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26 protocols using h1029

1

RLIP76 RBD-His Variants Binding Assay

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RLIP76 RBD-His variants (80 nM) were immobilized on Protein A SPA fluoromicrospheres (Perkin Elmer) via an anti-His antibody (H1029, Sigma-Aldrich) in 50 mM Tris-HCl pH 7.5, 2 mM DTT, 1 mM MgCl2, and 0.2 mg/ml BSA. [3H]GTP·Ral proteins were titrated at the concentrations indicated in the results. Experiments were performed as described previously (36 (link)). The equilibrium binding constants (Kd) for the effector–Ral interactions were determined by monitoring the SPA signal in the presence of varying concentrations of [3H]GTP·Ral and fitted using nonlinear regression with the computer program Grafit.
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2

Recombinant Erc1 Protein Expression in Pichia

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The Pichia pastoris KM71H-OCH protein expression system was used to produce N-terminally His and C-terminally Myc-His tagged U. maydis Erc1, Erc1M1x, and Erc1M2x recombinant proteins. All genes for each respective protein were cloned into the pGAPZαA vector (Invitrogen; Carlsbad, USA) under the control of a constitutive promotor with an α-factor signal peptide for secretion. Protein expression was performed by growing Pichia in 1 L buffered (100 mM sodium phosphate buffer, pH 6.0) YPD medium at 28 °C for 48 hours with 200 rpm shaking (pGAPZαA, B, & C Pichia pastoris Expression Vectors, Invitrogen; Carlsbad, USA). Recombinant protein purification was performed with a Ni-NTA-matrix (Ni-Sepharose™ 6 Fast-Flow, GE-Healthcare; Freiburg, Germany). After protein purification, each protein sample was applied to the NAP-25 column to exchange buffer with 20 mM potassium phosphate buffer pH 6.0. The proteins were stored at −20 °C for further experiments. Western blot analysis was performed by using anti-His (H1029, Sigma-Aldrich, Steinheim) and anti-Myc (M4439, Sigma-Aldrich, Steinheim) antibodies with 1:5000 and 1:3000 dilution, respectively20 (link). As a secondary antibody, anti-mouse IgG HRP (#7076, Cell Signaling Technology) was used in 1:3000 dilution20 (link).
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3

Western Blot Antibody Optimization

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Proteins were separated by SDS-PAGE and transferred to polyvinylidene fluoride membranes, which were sequentially incubated with primary and secondary antibodies The primary antibodies were used at the following dilutions: MYC (1:1,000; 2276 (9B11); Cell Signaling Technology), His (1:12,500; H1029; Sigma-Aldrich), FLAG (1:2,000; F1804; Sigma-Aldrich), GST (1:1,000; sc-459; Santa Cruz) α-tubulin (1:2,500; T6074; Sigma-Aldrich), Gβ (1:1,000; sc-261; Santa Cruz), Vangl2 (1:500; from S. Sokol; Ossipova et al., 2015 (link)), and p114RhoGEF (1:1,000; PA5-21429; Thermo Fisher Scientific). The secondary antibodies were goat anti-rabbit Alexa Fluor 680 (1:10,000; A21077; Invitrogen) and goat anti-mouse IRDye 800 (1:10,000; 926-32210; Li-Cor). Infrared imaging of immunoblots was performed using an Odyssey Infrared Imaging System (Li-Cor Biosciences). Images were processed using the ImageJ software and assembled for presentation using Photoshop and Illustrator.
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Recombinant Protein Expression and Purification

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Recombinant proteins HIS-14-3-3D2, GST-SCI1, and GST alone were expressed in E. coli BL21(DE3) Rosetta cells after induction with 0.1 mM IPTG for 2 h. Total soluble proteins were extracted with PBS Buffer [140 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, 1 mM PMSF, 50 μg/ml lysozyme, and 1% protease inhibitor cocktail for general use (Roche), pH 7.3], sonication, and centrifugation. Soluble proteins from the indicated extracts were mixed and incubated overnight at 4°C with equilibrated 100% Glutathione Sepharose 4 FastFlow bead slurry (GE Healthcare). Beads were washed three times with PBS supplemented with 1 mM PMSF. Bound proteins were eluted with 100 μl of 2x Laemmli Sample Buffer and boiled. The different fractions were resolved in 12% bis-acrylamide gel, immunoblotted with anti-GST (Sigma SAB4200055), or anti-HIS primary antibody (Sigma H1029), and visualized by enhanced chemiluminescence reaction (ECL) reaction.
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5

