What is Extinction coefficient of protein? what it indicates and its significance if it is closure to 1.000 or away from 1.000?
An extinction coefficient is a measure of how strongly a molecule absorbs light at a particular wavelength. There is no significance at all of its proximity to 1.00. See http://en.wikipedia.org/wiki/Molar_absorptivity
Thanks for your reply. I have seen basic information on wikipedia but in our bioinformatic study we found value is closure to 1.000 and I would like to know what does it indicate?
The value is an empirical constant specific to any given molecule, and the wavelength of absorbed light. Unless you are using the term 'extinction coefficient' for a different measurement, a value close to one simply indicates a value close to one!
What wavelength are you measuring at and what is the sample?
The extinction coefficient of a protein at a particular wavelength is the sum of the extinction coefficients of all the chromophores that absorb at that wavelength. For many proteins, the only chromophores are the aromatic amino acid side chains and disulfide bonds, which absorb in the UV range. The extinction coefficient of such proteins can be calculated based on the amino acid composition, but this is only valid when the protein is completely denatured in 8M guanidine hydrochloride.
Some proteins have bound ligands or prosthetic groups, however, that also contribute to the absorbance (heme, FAD, etc.).
The extinction coefficient of your protein of 1.000 is just coincidental. By the way, extinction coefficients have units of M-1cm-1 or (mg/ml)-1cm-1.
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