Lidstrom:Choosing a protein concentration quantification method

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General Considerations

From ISBN 0-19-963142-5

• Each method depends to varying degree on the amino acid composition of the protein you are measuring, and usually involves comparion with a protein standard.
  • The mismatch between the protein standards' composition and your protein's composition is a source of error.
• The only way to measure protein concentration directly is to weigh the protein in question after complete removal of water and contaminants, which is rarely possible or desirable.
• Highly purified proteins in aqueous solution can be estimated more easily than crude homogenates or membrane-bound proteins where many additional components in the mixture may interfere. ISBN 0-19-963142-5 pg 327

Major methods available

Spectrophotometer

• Absorbance at 280 nm gives a quick approximate estimation of protein in non-turbid solutions, which is often all that is required. ISBN 0-19-963142-5
  • Advantage" non-destructive.
• A280 varies from protein to protein:
  • A280 for a 1% protein solution varies from 0 for some parvalbumins to 26.5 for lysozyme ISBN 0-19-963142-5 pg 327 though most fall in the range of 4-15.
• A280 measurements can be inaccurate if other things (e.g. DNA) that absorb at 280nm are present. (citation)
  • A 1% BSA solution has A280 = 6.6.

Background info: ISBN 0-19-963142-5 pg 327

• Absorption at 280nm is due almost entirely to the aromatic amino acids: tryptophan and tyrosine.
• At 260 nm phenylalanine absorbs, and histidine, methionine, cystiene, and cystine absorb between 225 and 240 nm. At wavelengths less than 225 nm the peptide bond itself is the principal absorbing group, but the above amino acids also contribute.
• There are a number of reasons why these shorter wavelengths are not the most frequently used. At 192nm dissolved oxygen absorbs strongly, and thus measurements would have to be carried out in the absence of oxygen. 192 nm is below the working range of many spectrophotometers, since it requires a particularly good light source and stray radiation can be a problem. Wavelengths nearer 225 nm are used since, although the peptide bond absorbs less strongly, the interference by oxygen is limited.
• In a typical protein solution used in enzymatic studies, the main interfering substances likely to affect absorbance measurements are nucleic acids, nucleotides such as ATP or NAD(P), haem-containing compounds such as cytochromes, reagents containing sulphydryl groups such as 2-mercaptoethanol, dithiothreitol, glutathione or cystiene, and buffers.
• In general, the shorter the wavelength the larger the range of interfering substances. It is perhaps this reason that although A280 is less sensitive than some, and is dependent on the tyrosine and trypotphan content, it is one of the most used.
• The absorbance spectrum of tyrosine is pH dependent, but at 280nm both the protonated and unprotonated forms have similar absorption coefficients and so measurements do not have to be made at a particular pH.
• Some spectrophotometers used to measure column effluents use 206nm, which gives much greater sensitivity provided there is no interference.

• Before measuring the UV absorbance of a protein solution, it is important to check that the protein solution is not turbid, as this will cause light scattering. Clarification can be done by centrifugation. A clear protein solution (unless it contains prosthetic groups) will normally have zero A320. A significant A320 is usually due to light scattering and should be subtracted from A280.
  • After the absorbance of a suitable dilution of the protein has been made, and corrected if necessary, the approximate relationships for a protein at 1mg/mL of A280≈1.0, A215≈15, or A206≈30 can be used.

• Various corrections have been devised for interfering substances. These involve making measurements at two wavelengths, at the second of which there is a large difference in the absorbance coefficient between the interfering substance and the protein.
  • The oldest of these is one used by Warburg and Christian to correct for nucleic acid interference, and is expressed as a formula by Layne:
    • protein (mg/mL) = 1.55*A280 - 0.76*A260
  • A similar correction but using the A230 is:
    • protein (mg/mL) = 0.183*A230 - 0.075*A260
• If a particular substance is known to be present then a suitable correction may be devised along the above lines.
• Although the A205 is due mainly to the peptide bond and the absorbance coefficients for most proteins lie in the range of 28.5-33 there is some variation due to the tyrosine and tryptophan content.
  • A correction has been devised:
    • A205 for a 1% solution 10*[27+(120*A280/A205)]
  • The method of Wadell is based on differential measurements at 215 nm and 225 nm. By using these wavelengths some of the A215 due to buffers and other components is corrected for. The protein solution is diluted with sodium chloride solution (9g/L) until the A215 is less than 1.5. The relationship used is:
    • protein (mg/mL) = 0.144*(A215-A205)
• There are other less widely used methods not discussed here.

From Enzyme Activity and Assays:

• 

  Protein absorbance at 280nm

• 

  Protein absorbance at 205nm

Others

• Since the 1950s when Lowry et al. (8) modified the method originally devised by Wu (9) and Folin and Coicalteu (10), the Lowry method has become the most widely used for protein estimation. However, during the 1980s dye-binding assays based on Coomassie Blue (11,12) have become more popular because of their simplicity and because of certain shortcomings in the Lowry method. One of the oldest procedures, the Biuret test (13), is still used; it is quite satisfactory apart from the disadvantage of being relatively insensitive.
• Lowry depends to a significant extent on the aromatic amino acid content
  • The color yield for a protein like gelatin is about 1/4 the color that of trypsin. ISBN 0-19-963142-5 pg 327

Pierce Brand BCA assay

• The bicinchoninic acid assay (BCA assay), is a biochemical assay for determining the total concentration of protein in a solution (0.5 μg/mL to 1.5 mg/mL), similar to Lowry protein assay, Bradford protein assay or biuret reagent. wikipedia

Who uses what as of 2013

• Mila uses the spectrophotometer, with 235 and 280 nm and the formula: Protein concentration (mgl/ml) = (A235 - A280)/2.51
  • reference: An absolute method for protein determination based on difference in absorbance at 235 and 280 nm. Whitaker JR, Granum PE. Anal Biochem. 1980 Nov 15;109(1):156-9.
• Ceci/Amanda/Frances chose BCA, using a pierce brand kit.

Compatibility with your lysis solution

protein assay compatibility table from Pierce

Resources

• Thermo Scientific: Overview of Protein Assays Methods
• Thermo Scientific: Protein Assay Selection Guide
• Thermo Scientific: Protein Assay Technical Handbook