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21 protocols using hiload 16 60 superdex 200 pg

1

Purification of gp120 Glycoprotein

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FreeStyle 293F cells (Thermo Fisher Scientific, Waltham, MA, USA) were grown in FreeStyle 293F medium (Thermo Fisher Scientific, Waltham, MA, USA) to a density of 1 × 106 cells/mL at 37 °C with 8 % CO2 with regular agitation (150 rpm). Cells were transfected with recombinant gp120 expressors using ExpiFectamine 293 transfection reagent, as directed by the manufacturer (Thermo Fisher Scientific, Waltham, MA, USA). One week later, cells were pelleted and supernatants were filtered using a 0,22-µm-pore-size filter (Thermo Fisher Scientific, Waltham, MA, USA). The gp120 glycoproteins were purified by nickel affinity columns, as directed by the manufacturer (Thermo Fisher Scientific, Waltham, MA, USA). Monomeric gp120 was subsequently purified by fast protein liquid chromatography (FPLC), as previously reported [32 (link)]. The purification by FPLC was performed using an AKTA Prime Plus FPLC with a HILOAD 16/60 Superdex 200 PG (General Electric, Boston, MA, USA). The gp120 preparations (called later in the paper gp120core) were dialyzed against phosphate-buffered saline (PBS) and stored in aliquots at −80 °C until further use.
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2

Purification of Soluble Cav Protein

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The SEC spectrum of cavsol was acquired using a Bio-Rad BioLogic DuoFlow Chromatography system equipped with a GE HiLoad 16/60 Superdex 200 PG gel filtration column. The gel filtration standard (Bio-Rad) was dissolved in 50 mM Tris-HCl pH 8.0, and used for column calibration. Cavsol was refolded via dialysis into refolding buffer as described above, and was purified through the column described above.
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3

Expression and Purification of SARS-CoV-2 Nucleocapsid Protein

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The full-length SARS-CoV-2 NP gene was synthesized and cloned into a pET28a vector (Bionics, South Korea) with an N-terminal 6 × His tag. This was then transformed into E. coli BL21(DE3). Expression of recombinant NP was induced by adding 0.5 mM isopropyl β -D-1-thiogalactopyronoside to the bacterial culture. Bacterial cells were lysed by sonication, and soluble NP was purified using Ni2+ affinity chromatography (HisTrap FF; GE Healthcare, IL, USA) and a size-exclusion column (HiLoad 16/60 Superdex 200 PG, GE Healthcare). The purity and homogeneity of the recombinant protein were purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Finally, the protein was concentrated to 2 mg/ml in phosphate-buffered saline (PBS) using a 30 kDa molecular-weight cutoff centrifugal filter (Millipore, MA, USA).
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4

Crystallization of CesT/Re-CsrA Complex

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For crystallization experiments, the Re-CsrA and CesT proteins were first mixed at 1:1 molar ratio and then further purified via gel filtration on a Hiload 16/60 Superdex 200 pg (GE Healthcare) column to obtain stable CesT/Re-CsrA complex. The resultant protein complex was used to screen the commercial crystallization kits (Hampton Research) via the sitting drop vapor diffusion method. The conditions were then optimized. Diffractable crystals were obtained by mixing 1 μl of the protein complex (at 10 mg/ml) with 1 μl reservoir solution consisting of 20% PEG 3350 and 0.2 M sodium citrate tribasic dihydrate, pH 8.3, followed by incubation at 18 °C for about 1 week. Data collection were conducted at Shanghai Synchrotron Radiation Facility (SSRF) beamline BL18U1. The collected data were then processed with HKL200044 (link) for indexing, integration, and scaling.
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5

Purification of Recombinant HutZ Protein

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HutZ was expressed in Escherichia coli and purified as described previously.3 Briefly, the hutZ gene was subcloned into pET-28b (Merck Millipore, Darmstadt, Germany) via NdeI and EcoRI sites, and the thrombin recognition site (Leu-Val-Pro-Arg-Gly-Ser) in the pET-28b construct was mutated to the HRV 3C protease recognition site (Leu-Glu-Val-Leu-Phe-Gln-Gly-Pro).15 (link)E. coli strains transduced with HutZ expression plasmids were grown at 37 °C in LB broth supplemented with 50 μg/mL kanamycin. Expression of His-tagged fusion protein in E. coli BL21(DE3) was induced by adding isopropyl-β-D-thiogalactopyranoside to a final concentration of 0.4 mM, after which cells were further incubated at 28 °C overnight. His6-tagged HutZ was purified by affinity chromatography using a HisTrap HP column (GE Healthcare, Uppsala, Sweden). After cleavage of the His6-tag, the reaction mixture was applied to the HisTrap column. The column flow-through was collected and then applied to a gel-filtration column (HiLoad 16/60 Superdex 200 pg, GE Healthcare) equilibrated with 50 mM Tris-HCl and 150 mM NaCl (pH 8.0). The protein concentration was determined on the basis of absorbance at 411 nm using extinction coefficient (ε412) of 166 mM−1cm−1 16 (link)
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6