Liposome Association Assay for His-Tagged Protein

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The liposome association assay was performed as described25 (link)26 (link). Lipids were dried and incubated in Tris buffered saline (TBS) (50 mM Tris-HCl, pH 7.0, 0.1 M NaCl) at 37 °C for 1 h. The liposomes were formed by vigorous vortexing (5 min), pelleted by centrifugation at 20,000 × g for 10 min at 4 °C, and washed twice with ice-cold TBS. Purified His-FT was added to the liposomes to a final 100 μl volume, and the mixture was incubated at 30 °C for 30 min. After incubation, liposomes were pelleted again by centrifugation at 20,000 × g and washed twice with ice-cold TBS. The pellets were analysed by SDS–polyacrylamide gel electrophoresis and blotted onto nitrocellulose membrane (Bio-Rad, Hercules, CA) for protein gel blot analysis. His-FT was immunodetected by a monoclonal antibody against penta-His (H1029, Sigma-Aldrich; dilution 1:1,000) and horseradish peroxidase–coupled anti-mouse IgG (A3682, Sigma-Aldrich; dilution 1:10,000) with the West Pico chemiluminescence detection kit (Thermo Scientific, Rockford, IL) and signal intensity of each spot was quantified by image analyser (LAS4000, GE healthcare). An uncropped scan of a representative result is shown in Supplementary Fig. 6.
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6

Western Blotting of Cellular Fractions

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Western blotting of cell body or neurite homogenates were performed as described previously.27 (link) In addition to NAMPT (1 : 2000, Enzo Life Sciences, Exeter, UK), mouse monoclonal anti-histone H1 (1 : 500; Millipore, Nottingham, UK), and mouse monoclonal anti β-actin (1 : 5000; Abcam, Cambridge, UK) were used as loading controls for the cell body and the neurite fraction, respectively. For quantification, western blotting for NMNAT2 (2.0 μg/ml, Abcam) was performed as described in.16 (link) Western blotting band intensities were determined and analysed with the ImageJ software (National Institutes of Health, Bethesda, MD, USA). Western blotting of HEK293T or PC12 cell homogenates were performed as described,27 (link) and blots were probed with an anti-his antibody (Sigma, H1029).
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7

TrxR1 Protein Immunoblot Analysis

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Purified TrxR1 proteins were resuspended in 1 × SDS loading buffer (250 mM Tris/HCl pH 6.8, 40% glycerol [v/v], 10% SDS [w/v], 0.05% bromophenol blue [w/v], 5% 2-mercaptoethanol) and loaded in 10% SDS-polyacrylamide gel electrophoresis. The blot was carried out with a TransBlot Turbo Transfer System (BioRad). Anti-His antibodies (from Mouse, H1029; Sigma) and mouse immunoglobulin G horseradish peroxidase linked whole antibody (from sheep, GENA931; GE Healthcare) were used. Chemiluminescent signal detection was performed on a ChemiDoc MP system (BioRad).
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8

Detection of TAPBPR and UGT1 in MHC Class I Complexes

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TAPBPR was detected using either PeTe4, a mouse monoclonal antibody (mAb) specific for the native conformation of TAPBPR, raised against amino acids 22–406 of human TAPBPR (Boyle et al., 2013 (link)) that does not cross-react with tapasin (Hermann et al., 2013 (link)), or ab57411, a mouse mAb raised against amino acids 23–122 of TAPBPR that is reactive to denatured TAPBPR (Abcam, UK). UGT1 was detected using the rabbit mAb ab124879 (Abcam). MHC class I heavy chains were detected using mAb HC10 (Stam et al., 1986 ). Soluble TAPBPR variants were detected using the mouse anti-polyhistidine mAb H1029 (Sigma-Aldrich). A mouse IgG2a isotype control was also used as a control (Sigma-Aldrich).
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9

In vitro Validation of CTB4aKD-AtpB Interaction

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In order to confirm the interaction between CTB4aKD and AtpB in vitro, CTB4aKD and AtpB were amplified and sub-cloned into pGEX-4T-1 and pET28a, respectively. The plasmids were transformed into E.coli BL21. Then 5 μg of purified CTB4aKD-GST or GST and AtpB-His protein were incubated in 1 ml of PBS buffer (pH 7.4, 0.1% NP-40) at 4 °C with gentle agitation for 2 h before addition of 20 μl of Glutathione Sepharose 4B beads (GE healthcare, cat.no.17-0756-01), and continued incubation for 1 h. The Glutathione Sepharose beads was collected by brief centrifugation, washed five times in PBS buffer, re-suspended in SDS loading buffer, subjected to SDS-PAGE electrophoresis, and probed with an anti-GST (Sigma, SAB5300159, dilution, 1:1,000) and anti-His antibody (Sigma, H1029, dilution, 1:2,000). The original western blot images are provided in Supplementary Fig. 25. Primer sequences are provided in Supplementary Data 2.
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10

Antibody Purification and Western Blotting

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Anti-HA-agarose (A2095) and anti-FLAG affinity gel (A2220) were obtained from Sigma. For Western blotting, secondary antibody against mouse (A21057) was purchased from Invitrogen, and secondary antibody against rabbit (611-732-127) was from Rockland. Antibodies against FLAG (F1804), tubulin (T9026), and His tag (H1029) were purchased from Sigma; anti-HA (MMS-101P) was from Covance; anti-USP7 (sc-30164) was from Santa Cruz Biotechnology; anti-myc (2276) was from Cell Signaling Technology; anti-V5 (46-0705) and secondary antibodies for immunofluorescence were from Invitrogen. Anti-TRF1 has been described previously (26 ).
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