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Improved Native Isolation of Endogenous Protein A-Tagged Protein Complexes
John LaCava1, Nagarajan Chandramouli2, Hua Jiang1, and Michael P. Rout1
1Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
2Proteomics Resource Center, The Rockefeller University, New York, NY, USA
BioTechniques, Vol. 54, No. 4, April 2013, pp. 213–216
Full Text (PDF)
Supplementary Material
Protocol (.pdf)

Here we report a modified peptide reagent useful for the rapid, native elution of protein complexes containing a Protein-A-tagged component. We tested this reagent for the elution of tagged endogenous protein complexes from yeast (Nup53p/Nup170p dimer; Nup1p/Kap95p/Kap60p trimer; pentameric GINS complex) and bacteria (RNAP holoenzyme). The majority of the affinity-isolated material is released within 15 minutes under mild conditions, and the elution reagent itself is readily depleted from the elution mixture by simple spin column gel filtration. This reagent is ideal for eluting protein complexes after Protein A / IgG affinity isolation when protease cleavage is not possible or not desirable and facile depletion of the elution reagent is needed.

Affinity isolation methodologies have led the successful drive to capture endogenous protein complexes. Among these affinity systems, the S. aureus Protein A (SpA) / mammalian immunoglobulin G (IgG) interaction (1, 2) is widely utilized. Moreover, tandem affinity purification (TAP)-tagged (3) yeast strains available from genome-wide tagging efforts (4, 5) incorporate tandem repeats of the SpA-derived IgG binding Z-domain (6). Thus, a vast library of strains exist for the purification of diverse protein complexes via the SpA/IgG interaction.

To recover protein complexes in the most active and physiologically relevant state, it is desirable to work fast – minimizing the time between capture and assay. Native elution from SpA/IgG affinity systems generally follows two lines: competitive elution of the tagged bait protein and its coprecipitated interactors (7, 8), or protease cleavage of the tag from the bait protein, releasing the bait and its coprecipitated interactors (3). The efficiency of release of different protein complexes from the stationary phase by protease cleavage is not uniform, and cleavage requires long incubation times ranging from hours to overnight (9, 10). Improvement of these parameters, if at all possible, would likely require fundamental engineering of the protease. SpA binds to the hinge region on the Fc fragment of IgG; a bacteriophage display screen found a 13 amino acid peptide (FcIII peptide: DCAWHLGELVWCT) that bound competitively to the same region with high affinity (11). Our group previously developed a modified, higher solubility version of this peptide capable of competitively eluting protein complexes in their native state at high yield within ∼2 h (biotinylated FcIII peptide, termed Bio-Ox) (8). We reasoned that a larger increase in the solubility of FcIII could reduce the time to achieve competitive elution and therefore sought to improve this approach further.

Method summary

To improve isolation of Protein-A tagged protein complexes, we modified our previously described competitive elution peptide (Bio-Ox) with the addition of a polyethylene glycol moiety of four unit lengths to increase solubility. This new peptide (PEGylOx) enables elution of affinity-isolated material in less than 15 minutes under mild reaction conditions.

As the N terminus has previously been used to increase FcIII peptide solubility via conjugation to biotin (8), we tested several alternative N-terminal substitutions aimed at further solubility gains. Among our tested variants, a modification comprising a polyethylene glycol moiety of four units length (PEG[4]) proved to be the most effective at increasing and maintaining FcIII peptide solubility. Longer PEG modifications, up to eight units in length, exhibited problems with in-solution stability, precipitating out when held on ice. Coupling additional groups (e.g., biotin, arginine, poly-histidine) to the PEG moiety did not further improve performance (data shown for R-PEG[4], see below). The new reagent described here, termed PEGylOx, is an FcIII peptide N-terminally PEGylated with a four-unit polymer and cyclized by oxidation of the cysteines to cystine (Figure 1A).

