How do I calculate an extinction coefficient for a protein with known sequence for quantification by uv-measurements?
This answer comes from Song Tan (tan@mol.biol.ethz.ch): A good reference for determining protein concentration from UV absorption measurements is Gill.von.Hippel1989. These workers assume the proteins are fully denatured in 6 M GuHCl and calculate extinction coefficients of proteins based on their tryptophan, tyrosine and cysteine content. They also show that the difference between the calculated extinction coefficient for denatured protein and the measured extinction coefficient for native protein is very small (confirmed for a wide selection of proteins). If you have access to GCG, the command PEPTIDESORT will calculate the molar extinction coefficent based on the Gill and von Hippel formula.
