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Ni nta agarose beads

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Ni-NTA agarose beads are a type of affinity resin used for the purification of recombinant proteins containing a histidine (His) tag. The nickel-nitrilotriacetic acid (Ni-NTA) group on the beads binds to the His-tagged proteins, allowing them to be isolated from complex mixtures.

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47 protocols using ni nta agarose beads

1

Generation of Antibody Constructs and Neutralization Assays

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Sequences for the variable regions of antibody heavy and light chains were obtained from deposited antibody structures on the PDB and cloned into expression vectors to make full-length human IgG1 antibodies. Sequences for the heavy chain were modified with a C-terminal ybbR tag for enzymatic labeling (63 (link)) and, in the case of Fab fragments, a His6 tag for affinity purification using Ni-NTA Agarose Beads (Thermo Scientific Pierce). Full-length antibodies were purified using protein A agarose beads (Thermo Scientific Pierce). Antibodies were expressed in HEK-293T following transfection with heavy and light chains at >70% confluency. Cells were subsequently cultured for seven days in Opti-MEM with 1x Anti-Anti and with or without 2% FBS for Fab and IgG antibodies, respectively. Supernatants from the HEK-293T cells were collected for affinity purification. Full details on antibody purification and enzymatic labeling are described elsewhere (63 (link)).
Human convalescent sera was obtained through BEI Resources (NR-18964 and NR-18965 for Serum 001 and Serum 002, respectively) and used without further purification in virus counting assays and microneutralization assays. IC50 values for serum neutralization were measured as fold-dilutions from the initial undiluted stock.
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2

Antibody Expression and Purification

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Sequences for the variable regions of antibody heavy and light chains were obtained from deposited antibody structures on the PDB and cloned into expression vectors to make full-length human IgG1 antibodies. Sequences for the heavy chain were modified with a C-terminal ybbR tag for enzymatic labeling (56 (link)) and, in the case of Fab fragments, a His6 tag for affinity purification using Ni-NTA Agarose Beads (Thermo Scientific Pierce). Full-length antibodies were purified using protein A agarose beads (Thermo Scientific Pierce). Antibodies were expressed in HEK-293T following transfection with heavy and light chains at >70% confluency. Cells were subsequently cultured for 7 days in Opti-MEM with 1× Anti-Anti and with or without 2% FBS for Fab and IgG antibodies, respectively. Supernatants from the HEK-293T cells were collected for affinity purification. Full details on antibody purification and enzymatic labeling are described elsewhere (57 (link)).
Human convalescent sera were obtained through BEI Resources (NR-18964 and NR-18965 for Serum 001 and Serum 002, respectively) and used without further purification in virus counting assays and microneutralization assays. IC50 values for serum neutralization were measured as fold dilutions from the initial undiluted stock.
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3

Bacterial Expression and Purification of Fusion Proteins

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To construct the plasmids corresponding to GST-MoAA91 and GST-MoAA91DTB, His-MoMSN2, and His-CEBiP, full-length cDNA of MoAA91 lacking the signal peptide was amplified and inserted into the vector pGEX4T-2, full-length cDNA of MoMSN2 was amplified and inserted into the vector pET-32A, and full-length cDNA of CEBiP lacking the signal peptide and the transmembrane domain was amplified and inserted into the vector pET-32A, respectively. These plasmids were then expressed in E. coli strain BL21, and bacterial cells were collected and treated with lysis buffer (10 mM Tris-HCl [pH 7.5], 150 mM NaCl, 0.5 mM EDTA, 0.5% Triton X-100). To confirm the expression of the GST or His fusion proteins, bacterial lysates were separated by the use of SDS-PAGE gel followed by Coomassie blue staining (see Fig. S7A to D in the supplemental material). In the assay used for purification of protein (His-MoMsn2/CEBiP and GST-MoAa91/MoAa91DTB), bacterial lysate containing His-MoMsn2/CEBiP protein was incubated with 30 μl nickel-nitrilotriacetic acid (Ni-NTA) agarose beads (Invitrogen, Shanghai, China) and bacterial lysate containing GST-MoAa91/MoAa91DTB protein was incubated with GST beads for 1 h at 4°C. The beads were then washed five times, and the elution was reduced using glutathione (Abmart, Shanghai, China).
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4

