calculating extinction coefficient from protein sequence ???

Song Tan tan at mol.biol.ethz.ch
Wed Nov 16 14:29:02 EST 1994


In article <3ad81i$g23 at ra.ibr.cs.tu-bs.de>, Marcus Heller
<heller at ifr.ing.tu-bs.de> wrote:
 
> I'm looking for a formula which gives instruction how to calculate an
extinction
> coefficient for a protein with known sequence for quantification by
uv-measurements.

I think this question should go into the FAQ.

A good reference for determining protein concentration from UV absorption
measurements is:
Gill and von Hippel, Calculation of protein extinction coefficients from
amino acid sequence data, Analytical Biochemistry, (1989), 182, 319-326.  

They calculate extinction coefficients of proteins based on their
tryptophan, tyrosine and cysteine content, and assuming the proteins are
fully denatured in 6 M GuHCl.  But 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.

Song Tan
Institute for Molecular Biology and Biophysics
ETH-Honggerberg (Swiss Federal Institute of Technology)
8093 Zurich, Switzerland
email:  tan at mol.biol.ethz.ch

-- 
Song Tan
Institute for Molecular Biology and Biophysics
ETH-Honggerberg (Swiss Federal Institute of Technology)
8093 Zurich, Switzerland
email:  tan at mol.biol.ethz.ch



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