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8 protocols using tristar 5

1

Fluorescence Measurement Protocol

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The fluorescence of the supernatants was measured using a Tristar 5 plate reader (Berthold, Germany). Absorbance data were collected and processed using the MikroWin2010 program (Labsis Laborsysteme GmbH). The manufacturer's instructions were followed for operating the machine.
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2

Chiral-specific Enzymatic Luminescence

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Fifty microliters of a 10 ng mL−1 solution of a recombinant CypLase in 100 mM Tris–HCl (pH 7.5) containing 300 mM l-ascorbic acid sodium salt and 100 mM NaCl was automatically added to 50 μL of a 0.2 or 2 μM solution of chiral-separated (R)- or (S)-CypL in 100 mM Tris–HCl (pH 7.5) containing 300 mM l-ascorbic acid sodium salt and 100 mM NaCl on a black 96-well plate (FIA Plate; Greiner Bio-One, Kremsmunster, Austria) using an injector equipped with a multimode microplate reader (TriStar 5; Berthold Technologies, Bad Wildbad, Germany), followed by immediate measurement of luminescence intensity at room temperature. The luminescence intensity was recorded in relative light units (RLU) in 0.1 s intervals over 120 min.
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3

Quadriceps Protein Extraction and Western Blotting

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The quadriceps were homogenized in 60 µL/mg ice-cold RIPA buffer (10 mM Tris–HCl pH 7.4, 5 mM EDTA, 0.1% SDS, 150 mM NaCl, 1% sodium deoxycholate, 1% Triton) with 1 mM phenylmethanesulfonyl fluoride and a protease/phosphatase inhibitor cocktail (#5872, Cell Signaling, Danvers, MA, USA) using a Bead Mill 4 Homogenizer (Thermo Fisher Scientific, Waltham, MA, USA), and then centrifuged (15,000× g for 10 min at 4 °C). The supernatant protein concentration was determined with Bradford Reagent (Sigma, Burlington, VT, USA) using a microplate reader (Tristar 5, Berthold, Bad Wildbad, Germany). Forty micrograms of denatured proteins were separated in SDS polyacrylamide 12% and transferred onto polyvinylidene fluoride membranes according to the manufacturer’s instructions (Invitrogen, Waltham, MA, USA). After overnight incubation with primary antibodies and then horseradish peroxidase-conjugated secondary antibodies (see Table S3 for details), the protein complexes were revealed (Kit Clarity Western ECL substrate, Bio-Rad, Hercules, CA, USA) using chemiluminescence (Fusion X Spectra, Vilber, Marne-la-Vallée, France). The protein expression was quantified with ImageJ software (NIH, Bethesda, MD, USA, https://imagej.nih.gov/ij/) and normalized to glyceraldehyde 3-phosphate dehydrogenase (GADPH).
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4

FD-4 Permeability Assay on Airway-on-Chip

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Top and bottom channels of airway-on-a-chip were rinsed with Hank’s Balanced Salt Solution (HBSS). The 300 μl of HBSS containing 25 μg/ml FD-4 (average molecular weight 3000–5000; Sigma-Aldrich) was added to the top channel, and 150 μl of HBSS was added to the bottom channel. After 70 min of incubation at 37 °C, the HBSS was collected from the bottom channel. The FD-4 fluorescent signal was measured with a fluorescence plate reader (TriStar 5; Berthold Technologies) using 490 nm excitation and 520 nm emission filters. FD-4 concentrations were calculated using the standard curve generated by serial dilution of FD-4.
The Papp in FD-4 permeability test was calculated according to the following equation. Papp=δCr/δt×Vr/(A×C0) δCr/δt = permeability rate (δCr = final concentration in the bottom channel, δt = assay time); Vr = bottom channel volume; A = cell growth area; C0 = initial concentration in the top channel.
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5