Ubiquitination Assay Protocol

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For His ubiquitination assay, cells were co-transfected with the indicated plasmids for 48 h, followed by treatment with 20 μM MG132 (Selleck, S2619) for 6 h. Cells were collected and subjected to lyse in Buffer A (6 M guanidine-HCl, 10 mM imidazole, 0.1 M Na2HPO4/NaH2PO4; pH 8.0). The ubiquitinated proteins were pulled down with Ni-NTA agarose beads (Invitrogen, R901-15) for 4 h at room temperature, washed twice with Buffer A, followed by washed twice with Buffer A/TI (1:3, v/v), after which washed once with Buffer TI (25 mM Tris-HCl, 20 mM imidazole; pH 6.0) and boiled in 1 × SDS loading buffer for 10 min. The ubiquitinated proteins were detected with the indicated antibodies.
For HA ubiquitination assay, cells were prepared and lysed in ice-cold lysis buffer for 30 min and centrifugated. 10% of supernatants were used as input. The remaining supernatants were incubated with anti-Flag M2 agarose beads or anti-Myc magnetic beads for overnight at 4 °C. The beads were then washed five times with ice-cold lysis buffer and boiled in 2 × SDS loading buffer for 10 min. The ubiquitinated proteins were detected with anti-HA antibody.
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5

Detecting mTOR Ubiquitination via Ni-NTA Assay

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mTOR ubiquitination assays were determined by Ni-NTA affinity isolation as described previously [43 (link)]. Briefly, cells transfected with pCMV mTOR-His together with each of the indicated plasmids were washed with PBS, lysed in 200 μL of denaturing lysis buffer (50 mM Tris-HCl, pH 7.4, 0.5% SDS, 70 mM β-meraptoethanol) by vortexing, and boiled for 20 minutes at 95 °C. The lysates were diluted with 800 μL buffer A (50 mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH 8.0, protease inhibitor cocktail, and 10 μM MG132) and incubated overnight with 50 μL Ni-NTA Agarose Beads (Invitrogen, R901-15) at 4 °C. Beads were washed 5 times with buffer B (50 mM NaH2PO4, 300 mM NaCl, 20 mM imidazole, pH 8.0), and bound proteins were eluted by boiling in a mixture of 5× SDS-PAGE gel loading buffer and buffer C (50 mM NaH2PO4, 300 mM NaCl, 250 mM imidazole, pH 8.0) (1:4). Thereafter, ubiquitinated mTOR was identified with anti-His (Cell signaling) and anti-HA (Cell signaling) antibodies on Western blot.
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6

Purification of His-Tagged Proteins from E. coli

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His-MBP-AADs and His-FKBP F36V-AADs were purified from ArcticExpress E. coli. Cells were resuspended in Native Purification Buffer (50 mM NaH2PO4, 500 mM NaCl, 10 mM imidazole, 5 μg/ml aprotinin, 5 μg/ml leupeptin, 4 mm DTT) containing lysozyme and incubated on ice for 30 min. Cells were sonicated and lysates were cleared by centrifugation. Cleared lysates were incubated with Ni-NTA agarose beads (Invitrogen, R901–01) for 3 h at 4 °C. Beads were washed four times with native wash buffer (50 mM NaH2PO4, 500 mM NaCl, 20 mM imidazole, 5 μg/ml aprotinin, 5 μg/ml leupeptin, 4 mm DTT). Bound proteins were recovered by incubation with native elution buffer (50 mM NaH2PO4, 500 mM NaCl, 250 mM imidazole, 5 μg/ml aprotinin, 5 μg/ml leupeptin, 4 mm DTT) and dialyzed (20 mM HEPES-KOH pH 7.5, 50 mM NaCl, 1 mM DTT) for 2 h and then again overnight at 4 °C.
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7

