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The molar absorption coefficient, E, of a protein is usually based on concentrations measured by dry weight, nitrogen, or amino acid analysis. The studies reported here suggest that the Edelhoch method is the best method for measuring E for a protein. (This method is described by Gill and von Hippel [1989, Anal Biochem 182:319-3261 and is based on data from Edelhoch [1967, Biochemistry 6:1948-19541.) The absorbance of a protein at 280 nm depends on the content of Trp, Tyr, and cystine (disulfide bonds).
Note that only cystine, the historical term for a disulfide bond, contributes to absorption. The method org.biojava.nbio.aaproperties.PeptidePropertiesImpl#getExtinctionCoefficient uses the cystEine (Cys) count. It is an easy mistake to make; the code comments even reference "Ext(Cystine) = 125".
Assuming complete S-S cross linking occurs, the correct number of disulfide bonds should be 'N_cys / 2' (integer math, quotient only). Using this count then establishes consistency with ExPASy (https://web.expasy.org/protparam/).
Some test cases that can be replicated with protparam:
Sequence: CCCCC
Ext. coefficient: 250
Sequence: CCCCCC
Ext. coefficient: 375
Sequence: CCCCCCC
Ext. coefficient: 375
The text was updated successfully, but these errors were encountered:
From Pace et al, 1995:
Note that only cystine, the historical term for a disulfide bond, contributes to absorption. The method org.biojava.nbio.aaproperties.PeptidePropertiesImpl#getExtinctionCoefficient uses the cystEine (Cys) count. It is an easy mistake to make; the code comments even reference "Ext(Cystine) = 125".
Assuming complete S-S cross linking occurs, the correct number of disulfide bonds should be 'N_cys / 2' (integer math, quotient only). Using this count then establishes consistency with ExPASy (https://web.expasy.org/protparam/).
Some test cases that can be replicated with protparam:
Sequence: CCCCC
Ext. coefficient: 250
Sequence: CCCCCC
Ext. coefficient: 375
Sequence: CCCCCCC
Ext. coefficient: 375
The text was updated successfully, but these errors were encountered: