Methods and Uses of Calculating Protein Extinction Coefficient

The extinction coefficient of a protein describes its absorbance properties under a certain wavelength of light. It is an inherent attribute of a protein, linearly related to the concentration of protein and the light path length. The extinction coefficient is often used to estimate protein concentration.

 

Definition of Extinction Coefficient

The definition of an extinction coefficient is the absorbance under unit concentration and unit light path length.

A=ε×c×l

Where:

1. A is Absorbance.

2. ε is Extinction coefficient (units are usually cm^(-1)M^(-1) or L/(mol·cm)).

3. c is the concentration of protein (units are usually M or mol/L).

4. l is the light path length (units are usually cm).

 

Simplified Method to Estimate Extinction Coefficient

If you know the protein sequence, you can use the following simplified method to estimate its extinction coefficient at 280 nm:

ε280=(5500×W)+(1490×Y)+(125×C)

Where: 

W, Y, and C represent the number of residues of tryptophan, tyrosine, and cysteine in the protein, respectively.

 

It should be noted that this estimation method is only applicable in the absence of other substances that absorb light at 280 nm, and it does not account for the effects of the protein's structure and folding state on absorbance.The most accurate method involves measuring the absorbance of a protein sample of known concentration at a specific wavelength (e.g., 280 nm) and then using the above formula to calculate the extinction coefficient.