Luminescence Kinetics of Chiral CypL Interactions

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Fifty microliters of a 53 μg mL−1 solution of human AGP in 100 mM Tris–HCl (pH 9.0) was automatically added to 50 μL of a 0.2 or 2 μM solution of chiral-separated (R)- or (S)-CypL in water on a white 96-well plate (Eppendorf microplate 96/F-PP; Eppendorf, Hamburg, Germany) using the injector equipped with the multimode microplate reader (TriStar 5; Berthold Technologies), followed by immediate measurement of luminescence intensity at room temperature. The luminescence intensity was recorded in relative light units (RLU) in 0.1 s intervals over 180 min. As a point of caution, in this measurement, a white 96-well plate was used instead of the black 96-well plate described in Section 4.5. A white 96-well plate reflects light, but a black 96-well plate absorbs light. Therefore, the value of light intensity with a white 96-well plate is higher than that with a black 96-well plate.
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6

FITC-Peptide Binding to RAF Kinase

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Glutathione coated wells of a pre-blocked, black, clear bottom, 96-well plate (#15340, Thermo) were incubated with 50 ng of c-RAF kinase domain protein (#14-352, Merck) or GST protein (gifted by Prof. George Baillie) and incubated overnight at 4 °C. Wells were then incubated with increasing concentrations of FITC-labelled peptide [0.6–10 μM] for 2 h at room temperature. Excess protein/peptide was removed following each incubation step by washing three times in 1× TBS-T. Protein and peptides were diluted in binding buffer (200 mM NaCl, 50 mM Tris, 5 mM DTT, 5% Glycerol, protease cocktail inhibitor tablet (Roche), pH 7.5). FITC-peptide binding to c-RAF protein was measured using a Tristar 5 multimode microplate reader (Berthold Technologies). Binding affinities were measured via non-linear regression analysis (GraphPad Prism 8.0).
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7

Efficient mRNA Transfection in HeLa and JAWS II Cells

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HeLa cells (Riken Cell Bank, RCB0007) were grown in DMEM (Wako) supplemented with 10% FBS (Invitrogen) at 37 °C under a 5% CO2 atmosphere. JAWS II cells (ATCC, CRL-11904) were grown in MEM α, nucleoside (Gibco) supplemented with 10% FBS (Invitrogen) and 5 ng/mL murine GM-CSF (PeproTech) at 37 °C under a 5% CO2 atmosphere. One day before transfection, the cells were seeded in a 96-well cell culture plate, typically at 5 × 103 cells/well for HeLa cells or 1 × 104 cells/well for JAWS II cells. Just before transfection, the medium was replaced with Opti-MEM I medium (90 µL/well, Thermo). mRNA (10 ng/well) mixed with Lipofectamine MessengerMAX (0.15 µL/well) in Opti-MEM I medium (10 µL/well) was added to the cells. Three hours after the transfection, the growing medium was added to the cells (100 μL per well). At indicated time points, the cells were lysed, and the luciferase expression was measured using Nano-Glo Luciferase Assay System (Promega). The chemiluminescence was measured on the TriStar5 or TriStar2 plate reader (Berthold Technologies). Statistical analysis of the data was performed using GraphPad Prism 9 software.
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8

Quantifying Membrane Permeabilization by Proteins

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Calcein-filled PM vesicles were prepared from six-week-old N. benthamiana as described (Ottmann et al., 2009 (link)). Permeabilization of the vesicles (1 ng protein μL−1) induced by Hip1 or P. parasitica NLP (expressed as described; Ottmann et al., 2009 (link)) was assayed at RT in 20 mM 2-(N-morpholino)ethanesulfonic acid (MES), pH 5.8, 140-mM NaCl by measuring fluorescence (excitation 485 ± 14 nm, emission 535 ± 20 nm) in a microplate reader (TriStar 5, Berthold). The percentage of calcein release (R) was calculated according to the equation
R=(FmeasFinit)/(FmaxFinit)*100,
where Fmeas, Finit, and Fmax are the measured, initial, and maximal fluorescence, respectively. Fmax was obtained by the addition of Triton X-100 to 0.5% (v:v) final concentration at the end of each measurement.
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