shift in E2 molecular weight from 17 kDa (free UBE2D2) to 25 kDa (UBE2D2~ubiquitin conjugate), as detected by gel electrophoresis and silver stain. Vehicle lane contained 1.5% DMSO and control lane lacked UBE1 protein. The bar graph represents mean inhibition relative to vehicle control ± s.e.m., as quantified and averaged across three independent biological replicates. Uncropped gel for panel d is available online. Source data for the thioester transfer assay plot is available online.

Article Snippet: For UBA3 thioester transfer assays, 15 nM NAE1/UBA3 was substituted for UBE1 (Boston Biochem E-313), 135 nM UBE2M for UBE2D2 (Boston Biochem E2–656), and 1 μM NEDD8 (Boston Biochem UL-812) for ubiquitin.

Techniques: Binding Assay, Generated, Residue, Inhibition, Ubiquitin Proteomics, Activity Assay, Molecular Weight, Nucleic Acid Electrophoresis, Silver Staining, Control

Journal: Nature chemical biology

Article Title: Targeting a Helix-in-Groove Interaction Between E1 and E2 Blocks Ubiquitin Transfer

doi: 10.1038/s41589-020-0625-7

Figure Lengend Snippet: ( a ) Amino acid sequences of stapled peptides corresponding to the N terminus and alpha-1 helix of UBE2D2 (aa 1–16), UBE2G2 (aa 1–14), and UBE2A (aa 1–17), which incorporate the optimal staple position identified for SAH-Ubc15–11. X, S5-pentenyl alanine; 8, R5-octenyl alanine; B, norleucine. ( b ) Comparative dose-responsive inhibition of UBE1 by the indicated SAH-E2 h1 peptides, as monitored by thioester transfer assay, gel electrophoresis, and silver stain. ( c ) Quantitation of the data in b by ImageJ analysis. Data are mean percent inhibition ± s.e.m. for three independent biological replicates. ( d ) Circular dichroism spectra of UBE2A (BSTPARRRLBRDFKRLQ, where B is norleucine) and SAH-UBE2A, demonstrating induction of α-helicity by insertion of the i, i+7 staple. ( e ) Inhibition of UBE1-mediated thioester transfer of ubiquitin to the E2 enzyme UBE2D2 by SAH-UBE2A but not the corresponding unmodified template peptide, UBE2A. Data are mean inhibition ± s.e.m. for three independent biological replicates. ( f ) Comparative protease resistance of SAH-UBE2A and UBE2A upon treatment with proteinase K, as measured by HPLC analysis. SAH-UBE2A displays a 23-fold longer half-life than UBE2A. Data are mean ± s.d. for experiments performed in triplicate. ( g ) SAH-UBE2A but not UBE2A was significantly protected from deuterium exchange upon incubation with UBE1. The relative difference in deuterium uptake after 10 sec of labeling is shown. The difference in uptake was calculated from the mean deuterium level for UBE2A or SAH-UBE2A in the presence of UBE1 minus that of the peptide alone. Mean deuterium levels were obtained from at least two independent biological replicates of each condition. ( h ) C-terminally biotinylated SAH-UBE2A directly bound to recombinant human UBE1 (MW 118 kDa), as demonstrated by streptavidin capture, gel electrophoresis, and silver stain. ( i ) C-terminally FITCylated SAH-UBE2A bound to UBE1 with a K d of 384 ± 43 nM, as assessed by fluorescence polarization assay. Error bars are s.d. for assays conducted in technical triplicate and performed three times with independent preparations of peptide and protein (all 9 points for each dosing level are plotted). Uncropped gels for panels b , e , and h are available online. Source data for thioester transfer assays, CD spectra, protease resistance testing, HXMS analyses, and FP plot are available online.

Article Snippet: For UBA3 thioester transfer assays, 15 nM NAE1/UBA3 was substituted for UBE1 (Boston Biochem E-313), 135 nM UBE2M for UBE2D2 (Boston Biochem E2–656), and 1 μM NEDD8 (Boston Biochem UL-812) for ubiquitin.

