Fig 8. Estimate for the change in free energy of folding upon oxidation.

(a) Calculated ΔG_alch. for the transformation from methionine to methionine sulfoxide using FEP. The calculations were done with the tri-peptide Ala-Met-Ala to mimic the unfolded state (black bar) and for each methionine residue in the folded state of the A2 domain that is at least partially buried (colored bars). The residue Met¹⁵⁴⁵ was excluded because it is completely solvent exposed. The p-values for the difference in ΔG_alch. between folded and unfolded state were calculated from a one-tailed student t-test. (b) The estimated ΔΔG of folding due to the conversion of an individual methionine residue to methionine sulfoxide (see “Materials and methods” and Fig 2 for details about how it was calculated). A positive value indicates that oxidation of a specific methionine residue is thermodynamically unfavorable for folding. The reported values are averages over three simulations while error bars denote standard errors of the mean.