# Calculation of extinction coeffcient of GFP

I want to convert the absorption of a protein into concentration. Hence ı need to calculate the extinction coefficient of the protein (GFP). ı found the formula (nTrp)5500+(nTyr)1490 on the internet but not able to use it since ı dont understand what n in front of the amino acids stand for and how ı reach to the n value

## 1 Answer

Only the number ("n") of the aromatic amino acids Tryptophan (Trp) and Tyrosin (Tyr) in your protein contribute significantly to its absorption at 280 nm (and Cystein (Cys), albeit to a lesser extend), see also here.

You could retrieve the protein's amino acid sequence from uniprot (see GFP here). Looking through the GFP sequence, one can identify n=11 (4.6%) Tyr and n=1 (0.4%) Trp. Now you can insert those in your formula and end up with an extinction coeffient of 21'890 M^-1 * cm^-1. This formula is only valid if all Cys are reduced (GFP has n=2 Cys that could form a disulfide bridge).

If you want to avoid all the formulas I suggest you copy the sequence of GFP and paste it into ExPASy ProtParam. This way you get a nice overview of the amino acid distribution of your protein and also retrieve the extinction coefficient under oxidizing conditions, which BTW is 22'015 M^-1 * cm^-1.