General Troubleshooting Guide for Protein Synthesis

Q: What is protein expression and purification?

Protein expression is the biotechnological process of generating a specific protein. It can be done in prokaryotic, eukaryotic or In vitro E. coli expression system. Protein purification is a series of processes intended to isolate one or a few proteins from cells or organisms. The most popular method for protein purification is affinity chromatography, and which is designed by different protein tags. Other protein purification methods, including ion exchange chromatography, size-exclusion chromatography, polish purification and hydrophobic interaction chromatography are available to handle tag-free proteins with high purity.

Q: Why is there no/low protein expression?

a. Incorrect vector construction. You should confirm vector by sequencing or apply for our custom clone service.

b. Rare codons. You should optimize codons, use strains supplementing rare codons, induce at lower temperature or grow in poor media.

c. Protein toxicity. You should use promoters with tighter regulation or lower plasmid copy number. Use pLysS/pLysE bearing strains in T7-based systems or strains that are better for the expression of toxic proteins. Start induction at high OD and shorten induction time. Add glucose when using expression vectors containing lac-based promoters.

Q: How to avoid inclusion bodies and improve soluble expression?

a. Proteins with high hydrophobicity or transmembrane domains. You should add fusion tags or add heat shock chaperones. You should induce for a shorter time at low temperature or change to poor media. Generate truncated forms of protein or use membrane rich strains.

b. Incorrect disulfide bond formation. You should add fusion partners, including thioredoxin, DsbA, DsbC. Clone in a vector containing secretion signal peptide to cell periplasm. Use gamiB (DE3)strains with oxidative cytoplasmic environment. Lower inducer concentration and induction temperature.

c. Incorrect folding. You should use a fusion partner. Co-express with molecular chaperones. Use strains with cold-adapted chaperones. Supplement media with chemical chaperones and cofactors. Reduce the inducer concentration and add fresh media. Induce for a shorter time at low temperature.

Q: Why is the molecular weight of protein smaller than the predicted?

a. Rare amino acids selenocysteine (Sec) or pyrrolysine (Pyl) in protein sequence. You should use some other amino acids to instead these two unusual amino acids.

b. Imbalanced translation process of fusion protein. You should change another fusion tag or move fusion tag to C-terminal. You should induce for a shorter time at low temperature or change to poor media.

c. Protein degradation. You should replace specific protease sites. Use protease deficient strains. Induce at high OD. You should induce for a shorter time at low temperature or use protease inhibitors when breaking cells.

Q: Why is the actual band size different from the predicted?

a. Post-translational modification. Phosphorylation, glycosylation, etc which increases the size of the protein.

b. Post-translational cleavage. Many proteins are synthesized as pro-proteins, and then cleaved to give the active form.

c. Splice variants. Alternative splicing may create different sized proteins from the same gene.

d. Relative charge. The composition of amino acids have different relative charge which will affect the electrophoretic mobility.

e. Multimers such as dimerisation of a protein. This is usually prevented in reducing conditions, although strong interactions can result in the appearance of higher bands.

f. Protein structure such as disulfide bond, protein secondary structure or protein 3D structure formation.

g. Hydrophobic proteins, such as transmembrane proteins, may have difficulties in migrating into the gel, and thus resulting in different multi-banded patterns.

Q: How to express a protein with bioactivity? Why is the protein inactive?

For gaining a protein with bioactivity, you should choose a right expression system, a suitable expression vector, an appropriate purification method and a validation experiment. You can learn more from this link: Otherwise, you can check the problems below:

a. Low solubility of the protein. You should fuse desired protein to a fusion partners and lower temperature.

b. Lack of essential post translational modification. You should change another expression system.

c. Incomplete folding. You should use a fusion partner and use strains with cold-adapted chaperones. Co-express with molecular chaperones at lower temperature. Monitor disulfide bond formation and allow further folding in vitro.

d. Mutations in cDNA. You should sequence plasmid before and after induction or use a recA strain to ensure plasmid stability. Transform E. coli before each expression round.

Q: Why are our protein products almost invisible in pipes?