Techniques: Inhibition, Nucleic Acid Electrophoresis, Silver Staining, Quantitation Assay, Circular Dichroism, Ubiquitin Proteomics, Incubation, Labeling, Recombinant, Fluorescence

Journal: Nature chemical biology

Article Title: Targeting a Helix-in-Groove Interaction Between E1 and E2 Blocks Ubiquitin Transfer

doi: 10.1038/s41589-020-0625-7

Figure Lengend Snippet: (a) Sequence compositions of the unmodified UBE2A template peptide and stapled constructs SAH-UBE2A, SAH-UBE2A R7E , and SAH-UBE2A R7A/L9A/B10A . (b) Comparative effects of UBE2A, SAH-UBE2A, SAH-UBE2A R7E , and SAH-UBE2A R7A/L9A/B10A on UBE1-mediated thioester transfer of ubiquitin to the E2 enzyme UBE2D2. Whereas SAH-UBE2A (10 μM) completely inhibits UBE1 activity, triple mutagenesis abrogates the inhibitory effect and single R7E mutagenesis has an intermediate effect. (c) Progressive loss of UBE1 protection from deuterium exchange into SAH-UBE2A upon single R7E and triple R7A/L9A/B10A mutagenesis. The relative difference in deuterium uptake after 10 sec of labeling is shown. The difference in uptake was calculated from the mean deuterium level for each SAH-UBE2A peptide in the presence of UBE1 minus that of the peptide alone. Mean deuterium levels were obtained from at least two independent biological replicates of each condition. (d) Difference in deuterium uptake plots demonstrate the relative deuterium incorporation of SAH-UBE2A/UBE1, SAH-UBE2A R7E /UBE1, or SAH-UBE2A R7A/L9A/B10A /UBE1 minus the relative deuterium incorporation of UBE1 at 10 min of deuterium labeling. The shaded gray region indicates differences in deuteration that are below the meaningful differences threshold. Consistent with results of both the thioester transfer assay (b) and peptide deuterium exchange (c), and the predicted SAH-UBE2A/UBE1 binding mode, triple mutagenesis essentially abrogates the effect of SAH-UBE2A on UBE1 conformation, with single R7E mutagenesis having an intermediate influence. Data are representative of three independent replicates for SAH-UBE2A, and two independent replicates for SAH-UBE2A R7E and SAH-UBE2A R7A/L9A/B10A . Each peptide, from N- to C-terminus, was given a peptide number to simplify the presentation. The peptide list and residue identity of each peptide can be found in . Uncropped gel for panel b is available online. Source data for the HXMS analyses are available online.

Article Snippet: For UBA3 thioester transfer assays, 15 nM NAE1/UBA3 was substituted for UBE1 (Boston Biochem E-313), 135 nM UBE2M for UBE2D2 (Boston Biochem E2–656), and 1 μM NEDD8 (Boston Biochem UL-812) for ubiquitin.

Techniques: Sequencing, Construct, Ubiquitin Proteomics, Activity Assay, Mutagenesis, Labeling, Binding Assay, Residue

Journal: Reproductive Biology and Endocrinology : RB&E

Article Title: SERPINE2, an inhibitor of plasminogen activators, is highly expressed in the human endometrium during the secretory phase

doi: 10.1186/1477-7827-9-38

Figure Lengend Snippet: Antibody specificity and presence of the SERPINE2 protein in human uterine fluid . (A) Four hundred nanograms of recombinant human SERPINE2 was resolved on 10% SDS-PAGE and followed by Western blotting using anti-mouse SERPINE2 antiserum (lane 1), an anti-human SERPINE2 antibody (R&D) (lane2), or another anti-human SERPINE2 antibody (Abnova) (lane 3). (B) One hundred micrograms of the extract of endometrial curettage was analyzed by anti-mouse SERPINE2 antiserum (lanes 1 and 2) and an anti-human SERPINE2 antibody (R&D) (lanes 3 and 4). (C) Fifty micrograms of uterine fluid proteins collected from each individual patient ( n = 7) was Western-blotted using anti-mouse SERPINE2 antiserum (1:3000) (upper panel). EP, MP, and LP indicate early-, mid-, and late-proliferative phases, and ES and MS indicate early- and mid-secretory phases, respectively. The blot was also overexposed to clearly display the staining signal (lower panel).

Article Snippet: Membranes were blocked with 10% (w/v) skim milk in phosphate-buffered saline (PBS) (blocking solution) for 2 h, and then incubated with our homemade anti-mouse SERPINE2 antiserum (1: 5000) [ , ], anti-human SERPINE2 antibody (1: 1000, catalog no. AF2980, R&D Systems, Minneapolis, MN, USA), or another anti-human SERPINE2 antibody (1: 1000, product no. H00005270-B01, Abnova) in blocking solution for 2 h at 37°C.

