Include oxidations in hydrophobicity scales

[Stortebecker]

Hi,

when calculating peptide hydrophobicity, it would be nice to include the possibility of common modifications. For MS, especially oxidation of methionine would be of interest. M[ox] dramatically reduces the hydrophobicity of a peptide, as mentioned in Eichacker et al, 2004:

When compared with the Eisenberg scale (39), a single oxidation of methionine would reduce the hydrophobicity from 0.64 to –0.76 (Fig. 6A). A double oxidation would decrease the hydrophobicity of the peptide to –2.0 (Fig. 6A). Such a drastic shift of one single amino acid may contribute to the physical properties of the hydrophobic transmembrane peptide in a way that the peptide becomes detectable.

However, I am not sure, how we could provide this feature in the hydrophobicity function. Reading tags for oxidation / dioxidation like [+16] from the given sequence would be nice, but is so far not supported by any of the functions, I think. A workaround would be to use additional integer parameters like oxidated, dioxidated where the user can specify how many oxidations occur on the given peptide. For the hydrophobicity function, the exact localization of the oxidation would be rather insignificant.

Also, I do not know if all hydrophobicity scales define oxidations. Some research would be needed for correct implementation.

What is your opinion about this?

Greetings, Florian