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Incorrect extinction coefficient for oxidized Cys #766

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darnells opened this issue May 2, 2018 · 1 comment
Open

Incorrect extinction coefficient for oxidized Cys #766

darnells opened this issue May 2, 2018 · 1 comment

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@darnells
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@darnells darnells commented May 2, 2018

From Pace et al, 1995:

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
@josemduarte
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@josemduarte josemduarte commented May 2, 2018

Doesn't this method take care of that?

biojava/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java

Line 194 in 359dce8

private Map<AminoAcidCompound, Integer> getExtinctAACount(ProteinSequence sequence){

It does seem to count N_cys/2.

Would you be able to add a test case to demonstrate the issue?

There's actually a test here (it uses the expasy server as the standard of truth):

biojava/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java

Line 211 in 359dce8

public void testExtinctionCoefficient(){

Perhaps you can add those new test cases to that test?
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@darnells @josemduarte
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