Techniques: Recombinant, SDS Page, Western Blot, Staining

Journal: Reproductive Biology and Endocrinology : RB&E

Article Title: SERPINE2, an inhibitor of plasminogen activators, is highly expressed in the human endometrium during the secretory phase

doi: 10.1186/1477-7827-9-38

Figure Lengend Snippet: Localization of SERPINE2 in the human uterus . Longitudinal sections of the early secretory phase uterus (n = 5) on the slide were incubated with anti-mouse SERPINE2 antiserum and then treated with biotin-conjugated goat-anti-rabbit IgG and HRP-conjugated streptavidin (brown). For contrast, specimens were further stained with hematoxylin (blue). The representative picture is shown. Magnified pictures of the luminal epithelium (A), glandular epithelium (B), and myometrium (C) are shown. Bar = 50 μm. bv, blood vessel; ge, glandular epithelium; le, luminal epithelium; m, muscle; s, stroma.

Article Snippet: Membranes were blocked with 10% (w/v) skim milk in phosphate-buffered saline (PBS) (blocking solution) for 2 h, and then incubated with our homemade anti-mouse SERPINE2 antiserum (1: 5000) [ , ], anti-human SERPINE2 antibody (1: 1000, catalog no. AF2980, R&D Systems, Minneapolis, MN, USA), or another anti-human SERPINE2 antibody (1: 1000, product no. H00005270-B01, Abnova) in blocking solution for 2 h at 37°C.

Techniques: Incubation, Staining

Journal: Reproductive Biology and Endocrinology : RB&E

Article Title: SERPINE2, an inhibitor of plasminogen activators, is highly expressed in the human endometrium during the secretory phase

doi: 10.1186/1477-7827-9-38

Figure Lengend Snippet: Glandular epithelial expression of the SERPINE2 protein in the endometrium during the menstrual cycle . Sections prepared from endometrial curettage during early-proliferative (EP), mid-proliferative (MP), late-proliferative (LP), early-secretory (ES), mid-secretory (MS), and late-secretory (LS) phases were incubated with anti-mouse SERPINE2 antiserum and then treated as described in Figure 2. Bar = 50 μm. bv, blood vessel; ge, glandular epithelium; s, stroma.

Article Snippet: Membranes were blocked with 10% (w/v) skim milk in phosphate-buffered saline (PBS) (blocking solution) for 2 h, and then incubated with our homemade anti-mouse SERPINE2 antiserum (1: 5000) [ , ], anti-human SERPINE2 antibody (1: 1000, catalog no. AF2980, R&D Systems, Minneapolis, MN, USA), or another anti-human SERPINE2 antibody (1: 1000, product no. H00005270-B01, Abnova) in blocking solution for 2 h at 37°C.

Techniques: Expressing, Incubation

Journal: Reproductive Biology and Endocrinology : RB&E

Article Title: SERPINE2, an inhibitor of plasminogen activators, is highly expressed in the human endometrium during the secretory phase

doi: 10.1186/1477-7827-9-38

Figure Lengend Snippet: Quantification of SERPINE2 protein expression levels in endometrial glands . Representative samples were analyzed by automated cell acquisition and quantification software (A). The expression signal of a respective glandular gland was quantified using HistoQuest software and is presented as a scattergram. Each spot on the scattergram stands for the intensity of one cell (B). The relative SERPINE2 protein expression levels in patients' glandular glands at various sub-phases of the menstrual cycle are shown as bar diagrams (C). Differences are significant among patients at various groups (χ = 69.32, p < 0.0001).

Article Snippet: Membranes were blocked with 10% (w/v) skim milk in phosphate-buffered saline (PBS) (blocking solution) for 2 h, and then incubated with our homemade anti-mouse SERPINE2 antiserum (1: 5000) [ , ], anti-human SERPINE2 antibody (1: 1000, catalog no. AF2980, R&D Systems, Minneapolis, MN, USA), or another anti-human SERPINE2 antibody (1: 1000, product no. H00005270-B01, Abnova) in blocking solution for 2 h at 37°C.