Figure 1.  PEGylation of FcIII peptide increases solubility and maintains competitive displacement of S. aureus Protein A (SpA) from mammalian IgG. (A) The chemical structure of PEGylOx. (B) The concentrations of Bio-Ox, PEGylOx, and R-PEGylOx at room temperature (RT) or 4°C, as determined by UV280 spectrophotometry on three independent aliquots of lyophilized peptide suspended in the described buffered solution. Error bars indicate the standard deviation (SD) (C) The percentage of SpA retained by immobilized rabbit IgG after treatment with differing concentrations of Bio-Ox or PEGylOx for 1 h at RT – as determined by image densitometry of Coomassie stained SDS-PAGE gels (detailed in Supplementary Section S3). A buffer only control is included, and the IC50 for both reagents is indicated. All values are the average of duplicate experiments. (D (Click to enlarge)

For this study, Bio-Ox was synthesized as previously described (8). PEGylated peptides were synthesized by standard Fmoc solid-phase synthesis methods. Incorporation of PEG spacers into the peptide sequence was accomplished using N-Fmoc-amido-(PEG) n-acid building blocks (Detailed in Supplementary Section S1, or obtained from 21st Century Biochemicals, Marlboro, MA). Prior to use, lyophilized peptides were resuspended in a 40 mM Tris-Cl buffered solution at pH 8.0, with 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.01% v/v Tween 20, and 5% v/v ethanol. This solution was centrifuged at top speed in a bench-top microcentrifuge for 5 min at room temperature (RT) to remove any insoluble fraction. The resulting supernatant was assayed by UV spectrophotometry at a wavelength of 280 nm (UV280) to determine the final peptide concentration using an estimated molar extinction coefficient (12) (∊280) of 11125 M−1cm−1 (Supplementary Section S2A). We found that the addition of 5% v/v ethanol aided modified FcIII peptide solubility, increasing Bio-Ox solubility almost 3× (0.440 mM to 1.18 mM) (8), and exhibited no observable negative effect on the stability of any protein complex we have tested thus far (data not shown). PEGylOx was found to be 2.3× more soluble at saturation than Bio-Ox at RT and almost 3× more soluble at 4°C, demonstrating the advantage of the PEG[4] conjugate over biotin as a solubility enhancer. Although we reasoned that additional charged groups may provide further solubility gains, no such advantage was observed by the coupling of an R residue to the PEG[4] moiety (Figure 1B). Next, we conducted an assay for the competitive displacement of wild type (wt) SpA from immobilized IgG. Bio-Ox and PEGylOx each exhibited a similar IC50 (Figure 1C, Supplementary Section S2B) — consistent with the ability of both Bio-Ox and PEGylOx to effectively displace SpA, and the complete conservation of the mechanism of action of the peptide upon substitution of the biotin modification for PEG[4].

Macromolecular complexes tend to disintegrate with time after isolation; thus, to determine the shortest sensible time-scale of elution, we conducted a time course to displace SpA from immobilized IgG with a saturated PEGylOx solution. We found that > 70% of the SpA was released within 15 min (Figure 1D, Supplementary Section S2C). We then tested saturated solutions of PEGylOx and Bio-Ox for their ability to elute already well-defined SpA-tagged protein complexes (13-15) (Supplementary Section S4A) isolated from endogenous sources (Supplementary Protocol) and found that the saturated PEGylOx solution released numerous protein complexes with greater efficiency and uniformity between samples than the saturated Bio-Ox solution. While Bio-Ox is effective with longer incubation times (8), PEGylOx shows a distinct advantage at short elution times. Example protein complexes that we quantified exhibited approximately 60%-85% efficiency of release during a 15 minutes incubation with PEGylOx. In contrast, Bio-Ox was essentially unable to release two of the test complexes within this time, and one complex was released with only moderate efficacy (Figure 2). We conclude that PEGylOx is an improved, rapidly acting reagent for competitive native elution of SpA-tagged protein complexes.

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