After going through the final phases of the protocol, the next step is visualization of the extraction-precipitation outcome by SDS-PAGE analysis and Coomassie blue staining. When there is a lysis step prior to organic extraction, a prominent ELP band should be apparent. In the case of ELP-I-Cm2, this band appears at 100 kDa (Figure 3A).
Screening of different organic solvent combinations demonstrated variable extraction efficiencies (Figure 3B), with every combination producing different concentrations and purities. We select the best combinations for the extraction-precipitation based on the purity and functional assay of the fusion protein for use with subsequent larger-scale ELP purifications of that construct. The AG (isopropanol:acetonitrile) and BG (butanol:acetonitrile) 1:1 mixtures produced the highest protein recovery (2.2-2.6 g/L) compared to the other combinations for the case of ELP-I-Cm2.
To determine whether the purified ELP remains functional after organic extraction, a fusion protein activity assay should be performed. In the case of ELP-I-Cm2, a Cm2 enzyme activity assay was conducted (Figure 2C). This assay measures the conversion of chorismate into prephenate in the presence of the Cm2 enzyme, with subsequent conversion into phenylpyruvate (Figure 2D). Phenylpyruvate production is tracked by measuring the increase in absorbance at 320 nm as a direct indication of the reaction extent. The protein extracted with the AG solvent mix retained about 80% of the activity compared to ELP-I-Cm2 isolated by the standard ITC method; the BG mix retained around 50% activity. As expected, the V40 control, which has a similar molecular weight but lacks the Cm2 enzyme, showed almost no activity.
In summary, the ELP-I-Cm2 results suggest that a combination of a lysis step before extraction with the appropriate solvent mix (e.g., AG or BG) is effective in isolating pure ELP-I-Cm2 that retains much of its enzymatic activity, making this approach a viable alternative to ITC purification.

Figure 1: Organic solvent extraction and precipitation of elastin-like polypeptides from E. coli generates purified constructs in a manner that is independent of molecular weight and isoelectric point. This figure has been adapted with permission from Aayush, A., Darji, S., Estes, K. M., Yeh, E., Thompson, D. H. Development of an elastin-like polypeptide-based nucleic acid delivery system targeted to EGFR+ bladder cancer cells using a layer-by-layer approach. Biomacromolecules. 25 (9), 5729-5744 (2024)18. Copyright © 2024 American Chemical Society. Please click here to view a larger version of this figure.

Figure 2: Representative images of the ELP-I-Cm2 observed by atomic force microscopy (AFM) in organic solvent mix AG (1:1 isopropanol and acetonitrile) and aqueous medium. (A) Organic solvent mix AG (1:1 isopropanol and acetonitrile) and (B) Aqueous medium. Differences in enzyme activity of ELP-I-Cm2 in organic versus aqueous environments likely arise from distinct microphase arrangements, as visualized by AFM. (C) In organic solvent, Cm2 is retained within a hydrated reverse micellar core surrounded by solvated ELP chains, supporting activity by preserving structure and enabling substrate access. (D) In contrast, limited solvent compatibility causes ELP collapse and aggregation into amorphous assemblies, leading to structural disruption of Cm2 and reduced catalytic activity. This figure has been reprinted with permission from Darji S., Aayush, A., Estes, K. M., Strock, J. D., Thompson, D. H. Unravelling the mechanism of elastin-like polypeptide-enzyme fusion stabilization in organic solvents. Biomacromolecules. 25 (1), 272-281 (2024)9. Copyright © 2024 American Chemical Society. License Number: 6137271264771 Please click here to view a larger version of this figure.

Figure 3: Representative images of the ELP-I-Cm2 protein expression and purification via SDS-PAGE analysis, followed by its activity assay results. (A) SDS-PAGE electrophoresis analysis to showcase the comparison between E.coli pellet masses that are just vortexed versus a single-step cell lysis followed by organic extraction. (B) SDS-PAGE electrophoresis analysis of ELP-I-Cm2 proteins in different organic solvents. The AG and BG combinations showed maximum protein extraction. To ensure reproducibility, ELP-I-Cm2 was purified using organic extraction from at least three biological replicates. (C) Activity assay of ELP-I-Cm2 from organic extraction (AG and BG) in comparison to proteins extracted by standard ITC alone (positive control), while the negative control, V40 showing low activity (each condition had n = 3 replicates). (D) The Cm2 activity assay tracks the reaction by measuring the increase in absorbance at 320 nm, corresponding to the formation of phenylpyruvate product, as shown. This figure has been reprinted with permission from Darji S., Aayush, A., Estes, K. M., Strock, J. D., Thompson, D. H. Unravelling the mechanism of elastin-like polypeptide-enzyme fusion stabilization in organic solvents. Biomacromolecules. 25 (1), 272-281 (2024)9. Copyright © 2024 American Chemical Society. License Number: 6086020722974 Please click here to view a larger version of this figure.

Figure 4: Workflow for organic solvent-based extraction and precipitation of ELP fusion proteins. (A) Cell lysis and preparation. E. coli bacterial pellets expressing the protein of interest are suspended in lysis buffer to generate a bacterial lysate. The lysate is disrupted by sonication and then followed by centrifugation to separate soluble and insoluble fractions. (B) Organic Solvent Extraction. The soluble fraction (or pellet if the protein is insoluble) is mixed with organic solvents to extract the target protein. After centrifugation, the protein-containing supernatant is collected and precipitated with acetonitrile. The final centrifugation yields a pellet containing the purified protein of interest. Figure created with BioRender.com Please click here to view a larger version of this figure.
| Label | Solvent |
| A | Isopropanol |
| B | Butanol |
| C | Ethyl Acetate |
| D | Ethanol |
| E | Methanol |
| F | Acetone |
| G | Acetonitrile |
Table 1: Organic solvents employed to extract the ELP-I-Cm2 fusion protein from inclusion bodies.
Supplementary File 1: The plasmid DNA sequence for the ELP-I-Cm2 protein. Please click here to download this File.