CUSABIO protein product does not contain carrier protein or other additives (such as bovine serum albumin (BSA), human serum albumin (HSA) and sucrose, and lyophilized from low salt solution, so it often does not form a white grid structure, but a trace amount of protein deposit within the tube, forming a thin transparent or invisible protein layer.

Tips: Before opening the lid, we recommend to centrifuge in a small centrifuge for 20-30 seconds firstly to ensure that the contents are on the bottom of the tube. Our quality control steps ensure that the amount of protein contained in each tube is accurate, although sometimes you can’t see the protein powder, but the protein content in the tube is still very accurate.

Q: How is the protein purified? Is the purity guaranteed?

We will design the optimal purification scheme according to the tag type of the fusion protein and the physicochemical properties of the protein itself. Our common purification methods are: affinity chromatography, hydrophobic chromatography, ion exchange chromatography, molecular sieve, salting out, etc. We guarantee a minimum purity standard of >85%. If the initial purification does not meet this standard or customer has higher purity requirement, we also have AKATA purification instrument, which is highly automated, precise control, combining the use of various column, to ensure that the purity of our protein product is further enhanced and the final purity test results are displayed on the COA report.

Although we guarantee a minimum purity standard of >85%, some of the proteins we prepared have a purity of 95% or even 97%.

Q: How should I reconstitute and store the products?

Centrifugate the reagent tube before opening the cap.

As for short-term storage or usage, please use sterile deionized water to completely reconstitute proteins to 0.1-1.0 mg/mL. Aliquot after 10-15 minutes if needed and store at 4℃.

As for long-term storage, the cytokines or recombinant proteins are recommended to add 5-50% of glycerol (final concentration) and aliquot for long-term storage at -20℃/-80℃. Our default final concentration of glycerol is 50%. Customers could use it as reference.

Q: What types of tags do you use for fusion?

The common tags we provide include His-tag, FLAG-tag, GST-tag, MBP-tag, combination tags (His-GST-tag, His-sumo-tag, His-MBP-tag), etc. Sometimes, the tag of proteins will be determined during the manufacturing process. If you have specified tag type, please feel free to consult with us. Click here to learn more about the general information of different tags.

Q: What is the impact of a given tag type and any potential biological activity of the protein?

Theoretically small tags generally have very small influence on protein activity. However, the specific impact on protein activity can't be concluded (There is no impact on some proteins, small impact on some proteins, and relatively great impact on some proteins).

Q: Can you remove the endotoxin?

Not all endotoxin can be removed. Please communicate with us in advance if you need to remove the endotoxin which takes 2-3 business days. We could offer endotoxin removal service free of charge using PMB affinity chromatography, use LAL reagent to semi-quantitatively detect the content of endotoxin and guarantee endotoxin level within 0.1 ng/μg (1 EU/μg).

Q: Can you offer aseptic manufacture processing?

Yes, we can offer this service and it is free of charge, but you should remark this information when placing the order. We've performed aseptic processing for liquid protein before lyophilization, but there may exist contamination during lyophilization process, so we can't say germ-free for the whole process.

Q: How to determine species cross-reactivity of cytokines?

a. Apart from a few exceptions, most human cytokines are active on mouse cells.

b. Many mouse cytokines may also have effect on human cells, however, the activity may be lower than the corresponding human cytokines.

c. One of the few human cytokines will be more active than corresponding mouse cytokines when acting on mouse cells, such as IL-7.

d. Interferon, GM-CSF, IL-3 and IL-4 and other cytokines are species-specific and almost have no activity on non-homologous cells.

e. In contrast, fibroblast growth factor (FGF) and neurotrophin are highly conserved and both have good activity on cells of different species.

Q: What is the general preservative? Which kind of preservative do you usually add?

Commonly used preservative include Proclin 300, Sodium azide, etc. We do not add any preservative to our proteins.

Q: What is the general protectant? What kind of protectant do you usually add?

Commonly used protectant include saccharides, polyols, polymers, surfactants, some proteins and amino acids etc. We usually add 8% (mass ratio by volume) of trehalose and mannitol as lyoprotectant. Trehalose can significantly prevent the alter of the protein secondary structure, the extension and aggregation of proteins during freeze-drying process; mannitol is also a universal applied protectant and fillers, which can reduce the aggregation of certain proteins after lyophilization.

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