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6 protocols using mouse anti his

1

Truncation Analysis of CD99 Extracellular Domain

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Kunkel mutagenesis was utilized to make truncated CD99 ECD fragments (23-122, 33-122, and 43-122 ) and a combination of Kunkel mutagenesis and restriction and insertion cloning were utilized to produce the other CD99 fragments (53-122, 63-122, 73-122, 83-122, 93-122, 103-122, and 113-122) 77 (link). The proteins were expressed and purified as described above, except they were only purified using a Ni-Sepharose resin (Cytivia). SDS-PAGE of 50 ng of each purified protein was performed followed by transfer to Immobilon-PSQ PVDF membrane (ca# ISEQ00010, Millipore). For Western blot detection, the membranes were blocked with 5% skim milk overnight at 4°C, then washed three times with 1X TBST (50 mM Tris pH 7.5, 150 mM NaCl, and 0.05% Tween-20). The membranes were then incubated with 14 nM of clones 10, 22, and 30, 1 nM of HO36-1.1, or 1:1000 of mouse anti-His (ca# 37-2900, Invitrogen) for 1.5 hours at room temperature, then washed as described above. The membranes were then incubated with goat anti-mouse IgG Fc conjugated with horseradish peroxidase (HRP) (ca# 31437, Invitrogen) or goat anti-mouse IgM-HRP (ca# 626820, Invitrogen), for 1 hour at room temperature, then washed as described above. Pierce ECL 2 Western Blotting Substrate (ca# 80198, Thermo) was added according to manufacturer protocol. Signal detection was analyzed on ChemiDoc Touch imaging system (Biorad).
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2

Dephosphorylation and Fluorescent Detection of Circadian Proteins

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Cells were harvested 72 hrs after transfection. They were homogenized in protein extraction buffer (20 mM HEPES pH 7.5; 100 mM KCl; 5% glycerol; 10 mM EDTA; 0.1% Triton X-100; 20 mM β-glycerophosphate; 0.1 mM Na3VO4 pH 11) containing a protease inhibitor cocktail (c0mplete Mini EDTA-free; Roche) and loaded onto a 10% gel. For dephosphorylation we treated the protein extract with λ-Phosphatase (Thermo Scientific) for 1 hour. For visualizing the different proteins, we incubated the western blots in primary and secondary fluorescent antibodies with following dilutions: rabbit anti-CRY 1:10000 (kindly provided by T. Yoshii), Alexa Fluor goat-anti-rabbit 680 1:5000 (Invitrogen), rabbit anti-CRY 1:1000 (kindly provided by P. Emery)[31 (link)], Mouse Anti-HIS 1:5000 (Invitrogen) Alexa Fluor goat-anti-mouse 1:5000 (Invitrogen), mouse anti-GSK-3 1:5000 (4G-1E; Millipore).
Fluorescent signals were detected using the Odyssey Imaging System (Licor Bioscience).
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3

Antibodies for Protein Localization

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Primary antibodies were: polyclonal guinea pig anti- PLEKHA7 (in-house gp2737, 1:500 IF); monoclonal mouse anti-GFP (Roche Applied Science, 11814460001, 1:100 IF), polyclonal rabbit anti-PDZD11 (in-house r29958 28, 1:50 IF), mouse anti-HA (Zymed Laboratories Inc., 32-6700, 1:1000 IB), and mouse anti-His (Invitrogen, catalog number 37-2900, 1:1500 IB). Secondary antibodies were anti-mouse Alexa Fluor 488, anti-rabbit Alexa Fluor 488, anti-rabbit Cy3, anti-mouse Cy3, and anti-guinea pig Cy3 (Jackson ImmunoResearch Europe, 1:250 IF), and HRP-conjugated anti-mouse (Promega, 1:20000, IB).
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4

Quantifying TFPI-Tissue Factor Binding

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All reagents, unless noted, were from Sigma Aldrich (St Louis, MO). Human recombinant FVIIa and FX were purchased from Haematologic Technologies (Essex Junction, VT). Recombinant His-tagged human TFPI was purchased from R&D Systems (Minneapolis, MN). Protein G was purchased from EMD Millipore (Billerica, MA). Mouse anti-His, mouse IgG, and Alexa-488-conjugated secondary goat anti-mouse antibodies were purchased from Invitrogen (Carlsbad, CA). A mouse anti-TFPI antibody was purchased from Fitzgerald Industries International. Mouse monoclonal anti-TF antibodies (TF9-5B7 and TF9-10H10) were a generous gift from Dr. James Morrissey at University of Illinois.
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5

Stability of Recombinant Proteins at Varying Temperatures

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Aliquots of lyophilized sp79 and sp82 biomass were stored in sealed moisture-free chambers away from light for one year at −80 °C, −20 °C, 4 °C, 25 °C, 37 °C and 42 °C. Samples were brought to 1 mg/mL in SDS sample buffer, boiled for 5 min at 100 °C, and stored in −80 °C until analysis by SDS-PAGE followed by western blot with rabbit anti-Myc antibody (Rockland) at 1:3000 and donkey anti-rabbit (Invitrogen) at 1:10,000. ImageJ software was used to estimate band intensity relative to a sample taken to represent time zero (from fresh harvest). For sp648, biomass samples were processed and stored under identical conditions as above for 10 months. To harvest the total soluble protein, measured aliquots were resuspended in PBS with Halt Protease Inhibitor and lysed on a Precellys Evolution Homogenizer (Bertin Instruments) using Lysis Matrix B (MP Bio) beads, followed by centrifugation to collect the supernatant. Automated immunoblotting was done via the JessTM Simple Western nano-immunoassay system (ProteinSimple, San Jose, CA, USA), following the manufacturer’s protocol, using mouse anti-His (ThermoFisher Scientific) followed by goat anti-mouse HRP conjugate (ProteinSimple) and rabbit-NANP (Alpha Diagnostic) followed by goat anti-rabbit HRP conjugate (ProteinSimple).
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6

Isolation and Identification of FtsH12 Interactome

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Chloroplasts of six-week-old pftsh12::ftsh12CDS::4×c-myc in GABI_550G09 background were isolated as described above. Plastids were solubilized in PBS, 0.28% beta-DM and 1.86% digitonin. Immunoaffinity enrichment of c-myc tagged FtsH12 and mass spectrometry-based identification of co-precipitating proteins was performed according to Haselmann et al. (2018) (link). Antibodies used were monoclonal mouse anti-c-myc and mouse anti-His (Thermo Fisher Scientific). Briefly, proteins eluted after affinity capture were purified with SDS-PAGE and in-gel digested with trypsin (SERVA), as described earlier for proteome analysis by mass spectrometry.
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