Purification of S. cerevisiae Pex5 Protein

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Full‐length Saccharomyces cerevisiae Pex5 was cloned in a petM30 vector. Pex5 was expressed in autoinduction medium (Studier, 2005 (link)), with 5 h at 37°C and 26 h at 20°C. Cells were harvested, resuspended in lysis buffer (50 mM Hepes pH 7.5, 150 mM NaCl, 20 mM imidazole, protease inhibitor (Roche), DNAse (Sigma), and lysozyme (Sigma)), homogenized 1 h at 4°C and lysed by sonication. The lysate was then cleared by centrifugation and the supernatant was loaded onto Ni‐NTA resin. Bound proteins were washed with 50 mM Hepes pH 7.5, 750 mM NaCl, 20 mM Imidazole, and the protein was eluted with 50 mM Hepes pH 7.5, 150 mM NaCl, 250 mM Imidazole. The eluate was then dialyzed against Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP and simultaneously digested with 1 mg of TEV‐protease. Undigested protein and TEV protease were removed by a second Ni‐NTA step and flow through containing Pex5p was concentrated for gel filtration (Hiload 16/60 Superdex 200 pg, GE healthcare). Relevant fractions were pooled and the protein was concentrated, flash‐frozen in liquid nitrogen, and stored at −80°C.
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7

Size-Exclusion Chromatography of Protein Complexes

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Size‐exclusion chromatography was performed with a HiLoad® 16/60 Superdex® 200 pg (GE Healthcare) column, equilibrated with a assay buffer. 0.5 mg of pure protein or complexed proteins (10 minutes at 4°C under gentle mixing) were injected together with 1 mg of aprotinin (6.5 kDa) using a 2 mL loop and eluted with 1 mL/min flow rate. Protein elution was monitored by following the absorption at 280 nm (mAU).
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8

Determining Molecular Masses of Proteins

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The native molecular masses were determined by gel filtration on a HiLoad 16/60 Superdex 200 pg prepacked column (GE Healthcare) using 50 mM sodium phosphate pH 7.2 plus 150 mM NaCl as column buffer and according to the instructions in the Gel Filtration Calibration Kit (GE Healthcare) using the native protein standards: Ferritin (444 kDa), Aldolase (158 kDa), Conalbumin (75 kDa), Ovalbumin (43 kDa), Carbonic anhydrase (29 kDa), RNAse (13.7 kDa), Aprotinin (6.5 kDa). The molecular mass of the monomers of BvHb1.2 and BvHb2 were also determined by mass spectrometry [24 (link)].
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9

Generation of Fab-to-IgG Chimeric Antibody

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The HD5 Fab antibody was selected from a fully human Fab antibody library (kindly provided by Dyax, MA, USA) as previously described [32 (link)]. Fabs were expressed, purified and converted into chimeric IgG1 molecules comprising mouse Fc. A stable transfected NSO cell line carrying the HD5 Ab cassette in a glutamine synthetase gene expression system (LONZA, Switzerland) was generated as previously described [33 (link)]. The HD5 (5.1 clone) cell line was grown in DMEM (-/-) supplemented with L-Glutamine (Gibco, Carlsbad, CA), Penicillin-Streptomycin (Gibco), and 10% FBS IgG depleted (PAA, Austria) media. Antibody production was performed in Fibrastage cell culture systems (Eppendorf, Germany). Supernatants were purified using CaptureSelect Fab Kappa matrix (Life technologies, Carlsbad CA). Concentrated IgGs solutions ran through size exclusion chromatography (Hiload 16/60, Superdex 200 PG) (GE Healthcare, UK) in an ÄKTA Prime system (Amersham Pharmacia, UK) and recovered fractions of the purified IgG were desalted, concentrated and sterile filtered.
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10

Heterologous Protein Expression in E. coli

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The pET-CsyB/E. coli BLR (DE3) strain
was incubated to an OD600 of 0.6 at 37 °C in an LB
medium containing 50 mg mL–1 kanamycin. The target
protein expression was induced at 20 °C overnight by adding the
isopropyl d-1-thiogalactopyranoside (IPTG) to a final concentration
of 0.6 mM. The E. coli cells were harvested
by centrifugation at 7000g for 15 min. The cells
were suspended and disrupted by ultrasonication, and the lysate was
centrifuged at 10000g for 30 min. After protein was
purified by metal affinity chromatography, gel filtration chromatography
was used as the last step on a HiLoad 16/60 Superdex 200 pg (GE Healthcare).
All of the procedures were performed at 4 °C.
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