The molar extinction coefficient of a particular protein can be calculated quite accurately from the protein sequence and is quite useful to know since it allows you to accurately quantify the amount of protein, assuming you can obtain it in pure form. You can do this by measuring the absorbance of the protein at the ultraviolet wavelength of 280nm, which you can do accurately in a quartz cuvette in a UV spectrophotometer. How much a protein absorbs at 280nm is almost totally a function of the content of the aromatic rings of the amino acids Tyrosine and especially Tryptophan (the aromatic ring of Phenylalanine absorbs well at 260nm, but not 280nm). A solution to Tryptophan will give an absorbance of 5500 M-1 cm-1, while a solution of Tyrosine will give an absorbance of 1490 M-1 cm-1. The absorbance units are expressed per M per centimeter, so that a 1 M solution of Tryptophan in a typical 1 cm path length cuvette will have an absorbance of 5500. Since the absorbance of Tryptophan is so much higher than Tyrosine, the absorbance of a protein is very heavily influenced by the Tryptophan content. This can be a problem since this is the rarest amino acid, so that the average protein contains only ~1.3% Tryptophan. This means that many proteins contain little or none of this amino acid and so have very low absorbances at 280nm, while proteins which happen to have unususally high amounts of this amino acid will absorb unusually strongly at 280nm. Tyrosine is one of the rarer amino acids, at ~3.25% in the average protein, so the same problem can occur to a lesser degree here also. So proteins of similar molecular weight can have quite different absorbances, since they can have utterly different Tryptophan and Tyrosine content. However if you know the amino acid sequence and can get your protein pure you can correct for this problem and also quickly and conveniently measure the concentration. To calculate the absorbance of a 1M solution of a protein you simply count up the number of Tryptophan residues and multiply that by the absorbance of a one molar solution of Tryptophan. Then add that to the number of Tyrosine residues multiplied by the absorbance of a one molar solution of Tyrosine, and the sum is the absorbance of 1M of the whole molecule. So we use this simple equation;
Molar Extinction Coefficient = (Number of Tryptophan residues X 5500) + (Number of Tyrosine residues X 1490)
The Molar Extinction Coefficient is the absorbance of a 1M solution of the protein, which is not possible to achieve for most normal sized proteins; for example a 1M solution of the 66kDa protein bovine serum albumin would have a density of more than 66kg/L, almost three times that of Uranium, the densest substance on the surface of planet Earth. More useful is the absorbance of a 0.1%, equal to a 1g/L or 1mg/ml solution. This is usually referred to as the absorbance, and can be calculated by simply dividing the Molar Extinction Coefficient by the molecular weight. So this gives you the absorbance that a 1mg/ml solution of your protein would have. So all you have to do is measure the absorbance of your pure protein at 280nm and divide this by the absorbance value which a 1mg/ml solution would have, giving you the mgs/ml concentration of your protein solution.
Please type or paste your protein sequence in box below, can be upper or lowercase, program will read either and both.