Techniques: Expressing, Software

Journal: Oncotarget

Article Title: Serpin E2 promotes breast cancer metastasis by remodeling the tumor matrix and polarizing tumor associated macrophages

doi: 10.18632/oncotarget.12927

Figure Lengend Snippet: ( A ) Masson trichrome staining performed on 4T1 Ctrl and shSerpine2 tumors. Representative images show increased collagen encapsulation (blue) of SerpinE2 KD tumors. Scale bar100μm. ( B - C ) Intravital imaging using (IVI-MP) of 4T1 Ctrl and shSerpine2 tumors. (B) Representative images show collagen I fibers detected by the SHG signal (cyan) at the surface of 4T1 tumors; scale bar25μm. (C) Average SHG signal intensity was determined per 100μm z-stack; data are acquired from 19-30 separate z-stacks from 3 mice per cell line. * P < 0.00036. D. IVI-MP performed on mice bearing GFP-labeled 4T1 control and shSerpinE2 tumors. Representative images show GFP-labeled tumor cells (green), phagocytic dextran positive cells (red); SHG imaging identified collagen I fibers (cyan). Scale bars25μm. (E-F) ( E ) GFP-labeled 4T1 tumor-bearing mice were treated with control liposomes or clodronate-containing liposomes until IVI-MP was performed. Representative images are shown as in (D). ( F ) Quantification of SHG (cyan) signal intensity in 100 μm Z-stacks of tumors in treated animals. Data are mean ± SEM of measurements from 40-61 Z-stacks from at least 3 different tumors for each treatment group. * P < 0.016. All data are mean ± SEM.

Article Snippet: Anti-human SerpinE2 Ab (MAB2980) was from R&D systems.

Techniques: Staining, Encapsulation, Imaging, Labeling, Control, Liposomes

Journal: Oncotarget

Article Title: Serpin E2 promotes breast cancer metastasis by remodeling the tumor matrix and polarizing tumor associated macrophages

doi: 10.18632/oncotarget.12927

Figure Lengend Snippet: Conditioned medium (CM) from 4T1 and 168FARN ( A ) or MDA-MB435 ( B ) cultures was incubated overnight with Ab11, then bound serpinE2 was pulled-down with Protein G, and analyzed by western blot with the rodent-specific antibody, 4B3 (A), or a human-specific antibody (B). (A) The right panel shows a short exposure of serpinE2 complexes from 4T1 CM, but none in 168FARN CM (long exposure on the left), as well as an IP of the preformed tPA/serpinE2 complex. ( C ) SFM loaded with purified human serpinE2 or the preformed serpinE2/tPA complex was IP'd with Ab11 as in (A) & (B) and analyzed by western blot with a human serpinE2-specific antibody. The serpinE2 complex and uncomplexed serpinE2 are indicated with arrowheads.

Article Snippet: Anti-human SerpinE2 Ab (MAB2980) was from R&D systems.

Techniques: Incubation, Western Blot, Purification

Journal: Oncotarget

Article Title: Serpin E2 promotes breast cancer metastasis by remodeling the tumor matrix and polarizing tumor associated macrophages

doi: 10.18632/oncotarget.12927

Figure Lengend Snippet: The LRP1 receptor is expressed on tumor cells and on macrophages and we propose that serpinE2 targeting with Ab11 impacts on LRP1 signaling in both cell types. ( A ) In metastatic tumors, serpinE2-LRP1 binding stimulates ERK signaling and secretion of CCL2. Tumor cells display hyperactivation of receptor tyrosine kinases (RTKs); FGFRs, which are active in the 4T1 model, also stimulate ERK pathway activation. We speculate that in macrophages, the combination of high CCL2 levels and serpinE2-activated LRP1 promotes the M2 phenotype. Indeed, there are high levels of phagocytic, Texas-red positive M2 tumor associated macrophages (TAMs) in the metastatic tumors; they are known to be responsible for degrading the matrix during tumor development. ( B ) Ab11 or sepinE2 KD (not drawn in model) lowers ERK pathway activity and the secretion of CCL2, and stimulates TIMP1 secretion. Tyrosine kinase inhibitors (TKIs) block RTK signaling. The matrix-degrading M2 TAMs are decreased in Ab11-treated tumors. Moreover, depleting macrophages with clodronate liposomes results in deposition of a dense collagen matrix, similar to that observed in Ab11-treated tumors. Thus, we propose that the drop in CCL2, which contributes to a decrease in M2 TAMs, as well as blocking serpinE2, which skews the TAMs towards the M1 phenotype, causes the emergence of a dense collagen matrix that inhibits intravasation and metastatic dissemination.

Article Snippet: Anti-human SerpinE2 Ab (MAB2980) was from R&D systems.

Techniques: Binding Assay, Activation Assay, Activity Assay, Blocking Assay, Liposomes