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    Purification of recombinant Low Density Lipoprotein Receptor Related Protein Associated Protein 1 (LRPAP1, RAP) from Escherichia coli

    Patricia Yuste-Checa, F Ulrich Hartl, Silvia Gärtner

    Published: 2024-02-02 DOI: 10.17504/protocols.io.rm7vzxpb2gx1/v1
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    Abstract

    This protocol details how to efficiently purify LDL Receptor Related Protein Associated Protein 1 (LRPAP1 or RAP) from Escherichia coli.

    Attachments

    Purification of recombinant LRPAP1 from E. coli.docx

    Steps

    LRPAP1 express4ion

    1.

    Thaw RbCl-competent Escherichia coli Bl21 cells (DE3) On ice.

    2.

    Add 1µL of pQTEV-LRPAP1 plasmid without the signal peptide (1-35 amino acids) and incubate 0h 30m 0s On ice.

    3.

    Heat shock 0h 0m 45s at 42°C.

    4.

    Incubate On ice 0h 2m 0s, then add 850µL Lysogeny broth (LB) or Super Optimal broth with Catabolite repression (SOC) medium.

    5.

    Shake for 1h 0m 0s at 37°C.

    6.

    Centrifuge for 3000x g and remove most of the supernatant.

    7.

    Resuspend the pellet with the remaining supernatant and plate the bacteria on LB /Ampicillin agar plates and incubate 1h 0m 0s at 37°C.

    8.

    Prepare preculture: Scrap all colonies with the scraper and inoculate 25-50 mL LB/Ampicillin. Shake at 37°C for 4-6 h.

    9.

    Measure OD600 of the preculture and inoculate 6L of LB media to an OD600 = 0.05.

    10.

    Shake flasks at 37°C until approx. OD600 = 0.5-0.8. (2-4 h).

    11.

    Add isopropyl β-D-1-thiogalactopyranoside (IPTG) at final concentration of 1millimolar (mM).

    12.

    Shake flasks 1h 0m 0s at 22°C.

    13.

    Centrifuge bacterial culture at 4000rpm. Discard supernatant.

    14.

    Resuspend each pellet with Lysis buffer (20 mL/1L bacteria) supplemented with Complete EDTA-free protease inhibitor cocktail (Merck). Flash-freeze in liquid nitrogen for storage at -80°C.

    Lysis

    15.

    Thaw the cell pellets in a water bath at 22°C and add lysis buffer (final volume 200 mL lysis buffer/ 6L bacteria) supplemented with Complete EDTA-free protease inhibitor cocktail (Merck) and Sm DNase 50.

    16.

    Add 1 lysozyme and incubate gently shaking for 0h 30m 0s at 4°C.

    17.

    Sonicate lysate On ice, 8 cycles 0h 0m 20s ON, 0h 0m 30s OFF.

    18.

    Centrifuge lysate at 40000rpm,4°C.

    Ni-NTA chromatography

    19.

    Equilibrate the Ni-NTA column with 10 column volumes (CV, 20 mL) Lysis buffer.

    20.

    Load lysate supernatant to the Ni-NTA column.

    21.

    Wash the Ni-NTA column with 10 CV Lysis buffer.

    22.

    Elute His7-TEV-RAP with 5 CV 100% High salt buffer and collect elution fractions.

    23.

    Analyze eluted fraction by SDS-PAGE and Coomassie blue staining.

    Ni-NTA chromatogram and SDS PAGE analysis.  P: 20 µL resuspended pellet + 20 µL 2x SDS sample buffer, loaded 15 µL. S: 20 µL diluted supernatant + 20 µL 2x SDS sample buffer, loaded 15 µL. Fractions of interest: 10 µL + 10 µL 2x SDS sample buffer; loaded 6 µL. Green box: Collected elution fractions (Fractions 29-41, 65mL).
    Ni-NTA chromatogram and SDS PAGE analysis. P: 20 µL resuspended pellet + 20 µL 2x SDS sample buffer, loaded 15 µL. S: 20 µL diluted supernatant + 20 µL 2x SDS sample buffer, loaded 15 µL. Fractions of interest: 10 µL + 10 µL 2x SDS sample buffer; loaded 6 µL. Green box: Collected elution fractions (Fractions 29-41, 65mL).

    Desalting

    24.

    In order to reduce the salt concentration, load the eluted protein onto a HiPrep 26/10 desalting column equilibrated with the Low salt buffer.

    His-TEV cleavage

    25.

    Collect eluted fraction containing protein and add glycerol at final concentration of 10%, DTT at final concentration of 1millimolar (mM), EDTA at final concentration of 0.25millimolar (mM) and His-TEV at final concentration of 93U per mg of protein.

    26.

    Incubate at 4°C 0h 0m 30s.

    Ni-NTA chromatography (Collect flow through)

    27.

    Load the cleavage mixture onto a Ni-NTA column previously equilibrated with Lysis buffer and collect the flow through where the cleaved RAP protein should elute.

    28.

    Wash the column with 5 CV (CV, 20 mL) of Lysis buffer and collect eluted fractions.

    29.

    Analyze flow though fractions by SDS-PAGE and Coomassie blue staining.

    Ni-NTA chromatogram and SDS PAGE analysis.  TEV digest: 10 µL sample + 10 µL 2x SDS sample buffer, loaded 2.0 µL. Fractions of interest: 10 µL sample + 10 µL 2x SDS sample buffer, loaded 5 µL. Green boxes: Collected flow through (Fractions 20-21, 16 mL), and uncleaved His7-TEV-RAP protein eluted from the Ni-NTA column (Fractions 33-34).
    Ni-NTA chromatogram and SDS PAGE analysis. TEV digest: 10 µL sample + 10 µL 2x SDS sample buffer, loaded 2.0 µL. Fractions of interest: 10 µL sample + 10 µL 2x SDS sample buffer, loaded 5 µL. Green boxes: Collected flow through (Fractions 20-21, 16 mL), and uncleaved His7-TEV-RAP protein eluted from the Ni-NTA column (Fractions 33-34).

    Note
    Some uncleaved His7-TEV-RAP protein may be eluted from the Ni-NTA column. Those fractions can be pooled, desalted and TEV digested again.

    Size exclusion chromatography

    30.

    Load RAP-containing fractions onto a Superdex-200 column previously equilibrated with SEC buffer.

    31.

    Analyze eluted fractions by SDS-PAGE and Coomassie blue staining.

    Size exclusion chromatogram and SDS PAGE analysis. 10 µL fraction of interest + 10 µL 2x SDS sample dye, loaded 2.0 µL. Green box: Collected eluted fractions (72-77, 12mL).
    Size exclusion chromatogram and SDS PAGE analysis. 10 µL fraction of interest + 10 µL 2x SDS sample dye, loaded 2.0 µL. Green box: Collected eluted fractions (72-77, 12mL).
    32.

    Pool fractions containing RAP aliquot and flash-freeze in liquid nitrogen for storage at -80°C.

    Note
    The protein can be concentrated with a filter device like a VivaSpin20, MWCO 10,000 Da. Approximate yield : from 6L of bacterial culture around 95mg of pure RAP are obtained.

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