Extinction coefficient

This measure indicates how much light is absorbed by a protein at a particular wavelength. The extinction coefficient is measured by UV spectrophotometry, but can also be calculated. The amino acid composition is important when calculating the extinction coefficient. The extinction coefficient is calculated from the absorbance of cysteine, tyrosine and tryptophan using the following equation:

$ \displaystyle Ext(Protein) = count(Cystine)*Ext(Cystine) + count(Tyr)*Ext(Tyr) + count(Trp)*Ext(Trp)$

where Ext is the extinction coefficient of amino acid in question. At 280nm the extinction coefficients are: Cys=120, Tyr=1280 and Trp=5690.

This equation is only valid under the following conditions:

The extinction coefficient values of the three important amino acids at different wavelengths are found in [Gill and von Hippel, 1989].

Knowing the extinction coefficient, the absorbance (optical density) can be calculated using the following formula:

$ \displaystyle Absorbance(Protein) = \frac{Ext(Protein)}{Molecular ~ weight}$

Two values are reported. The first value is computed assuming that all cysteine residues appear as half cystines, meaning they form di-sulfide bridges to other cysteines. The second number assumes that no di-sulfide bonds are formed.