Chapter 4 │ Page 124 acids in solution through treatment with a plasma jet. A similar study was performed by Zhou et al. [53]. Wenske et al. [28, 54] reported the PTMs caused by plasma treatment, with both the kINPen and COST-jet, in di erent peptides, representing a more realistic environment for the di erent amino acids. It is clear that the amino acids that are most susceptible to plasma-induced PTM are the sulfur-containing methionine and cysteine. They are followed by the aromatic amino acids tryptophan, tyrosine and phenylalanine. Though NTP-induced modifications have been reported for most of the remaining amino acids, they exhibit a far lower susceptibility, e.g. only showing signs of PTM after lengthy NTPtreatment. Which PTM occurs depends on various factors, including the plasma working gas, the plasma device, and the amino acid environment. The most common PTM induced by plasma, however, seems to be oxidation of the amino acid side chains [28]. Based on this, Figure 2 shows the plasma-induced PTMs we considered in our investigation. To determine which of these amino acids specifically in our investigated complexes would be available for oxidation by plasma treatment, we analyzed the solvent accessible surface area (SASA) of the proteins. For this, we repeated all simulation steps outlined in section 2.1 for only the ligands of the complexes, i.e. HLA-E and HLA-Cw4. Indeed, in an experimental setting, plasma treatment of cancer cells would cause oxidation of only the ligands expressed on the cancer cells. The last 20 ns of the equilibrations were used for the SASA analysis. By comparing the SASA to the hydrophilic surface area of the amino acids in question [55], we can determine which amino acids can be easily reached by the solvent, and thus, by plasmaproduced RONS.
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