Purification and Utilization of Lack Antigen

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The Lack antigen was produced and purified from bacteria through histidine tag purification with Ni-NTA agarose beads (Invitrogen), and the Lack peptide (aa 156–173) was synthetized by PolyPeptide Group. CypHer5E was purchased from Amersham Bioscience and used according to the manufacturer’s instructions. For cytoskeleton-disrupting drugs, we used 10 µM nocodazole, 5 µM Latrunculin A, and 20 µM paclitaxel (Merck). For histone deacetylase inhibition, we used 1 µM SAHA (Cayman Chemical Company).
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8

Purification of Spc105 Protein Fragment

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The 6xHIS-MBP-Spc1052-455,222::GFP fusion construct was expressed in BL21-Rosetta 2 (DE3; Novagen) or T7 expression Escherichia coli cells (NEB) using 0.25 mM IPTG for 16 h at 18°C. Cells were then harvested and resuspended in the lysis buffer (20 mM Tris, pH 7.5, 300 mM NaCl, 5 mM imidazole, 0.1% Triton X-100 [Sigma-Aldrich], 5% glycerol, and 1 mM PMSF) supplemented with complete EDTA-free protease inhibitor mix (Roche). Cells were lysed by sonication (3× for 3 min with 30-s pulse on and 30-s pulse off). Cleared supernatant was incubated with Ni-NTA agarose beads (Invitrogen) for 2 h at 4°C. Beads were washed with lysis buffer containing 500 mM NaCl and 30 mM imidazole, and protein was eluted with lysis buffer containing 150 mM NaCl and 250 mM imidazole. Subsequently, the protein was loaded onto a 16/60 Superdex 200 size exclusion column (GE) equilibrated with gel filtration buffer (20 mM Tris, pH 7.5, 100 mM NaCl, 5% glycerol, and 1 mM DTT). Fractions were analyzed by SDS-PAGE and Coomassie staining, and peak fractions were aliquoted and stored at −80°C.
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9

Recombinant Expression and Purification of Sr43

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The native CDS of Sr43 plus two additional nucleotides (CC) at the beginning of the CDS (to maintain the open reading frame with His6 tag) was commercially synthesized (Twist Bioscience) and cloned into the Gateway entry vector pTwist_ENTR. For recombinant protein expression, Sr43 was transferred into the expression vector pDEST-His6-MBP by Gateway LR clonase reaction (Invitrogen). The resulting clone was verified by Sanger sequencing.
His6-MBP-Sr43 tagged protein was expressed in the E. coli Rosetta strain by growing the bacterial culture to an optical density OD600 of 0.8 at 37 °C and then inducing the protein expression by addition of 0.5 mM isopropyl β-d-thiogalactopyranoside at 18 °C and further incubating the culture for 14–16 h. The recombinant protein was purified under native conditions using Ni-NTA agarose beads (Invitrogen catalog no. R901-15) following the manufacturer’s instructions.
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10

Affinity Purification of His-tagged COA7

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HEK293 cells were grown in low‐glucose DMEM for 24 h. The cells were then transferred to DMEM and transfected with pcDNA3.1(+)‐COA7HIS using Gene Juice Transfection Reagent (Merck Millipore) according to the manufacturer's protocol. The cells were harvested 24 h after transfection and solubilized in ice‐cold digitonin buffer (1% digitonin, 10% glycerol, 20 mM Tris–HCl [pH 7.4], 100 mM NaCl, and 20 mM imidazole [pH 7.4]) supplemented with 2 mM PMSF and 50 mM IAA for 20 min at 4°C. The lysate was clarified by centrifugation at 20,000 g for 15 min at 4°C. The supernatant was then incubated with Ni‐NTA agarose beads (Invitrogen) with mild rotation for 1.5 h at 4°C. After binding, the beads were washed three times with wash buffer (20 mM Tris–HCl [pH 7.4], 100 mM NaCl, and 35 mM imidazole [pH 7.4]). Bead‐bound proteins were eluted with Laemmli buffer that contained either 50 mM DTT or 50 mM IAA for reducing and non‐reducing conditions, respectively. The samples were denatured and subjected to SDS–PAGE and Western blot.
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